Citrus Sinensis ID: 005698

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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--
Protein Sequence
MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQTLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADGKHHRGSRSPRGLDESRTKLGRRSRSKSIERKLYRNRGRSRSADGRRRKSMLSPANLDRSESNRRRHSASQSKDHANSESAETRDYKSMHHPHNWDKTEGELNASLKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTDPLMLNSDDVNLVSQSNAFPSM
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHcccEEEEEcccccccHHHHHHHHHccccEEEEEEcccccEEEEEEccHHHHHHHHHHcccccccccEEEEccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEccccHcHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHEEEEcccccHcHHHHHHHHHHHcccEEEEEEcccccEEEEEEccHHHHHHHHHHcccccccccccHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccEEccccccccccccccHHHHHHccccccccccEEccccEcccccccEEccccccccc
Coil and Loop (DISEMBL)
MTALAatttmgtlsqvpmapSAAAMAAAQAIVAAQALQAHAAQVQAQQSakdlsgspdkagkaDALKKtlqvsnlspllTVEQLRQLFSFCGTVVectitdskhfayieyskpeEATAALALNnmdvggrplnvemaksfpqkpshlnsslagsslPMMMQQAVAMQQMQFQQALLMQQTLTAQQAANRAASMKSATELAAARAAEISKKLKadglvdedketkqksrspstsrarsrsksrspvhyqrtyrarsrsksrspvsfhrrrrsrsfsppyrhrrghrsrsplrsrhyskydnerlstrdtrdgadrsrresdishhspvprrrksrsvsphsrksyrsdsgspkhrqessarkssrahskspkrhrgnrnsprnddakpkyrhrsrsksmerhdeekdeardgksqhrerkrsrslsredehhgrgrspagnvdenksklrgrsrsvsaldkyksseiaddsrddrlrnrhkrrsrsksvegkmgggsrdkkpkhhdrrrsrsisadgkhhrgsrsprgldesrtklgrrsrsKSIERKLYrnrgrsrsadgrrrksmlspanldrsesnrrrhsasqskdhansesaetrdyksmhhphnwdktegelnaslkdptvmeddgflsskqknydLKKSMENVsahenhgikstdplmlnsddvnlvsqsnafpsm
Flexible Loop (DISEMBL)
mtalaatttmgtlsqVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQTLTAQQAANRAASMKSATELAAARAAEISKklkadglvdedketkqksrspstsrarsrsksrspvhyqrtyrarsrsksrspvsfhrrrrsrsfsppyrhrrghrsrsplrsrhyskydnerlstrdtrdgadrsrresdishhspvprrrksrsvsphsrksyrsdsgspkhrqessarkssrahskspkrhrgnrnsprnddakpkyrhrsrsksmerhdeekdeardgksqhrerkrsrslsredehhgrgrspagnvdenksklrgrsrsvsaldkyksseiaddsrddrlrnrhkrrsrsksvegkmgggsrdkkpkhhdrrrsrsisadgkhhrgsrsprgldesrtklgrrsrsksierklyrnrgrsrsadgrrrksmlspanldrsesnrrrhsasqskdhansesaetRDYKSMHHPHNWDKTEGELNASLKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHenhgikstdplmlnsDDVNLVSQSNAFPSM
Low Complexity Region (SEG)
mtalaatttmgtlsqvpmapsaaamaaaqaivaaqalqahaaqvqaqqsaKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPmmmqqavamqqmqfqqallmqqtltaqqaaNRAASMKSATELaaaraaEISKKLKADGLVDEDKETKQKsrspstsrarsrsksrsPVHYQRTYRARSRSKsrspvsfhrrrrsrsfsppyrhrrGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDIshhspvprrrksrsvsphsrksYRSDSGSPKHRQEssarkssrahskspkrhrGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHrerkrsrslsredeHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDsrddrlrnrhkrrsrsksVEGKMGGGsrdkkpkhhdrrrsrsISADGKHHRGSRSPRGLDESRTKLGRRSRSKSIERKLYrnrgrsrsadgrrrKSMLSPANLDRSESNRRRHSASQSKDHANSESAETRDYKSMHHPHNWDKTEGELNASLKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTDPLMLNSDDVNLVSQSNAFPSM
Disordered region (IsUnstruct)
******************************IV**************************************QVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALN*******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*****************************AIV***A**************************ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA*****************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
**********GTLSQVPM**********QAIVA*******************************ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS*********SSLAGSSLPMMMQQAVAMQQMQFQQALLMQQT*********************ARAAEISKKLKADG***************************************************************************RSRHYSKYDNERL***********************************************************************************************************************************************************DKYKSSEIAD**************************************************************************SIERKLYR*******************************************************HPHNWDKTEGELNASLKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTDPLMLNSDDVNLVSQSNAFPSM
Disordered Region (DISPRO)
**********GTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQ******************KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKP********GSSLPMMMQQAVAMQQMQFQQALLMQQTLTAQQAANR*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************ASLKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTDPLMLNSDDVNLVS********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQTLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSxxxxxxxxxxxxxxxxxxxxxKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADGKHHRGSRSPRGLDESRTKLGRRSRSKSIERKLYRNRGRSRSADGRRRKSMLSPANLDRSESNRRRHSASQSKDHANSESAETRDYKSMHHPHNWDKTEGELNASLKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTDPLMLNSDDVNLVSQSNAFPSM
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	682	2.2.26 [Sep-21-2011]
Q8WXA9	508	Splicing regulatory gluta	yes	no	0.211	0.283	0.269	2e-05
Q9JKL7	494	Splicing regulatory gluta	yes	no	0.158	0.218	0.289	0.0001

>sp|Q8WXA9|SREK1_HUMAN Splicing regulatory glutamine/lysine-rich protein 1 OS=Homo sapiens GN=SREK1 PE=1 SV=1

 Score = 52.0 bits (123), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/152 (26%), Positives = 70/152 (46%), Gaps = 8/152 (5%)

Query: 17  PMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNL- 75
           P+     ++++  AI AA AL  + A +  +     L G+ D + K D +++T+ V NL 
Sbjct: 18  PLTTLGVSLSSLGAIPAA-ALDPNIATL-GEIPQPPLMGNVDPS-KIDEIRRTVYVGNLN 74

Query: 76  SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAYIEYSKPEEATAALALNNMDVGGRP 131
           S   T +QL + F   G V    +    T    FA++E++       ALA N +  G RP
Sbjct: 75  SQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPRALAFNGVMFGDRP 134

Query: 132 LNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQA 163
           L +  + +   KP  +    A   L  +M++ 
Sbjct: 135 LKINHSNNAIVKPPEMTPQAAAKELEEVMKRV 166

Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3.
Homo sapiens (taxid: 9606)

>sp|Q9JKL7|SREK1_RAT Splicing regulatory glutamine/lysine-rich protein 1 OS=Rattus norvegicus GN=Srek1 PE=1 SV=1

 Score = 48.9 bits (115), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/114 (28%), Positives = 53/114 (46%), Gaps = 6/114 (5%)

Query: 53  LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
           L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct: 55  LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 113

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQ 161
           +E++       ALA N +  G RPL +  + +   KP  +    A   L  +M+
Sbjct: 114 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKELEEVMK 167

Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3.

Rattus norvegicus (taxid: 10116)

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	682
255554000	946	conserved hypothetical protein [Ricinus	0.768	0.553	0.677	1e-125
224128984	950	predicted protein [Populus trichocarpa]	0.909	0.652	0.583	1e-123
224060343	892	predicted protein [Populus trichocarpa]	0.862	0.659	0.608	1e-112
225466283	926	PREDICTED: uncharacterized protein LOC10	0.724	0.533	0.640	1e-111
296088276	888	unnamed protein product [Vitis vinifera]	0.684	0.525	0.586	1e-100
449433175	936	PREDICTED: uncharacterized protein LOC10	0.816	0.595	0.577	2e-96
449487626	936	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.816	0.595	0.574	2e-95
356525215	975	PREDICTED: uncharacterized protein LOC10	0.925	0.647	0.5	2e-94
356510930	969	PREDICTED: uncharacterized protein LOC10	0.925	0.651	0.504	6e-90
30687254	987	RNA recognition motif (RRM)-containing p	0.840	0.580	0.500	1e-68

>gi|255554000|ref|XP_002518040.1| conserved hypothetical protein [Ricinus communis] gi|223542636|gb|EEF44173.1| conserved hypothetical protein [Ricinus communis]

 Score =  457 bits (1175), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 379/559 (67%), Positives = 438/559 (78%), Gaps = 35/559 (6%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSA-KDLSGSPDK 59
           MTALAATT+MGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQ  + KD SGSPDK
Sbjct: 282 MTALAATTSMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQAQSAKDSSGSPDK 341

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA 119
           AGK D LKKTLQVSNLSPLLTV+QL+QLFS+ G+VVEC+ITDSKHFAYIEYSKPEEATAA
Sbjct: 342 AGKEDTLKKTLQVSNLSPLLTVDQLKQLFSYFGSVVECSITDSKHFAYIEYSKPEEATAA 401

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
           LALNNMDVGGRPLNVEMAKS PQK S LNSS+A SSLP+MMQQAVAMQQMQFQQALLMQQ
Sbjct: 402 LALNNMDVGGRPLNVEMAKSLPQK-SLLNSSVASSSLPLMMQQAVAMQQMQFQQALLMQQ 460

Query: 180 TLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRS 239
           T+TAQQAANRAA+MKSATELAAARAAEISKKLKADG VDE+KET++KSRSPS SR RS+S
Sbjct: 461 TMTAQQAANRAATMKSATELAAARAAEISKKLKADGFVDEEKETERKSRSPSASRVRSKS 520

Query: 240 KSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYD 299
           KS+SPV Y+R  R+     SR                     R HRSRSP RSRH S+YD
Sbjct: 521 KSKSPVSYRRRRRSPYSPPSRR-------------------HRDHRSRSPFRSRHLSRYD 561

Query: 300 NERLSTRDTRDGADRSRR-ESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESS 358
            ER S RD+RD + R+RR +      SPV RR +SRSVSP  ++SYR+DSGSPK R+ESS
Sbjct: 562 IERRSFRDSRDDSGRTRRGDRSFDRRSPVSRRNRSRSVSPRMKRSYRADSGSPKRRRESS 621

Query: 359 ---ARKSSRAHSKSPKRHRGNRNSPRND-DAKPKYRHRSRSKSMERHDEEKDEARDGKSQ 414
              ARKSS   S+SP+ HRG+R+SPRND D K KYR RSRSKS+E   E+  EA+D K +
Sbjct: 622 PRRARKSSHGGSRSPRHHRGSRSSPRNDSDNKLKYRKRSRSKSVEDSKEKAKEAQDEKFK 681

Query: 415 HRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDR 474
            +ER RSRSLS E E +   +S + ++DEN+ K RGRSRS S ++  +S+E  +++RD R
Sbjct: 682 KQER-RSRSLSVE-EKNNVSKSSSRSIDENEPKHRGRSRSKS-VEARRSTEKVNETRDGR 738

Query: 475 LRNRHKRRSRSKSVEGK-----MGGGSRDKKPKHHDRRRSRSISADGKHHRGSR-SPRGL 528
           L+NR ++RSRSKSVE +      G  SRDKK KH DR+RSRSISADGKHHRGSR SPR  
Sbjct: 739 LKNRDRKRSRSKSVEVRRHSREKGNESRDKKSKHRDRKRSRSISADGKHHRGSRSSPRVA 798

Query: 529 DESRTKLGRRSRSKSIERK 547
           D+ ++K  R SRS+S E K
Sbjct: 799 DDIKSKHRRHSRSRSPESK 817

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128984|ref|XP_002328861.1| predicted protein [Populus trichocarpa] gi|222839291|gb|EEE77628.1| predicted protein [Populus trichocarpa]

 Score =  449 bits (1156), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 405/694 (58%), Positives = 480/694 (69%), Gaps = 74/694 (10%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQ-QSAKDLSGSPDK 59
           MT LA TT+MGTLSQVPMAPSAAAMAAAQAIVAA+ALQAHAAQ+QAQ +SAKD SGSPDK
Sbjct: 281 MTLLAPTTSMGTLSQVPMAPSAAAMAAAQAIVAAKALQAHAAQLQAQARSAKDSSGSPDK 340

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA 119
           A K DALKKTL VSNLSPLLTVEQL+QLFSFCGTVVECTI DSKH AYIEYSKPEEATAA
Sbjct: 341 ARKEDALKKTLHVSNLSPLLTVEQLKQLFSFCGTVVECTIADSKHSAYIEYSKPEEATAA 400

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
           LALNNMDVGGRPLNVE AKS PQKP  LNSS A SSLPMMMQQAVAMQQMQFQQALLMQQ
Sbjct: 401 LALNNMDVGGRPLNVETAKSLPQKPI-LNSSFASSSLPMMMQQAVAMQQMQFQQALLMQQ 459

Query: 180 TLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRS 239
           T+TAQQAAN+AA+MKSATELAAARAAEISKKLK DGLV  + ETK +S+SP   RARSRS
Sbjct: 460 TMTAQQAANKAATMKSATELAAARAAEISKKLKDDGLVTGEGETKAESKSPPPPRARSRS 519

Query: 240 KSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYD 299
           KSRSP++Y+                  RR RS S+SPP RH R  RSRSP+R R++S+Y+
Sbjct: 520 KSRSPINYR------------------RRMRSPSYSPPSRHNRDRRSRSPVRFRYHSRYN 561

Query: 300 NERLSTRDTRDGA----------DRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSG 349
            ER S RD               DRSR      HHSPV RR +SRS SP +RKSYR+DSG
Sbjct: 562 YERRSYRDRDSRDDGDRTRRRELDRSR-----DHHSPVSRRNRSRSASPRTRKSYRADSG 616

Query: 350 SPKHRQESSA---RKSSRAHSKSPKRHRGNRNSPRND---DAKPKYRHRSRSKSMERHDE 403
           SPKHRQESSA   RK+S + S+SP+ H G+R+SPRN+     + + R RSRSKS+E  ++
Sbjct: 617 SPKHRQESSAHRSRKASDSGSRSPRHHGGSRSSPRNNPDSKLRYRRRSRSRSKSVEEAND 676

Query: 404 EKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKS 463
           + DE R+ KS+  ER RSRSLS E +HHGR  SP  + +E+ SK R RSRS S   K  S
Sbjct: 677 KVDEIREKKSKQHER-RSRSLSVELKHHGRRPSPRSS-NEDDSKHRSRSRSKSVEVKRHS 734

Query: 464 SEIADDSRDDRLRNRHKRRSRSKSVEGKM-----GGGSRDKKPKHHDRRRSRSISADGKH 518
           +E  D + D +L++RH RRSRSKSV+ +      G  +RDKK KH DR RSRSI+A+GKH
Sbjct: 735 NEKVDKTGDGKLKHRH-RRSRSKSVDDRHHYKERGNETRDKKTKHQDRGRSRSITAEGKH 793

Query: 519 HRGSRSPRGLDESRTKLGRRSRSKSIERK---------------LYRNRGRSRSADGRRR 563
           HR   SPRG D S++K  R SRS S E K                +R+R RS SA+G+  
Sbjct: 794 HRSRSSPRGRDGSKSKHRRHSRSISPEGKRRSSHRVDQNKDEKSKHRHRRRSPSAEGKHG 853

Query: 564 KSMLSPANLDRSESNRRRHSASQS---KDHANSESAETRDYKSMHHPHNWDKTEGELNAS 620
           +   SP + + ++S  RR   S+S   K H+N E    R     HH H  DKTE   +A+
Sbjct: 854 R---SPRSSEENKSKHRRRPRSKSAERKRHSNDEKDIRRGENETHHEHGSDKTE---DAN 907

Query: 621 LKDPTVMEDDGFLSSKQKNYDLKKSMENVSAHEN 654
            +    M ++  +  K K  D K+ +E++    N
Sbjct: 908 EEKKYFMNEE-MVDLKHKGCDSKELVEDMVTGSN 940

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060343|ref|XP_002300152.1| predicted protein [Populus trichocarpa] gi|222847410|gb|EEE84957.1| predicted protein [Populus trichocarpa]

 Score =  412 bits (1060), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 392/644 (60%), Positives = 455/644 (70%), Gaps = 56/644 (8%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSA-KDLSGSPDK 59
           MT LA TTTMGTLS  PMAPSAAAMAAAQAIVAA+ALQAHAAQVQAQ  + KD SGSPDK
Sbjct: 255 MTLLAPTTTMGTLSHAPMAPSAAAMAAAQAIVAAKALQAHAAQVQAQAQSAKDSSGSPDK 314

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA 119
           A K DALKKTL VSNLSPLLTVEQL+QLFSFCGTVVEC I DSKH AYIEYSKPEEATAA
Sbjct: 315 ARKEDALKKTLHVSNLSPLLTVEQLKQLFSFCGTVVECAIADSKHSAYIEYSKPEEATAA 374

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
           LALNNMDVGGRPLNVEMAKS PQKP   +S  + SSLPMMMQQAVAMQQMQFQQAL+MQQ
Sbjct: 375 LALNNMDVGGRPLNVEMAKSLPQKPLLNSSLAS-SSLPMMMQQAVAMQQMQFQQALIMQQ 433

Query: 180 TLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRS 239
           T+TAQQAAN+AASMKSATELAAARAAEISKKLKADG V  ++ETK +++SPS  +ARSRS
Sbjct: 434 TMTAQQAANKAASMKSATELAAARAAEISKKLKADGFVIGEEETKAETKSPSPPQARSRS 493

Query: 240 KSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYD 299
           KSRSP++YQ                  RR RS S+SPP R  R  RSRSP R R++S+Y+
Sbjct: 494 KSRSPINYQ------------------RRLRSPSYSPPSRRNRDRRSRSPFRFRYHSRYN 535

Query: 300 NERLSTRDTRDGADRSR-RESDIS--HHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQE 356
             R S RD+RD  DR R ++SD S   HSPV RR +SRS SP +RKSYR DSGSPK R E
Sbjct: 536 YGRRSYRDSRDIVDRMRMQDSDRSRGRHSPVSRRSRSRSASPRTRKSYRDDSGSPKRRLE 595

Query: 357 SSA---RKSSRAHSKSPKRHRGNRNSPRN-DDAKPKY-RH-RSRSKSMERHDEEKDEARD 410
           SSA   RK++ + S+SP+ H G R S RN  D+K +Y RH RSRSKS+E  ++  +E +D
Sbjct: 596 SSAQRSRKAADSGSRSPRSHGGRRLSRRNITDSKLRYKRHSRSRSKSVEESNDRVNEIQD 655

Query: 411 GKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDS 470
            KS+  ER RSRSLS E +HHGR R    + DE++S  R RSRS S   K  S E    +
Sbjct: 656 KKSKQHER-RSRSLSVELKHHGR-RPSHRSSDEDESNHRSRSRSKSVEVKRHSYEKVGKT 713

Query: 471 RDDRLRNRHKRRSRSKSVEGKM-----GGGSRDKKPKHHDRRRSRSISADGKHHRGSR-S 524
            D RL++R  RRSRSKSV+ +      G  SRDKK KH DR +SRSISA+  HHR SR S
Sbjct: 714 EDGRLKHR-DRRSRSKSVDDRHCYKERGNESRDKKTKHRDRVQSRSISAESNHHRRSRSS 772

Query: 525 PRGLDESRTKLGRRSRSKSIERKLYRN-----------RGRSRSADGRRRKSMLSPANLD 573
           P+G DES++K  R SR  S E K   N           R RS SA+G   K + SP + +
Sbjct: 773 PKGRDESKSKHRRHSRPISPEGKRRSNHRIDEKSKHCSRRRSVSAEG---KHIRSPRSSE 829

Query: 574 RSESNRRRHSASQS---KDHANSESAETRDYKSMHHPHNWDKTE 614
            ++S RRRHS S+S   K H+N E  + R+     H H  DKTE
Sbjct: 830 ENKSKRRRHSRSKSAEHKRHSNDEEIK-REENETRHEHTSDKTE 872

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225466283|ref|XP_002270255.1| PREDICTED: uncharacterized protein LOC100244513 [Vitis vinifera]

 Score =  408 bits (1049), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 344/537 (64%), Positives = 396/537 (73%), Gaps = 43/537 (8%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSA-KDLSGSPDK 59
           MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQ  + KD +GSPDK
Sbjct: 275 MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQAQSAKDSAGSPDK 334

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA 119
            GKADALKKTLQVSNLSPLLTVEQL+QLFSFCGTVVEC+ITDSKHFAYIEYSKPEEATAA
Sbjct: 335 VGKADALKKTLQVSNLSPLLTVEQLKQLFSFCGTVVECSITDSKHFAYIEYSKPEEATAA 394

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
           LALNNMDVGGRPLNVEMAKS P KP+ LNS LA  SLPM+MQQAVAMQQMQFQQALLMQQ
Sbjct: 395 LALNNMDVGGRPLNVEMAKSLPPKPAILNSPLASPSLPMVMQQAVAMQQMQFQQALLMQQ 454

Query: 180 TLTAQQAANRAASMKSATELAAARAAEISKKLKADGLV---DEDKETKQKSRSPSTSRAR 236
           T+TAQQAANRAA+MKSATELA+ARAAEISKKLKADG V    E+KE  +KSRSPS S AR
Sbjct: 455 TMTAQQAANRAATMKSATELASARAAEISKKLKADGFVEEEKEEKEENRKSRSPSISHAR 514

Query: 237 SRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYS 296
           S+S+S+SP+HY+R  R+RS S                      + R HRSRSP RS HYS
Sbjct: 515 SKSRSKSPLHYRRRRRSRSFSPPSR------------------YSREHRSRSPFRSHHYS 556

Query: 297 KYDNERLSTRDTRDGADRSRRESDIS---HHSPVPRRRKSRSVSPHSRKSYRSDSGSPKH 353
            +D+   S RD +DG+DRSRR        HH    RR +SRS SP +RKSYR+DS SPK 
Sbjct: 557 IHDHGSRSYRDNKDGSDRSRRRDLDRSHDHHLSSSRRNRSRSRSPRTRKSYRADSESPKR 616

Query: 354 RQESSA---RKSSRAHSKSPKRHRGNRNSPRNDD----AKPKYRHRSRSKSMERHDEEKD 406
           R ESS+   RKSSR   KSP+ HRG+R+SPRNDD     + +       +     +E+ D
Sbjct: 617 RVESSSHRTRKSSRVSPKSPRHHRGSRSSPRNDDDNKSKRRRRSRSKSVEGKHYSNEKID 676

Query: 407 EARDGKSQHRERKRSRSLSREDEHH-GRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSE 465
           E RD KS+HR+R+RSRS+S E +HH G G SP  + D++KSK R RSRS SA  K   S+
Sbjct: 677 ERRDKKSKHRDRRRSRSISAEGKHHKGSGFSPR-SFDDSKSKHRKRSRSKSAEGKRVLSD 735

Query: 466 IADDSRDDRLRNRHKRRSRSKSVEGKMG-------GGSRDKKPKHHDRRRSRSISAD 515
             D+ RD++ ++  KRRSRS+S EGK           S + +PKH  RR SRS SA+
Sbjct: 736 KTDEGRDEKGKHHEKRRSRSRSAEGKYCRLNRLSPKSSDEIRPKH--RRHSRSRSAE 790

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088276|emb|CBI36502.3| unnamed protein product [Vitis vinifera]

 Score =  374 bits (960), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 326/556 (58%), Positives = 374/556 (67%), Gaps = 89/556 (16%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSA-KDLSGSPDK 59
           MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQ  + KD +GSPDK
Sbjct: 275 MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQAQSAKDSAGSPDK 334

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA 119
            GKADALKKTLQVSNLSPLLTVEQL+QLFSFCGTVVEC+ITDSKHFAYIEYSKPEEATAA
Sbjct: 335 VGKADALKKTLQVSNLSPLLTVEQLKQLFSFCGTVVECSITDSKHFAYIEYSKPEEATAA 394

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
           LALNNMDVGGRPLNVEMAKS P KP+ LNS LA  SLPM+MQQAVAMQQMQFQQALLMQQ
Sbjct: 395 LALNNMDVGGRPLNVEMAKSLPPKPAILNSPLASPSLPMVMQQAVAMQQMQFQQALLMQQ 454

Query: 180 TLTAQQAANRAASMKSATELAAARAAEISKKLKADGLV---DEDKETKQKSRSPSTSRAR 236
           T+TAQQAANRAA+MKSATELA+ARAAEISKKLKADG V    E+KE  +KSRSPS S AR
Sbjct: 455 TMTAQQAANRAATMKSATELASARAAEISKKLKADGFVEEEKEEKEENRKSRSPSISHAR 514

Query: 237 SRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYS 296
           S+S+S+SP+HY+R  R+RS S                      + R HRSRSP RS HYS
Sbjct: 515 SKSRSKSPLHYRRRRRSRSFSPPSR------------------YSREHRSRSPFRSHHYS 556

Query: 297 KYDNERLSTRDTRDGADRSRRESDIS---HHSPVPRRRKSRSVSPHSRKSYRSDSGSPKH 353
            +D+   S RD +DG+DRSRR        HH    RR +SRS SP +RKSYR+DS SPK 
Sbjct: 557 IHDHGSRSYRDNKDGSDRSRRRDLDRSHDHHLSSSRRNRSRSRSPRTRKSYRADSESPKR 616

Query: 354 RQESSA---RKSSRAHSK------------------------SPKRHRGNRNSPRN-DDA 385
           R ESS+   RKSSR +S                           K H+G+  SPR+ DD+
Sbjct: 617 RVESSSHRTRKSSRHYSNEKIDERRDKKSKHRDRRRSRSISAEGKHHKGSGFSPRSFDDS 676

Query: 386 KPKYRHRSRSKSMERH---DEEKDEARDGKSQHRERKRSRSLSREDEHHGRGR-SPAGNV 441
           K K+R RSRSKS E      ++ DE RD K +H E++RSRS S E ++    R SP    
Sbjct: 677 KSKHRKRSRSKSAEGKRVLSDKTDEGRDEKGKHHEKRRSRSRSAEGKYCRLNRLSP---- 732

Query: 442 DENKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKP 501
                               KSS        D +R +H+R SRS+S E +      D+K 
Sbjct: 733 --------------------KSS--------DEIRPKHRRHSRSRSAEYRRSDNKGDEKL 764

Query: 502 KHHDRRRSRSISADGK 517
            HH   + R ++ D K
Sbjct: 765 MHHKEPKEREVTEDLK 780

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433175|ref|XP_004134373.1| PREDICTED: uncharacterized protein LOC101203535 [Cucumis sativus]

 Score =  359 bits (922), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 367/635 (57%), Positives = 439/635 (69%), Gaps = 78/635 (12%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKA 60
           MTA+AATT+MGT+SQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQ+      S    
Sbjct: 268 MTAIAATTSMGTISQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQAQSAKDSSGSSD 327

Query: 61  GK---ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEAT 117
                ADALK+TLQVSNLSPLLTVEQL+QLFSFCGTVVECTITDSKHFAYIEYSKPEEAT
Sbjct: 328 KSGKAADALKRTLQVSNLSPLLTVEQLKQLFSFCGTVVECTITDSKHFAYIEYSKPEEAT 387

Query: 118 AALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLM 177
           AALALNNMDVGGRPLNVEMAKS PQKP+  N SLA SSLPMMMQQAVAMQQMQFQQALLM
Sbjct: 388 AALALNNMDVGGRPLNVEMAKSLPQKPAAANPSLASSSLPMMMQQAVAMQQMQFQQALLM 447

Query: 178 QQTLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARS 237
           QQT+TAQQAANRAA+MKSATELAAARAAEISKKLK DG+ +E+ ETK+KSRSPS  R RS
Sbjct: 448 QQTMTAQQAANRAATMKSATELAAARAAEISKKLKVDGIGNEETETKEKSRSPSLPRERS 507

Query: 238 RSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSK 297
           +SKS+SP+ Y+                   RRRS ++SPPYRH R HRSRSP+RSRHYS+
Sbjct: 508 KSKSKSPIKYR------------------SRRRSPTYSPPYRHSRDHRSRSPVRSRHYSR 549

Query: 298 YDNER---LSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHR 354
           Y+++R     +R+  + + R   +   S  SP+ R+ +SRS+SP  RKSYR+ S SP H+
Sbjct: 550 YEDDRRGYRESREASERSRRRDLDRSRSRRSPISRKNRSRSISPRRRKSYRAGSDSPSHQ 609

Query: 355 QESS---ARKSSRAHSKSPKRHRG-NRNSPRNDDA-KPKYRHRSRSKSME-RH--DEEKD 406
           +E S    RKS  +  +SP RH G +R+SPR DD+ K K+R RSRSKS+E +H  DE+ +
Sbjct: 610 RERSPQRGRKSDHSDLRSPIRHHGKSRSSPRKDDSDKLKHRRRSRSKSVETKHHSDEKIN 669

Query: 407 EARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVS---ALDKYKS 463
           E + GK ++RER+RSRS S ED+H  R  SP  ++D+N SK R RSRS S     DKY  
Sbjct: 670 EMQHGKLKNRERRRSRSASLEDKHSKRRPSPR-SLDKNISKHRRRSRSNSREKVDDKYHG 728

Query: 464 SEI---------------ADDSRDDRLRNRHKRRSRSKSVEGK-----MGGGSRDKKPKH 503
                              D +R ++L+NR +RRSRSKSV+GK         SRDK+ +H
Sbjct: 729 RRRSRSSSSDSKHLPDSKVDSTRYEKLKNRSRRRSRSKSVDGKHRRREKSDRSRDKRLRH 788

Query: 504 HDRRRSRSISADGKHHRGSR-SPRGLDESRTKLGRRSRSKSIERK--------------- 547
            DRR SRSIS +  H R +R SP   DE+++K  RR RS S E K               
Sbjct: 789 RDRRSSRSISPEAGHQRVTRLSPTSSDETKSK--RRRRSLSPEDKPSDIDNGCIAENPKN 846

Query: 548 LYRNRGRSRSADGRRRKSMLSPANLDRSESNRRRH 582
           L R + RS S  G   +S LSP+    +E N  +H
Sbjct: 847 LGRQQSRSNSISGENGESNLSPS----TEENEFKH 877

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487626|ref|XP_004157720.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized LOC101203535 [Cucumis sativus]

 Score =  356 bits (914), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 365/635 (57%), Positives = 437/635 (68%), Gaps = 78/635 (12%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKA 60
           MTA+AATT+MGT+SQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQ+      S    
Sbjct: 268 MTAIAATTSMGTISQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQAQSAKDSSGSSD 327

Query: 61  GK---ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEAT 117
                ADALK+TLQVSNLSPLLTVEQL+QLF FCGTVVECTITDSKHFAYIEYSKPEEAT
Sbjct: 328 KSGKAADALKRTLQVSNLSPLLTVEQLKQLFXFCGTVVECTITDSKHFAYIEYSKPEEAT 387

Query: 118 AALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLM 177
           AALALNNMDVGGRPLNVEMAKS PQKP+  N SLA SSLPMMMQQAVAMQQMQFQQALLM
Sbjct: 388 AALALNNMDVGGRPLNVEMAKSLPQKPAAANPSLASSSLPMMMQQAVAMQQMQFQQALLM 447

Query: 178 QQTLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARS 237
           QQT+TAQQAANRAA+MKSATELAAARAAEIS KLK DG+ +E+ ETK+KSRSPS  R RS
Sbjct: 448 QQTMTAQQAANRAATMKSATELAAARAAEISXKLKVDGIGNEETETKEKSRSPSLPRERS 507

Query: 238 RSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSK 297
           +SKS+SP+ Y+                   RRRS ++SPPYRH R HRSRSP+RSRHYS+
Sbjct: 508 KSKSKSPIKYR------------------SRRRSPTYSPPYRHSRDHRSRSPVRSRHYSR 549

Query: 298 YDNER---LSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHR 354
           Y+++R     +R+  + + R   +   S  SP+ R+ +SRS+SP  RKSYR+ S SP H+
Sbjct: 550 YEDDRRGYRESREASERSRRRDLDRSRSRRSPISRKNRSRSISPRRRKSYRAGSDSPSHQ 609

Query: 355 QESS---ARKSSRAHSKSPKRHRG-NRNSPRNDDA-KPKYRHRSRSKSME-RH--DEEKD 406
           +E S    RKS  +  +SP RH G +R+SPR DD+ K K+R RSRSKS+E +H  DE+ +
Sbjct: 610 RERSPQRGRKSDHSDLRSPIRHHGKSRSSPRKDDSDKLKHRRRSRSKSVETKHHSDEKIN 669

Query: 407 EARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVS---ALDKYKS 463
           E + GK ++RER+RSRS S ED+H  R  SP  ++D+N SK R RSRS S     DKY  
Sbjct: 670 EMQHGKLKNRERRRSRSASLEDKHSKRRPSPR-SLDKNISKHRRRSRSNSREKVDDKYHG 728

Query: 464 SEI---------------ADDSRDDRLRNRHKRRSRSKSVEGK-----MGGGSRDKKPKH 503
                              D +R ++L+NR +RRSRSKSV+GK         SRDK+ +H
Sbjct: 729 RRRSRSSSSDSKHLPDSKVDSTRYEKLKNRSRRRSRSKSVDGKHRRREKSDRSRDKRLRH 788

Query: 504 HDRRRSRSISADGKHHRGSR-SPRGLDESRTKLGRRSRSKSIERK--------------- 547
            DRR SRSIS +  H R +R SP   DE+++K  RR RS S E K               
Sbjct: 789 RDRRSSRSISPEAGHQRVTRLSPTSSDETKSK--RRRRSLSPEDKPSDIDNGCIAENPKN 846

Query: 548 LYRNRGRSRSADGRRRKSMLSPANLDRSESNRRRH 582
           L R + RS S  G   +S LSP+    +E N  +H
Sbjct: 847 LGRQQSRSNSISGENGESNLSPS----TEENEFKH 877

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525215|ref|XP_003531222.1| PREDICTED: uncharacterized protein LOC100790138 [Glycine max]

 Score =  353 bits (906), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 360/720 (50%), Positives = 439/720 (60%), Gaps = 89/720 (12%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKA 60
           MTALAATT+MGTLSQ PMA  +AA  AA   + A       A     QSAKD +GSP+KA
Sbjct: 279 MTALAATTSMGTLSQAPMA-PSAAAMAAAQAIVAAQALQAHAAQVQAQSAKDSTGSPEKA 337

Query: 61  GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL 120
            K DALKKTLQVSNLSPLLTVEQL+QLF FCGTVVECTITDSKHFAYIEYSKPEEATAAL
Sbjct: 338 SKDDALKKTLQVSNLSPLLTVEQLKQLFGFCGTVVECTITDSKHFAYIEYSKPEEATAAL 397

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQT 180
           ALNN+DVGGRPLNVEMAKS P KPS  NSSLA SSLP+MMQQAVAMQQMQFQQALLMQQ+
Sbjct: 398 ALNNIDVGGRPLNVEMAKSLPPKPSVANSSLASSSLPLMMQQAVAMQQMQFQQALLMQQS 457

Query: 181 LTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRSK 240
           +TAQQAANRAA+MKSATELAAARAAEISKKL  DG+  E+KETKQKSRSPS    RSRSK
Sbjct: 458 MTAQQAANRAATMKSATELAAARAAEISKKLNPDGVGTEEKETKQKSRSPSPPHGRSRSK 517

Query: 241 SRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDN 300
           SRSP++Y+R  R+RS S                   P RH + HRSRSPLRS HYS YD 
Sbjct: 518 SRSPINYRRRRRSRSYS-------------------PARHSKDHRSRSPLRSHHYSSYDR 558

Query: 301 ERLSTRDTRD---GADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQES 357
           ER S RD R+      R   +  + HHS   RR +SRSVSP++RKS    S SPK  +E+
Sbjct: 559 ERRSFRDIREHSDRYRRRDLDRSLDHHSSASRRNRSRSVSPYTRKS----SVSPKRHRET 614

Query: 358 S---ARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMER--HDEEKDEARDGK 412
           S    RK SRA S SP R RG+R+SP+ D+ K + R RSRS+S +   H  + +E   GK
Sbjct: 615 SPHRGRKQSRADSGSPSRRRGSRSSPKIDEKKLRNRRRSRSRSSDDRLHSIKNEEISHGK 674

Query: 413 SQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRD 472
           S+HRER+RSRSLS +++ H R RS    VDE++S+ + R RS S  D++ S E  D++R 
Sbjct: 675 SKHRERRRSRSLSVDEKPHRRSRSSPRKVDESRSRHKKRLRSKSVDDRHGSPERLDENRT 734

Query: 473 DRLRNRHKRRSRSKSVEGKMGGGSRD-----KKPKHHDRRRSRSISADG----------- 516
            R R+  KR SRS+S E +     R+     +K KH D +RSRS S +G           
Sbjct: 735 RRSRHSDKRHSRSRSTETRDQTDVREDERKNQKSKHRDTKRSRSKSVEGKHRFKDKSGEN 794

Query: 517 --------------------KHHRGSRSPR-GLDESRTKLGRRSRSKSIERKLYRNRGRS 555
                               KH +G  SP    DE   +  +    K+     Y +RG  
Sbjct: 795 RDKKSKRRDRKRSRSISLEDKHDKGDTSPHINFDERNFEPTKSPEGKNHSSDKYGSRGE- 853

Query: 556 RSADGRRRKSMLSPANLDRSESNRRRHSA--SQSKDHANSESAETRDYKSMHHPHNWDKT 613
           +S   ++  S       D S   R  +    S+ K  ++S SAE +     HH  + +  
Sbjct: 854 KSEHQKKTPSKSKSEQFDGSGPLRGNYKEYDSKGKSPSDSGSAEVK-----HHLSDGENA 908

Query: 614 EGELNASL------------KDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTD 661
             E N+ L            KD T++ D+G L+S   NY  ++S EN  A +N G  S +
Sbjct: 909 TSEENSKLFGDVFQEPIRTAKDSTILNDNGTLTSVNGNYKSEESSENAGADDNPGWISVE 968

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356510930|ref|XP_003524186.1| PREDICTED: uncharacterized protein LOC100796921 [Glycine max]

 Score =  338 bits (867), Expect = 6e-90,   Method: Compositional matrix adjust.
 Identities = 363/720 (50%), Positives = 438/720 (60%), Gaps = 89/720 (12%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKA 60
           MTALAATT+MGTLSQ PMA  +AA  AA   + A       A     QSAKD +GSP+KA
Sbjct: 273 MTALAATTSMGTLSQAPMA-PSAAAMAAAQAIVAAQALQAHAAQVQAQSAKDSAGSPEKA 331

Query: 61  GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL 120
            K DALKKTLQVSNLSPLLTVEQL+QLF FCGTVVEC ITDSKHFAYIEYSKPEEATAAL
Sbjct: 332 SKDDALKKTLQVSNLSPLLTVEQLKQLFGFCGTVVECAITDSKHFAYIEYSKPEEATAAL 391

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQT 180
           ALNN+DVGGRPLNVEMAKS PQKPS  NSSLA SSLP+MMQQAVAMQQMQFQQALLMQQ+
Sbjct: 392 ALNNIDVGGRPLNVEMAKSLPQKPSVANSSLASSSLPLMMQQAVAMQQMQFQQALLMQQS 451

Query: 181 LTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRSK 240
           +TAQQAA RAA+MKSATELAAARAAEISKKL  DG+  E+KETKQ SRS S  R RSRSK
Sbjct: 452 MTAQQAATRAATMKSATELAAARAAEISKKLNPDGVGSEEKETKQNSRSSSPPRGRSRSK 511

Query: 241 SRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDN 300
           SRSP+ Y+R  R+RS S +                   RH + HRSRSPLR  HYS YD 
Sbjct: 512 SRSPISYRRRRRSRSYSPA-------------------RHSKDHRSRSPLRPHHYSSYDR 552

Query: 301 ERLSTRDTRD---GADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQES 357
           ER S RD R+      R   +  + H S   RR +SRSVSP++RKS      SPK  +E+
Sbjct: 553 ERRSYRDIREHSDRYRRRDSDRSLDHRSSASRRNRSRSVSPYTRKSPV----SPKCHRET 608

Query: 358 S---ARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMER--HDEEKDEARDGK 412
           S    RK SR  S SP   RG+R SP+ D+ K + R RSRS+S +   H  + +E   GK
Sbjct: 609 SPHRGRKQSRVDSGSPSHRRGSRPSPKIDEKKLRNRRRSRSRSSDDRLHSSKNEEVLHGK 668

Query: 413 SQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRD 472
           S+ RER+RS+SLS +++ H R RS    VDE++S+ + RS S S  D++ S E  D++R+
Sbjct: 669 SKRRERRRSKSLSVDEKPHRRSRSSPRKVDESRSRHKKRSSSKSVDDRHDSPERLDENRN 728

Query: 473 DRLRNRHKR-------------------------------RSRSKSVEGK-----MGGGS 496
            RLR+  KR                               RSRSKSVEGK       G +
Sbjct: 729 RRLRHSDKRHSRSRSTDNRDQTDVREDESKNEKSKHRDTKRSRSKSVEGKRRSKDKSGEN 788

Query: 497 RDKKPKHHDRRRSRSISADGKHHRGSRSPR-GLDESRTKLGRRSRSKSIERKLYRNRGRS 555
           RDKK KHHDRRRSRSIS + KH +G  S    LDE   +L +    K+     Y NRG  
Sbjct: 789 RDKKSKHHDRRRSRSISLEDKHDKGGTSLHINLDERNFELTKSPEGKNHYSDKYGNRGE- 847

Query: 556 RSADGRRRKSMLSPANLDRSESNRRRHSA--SQSKDHANSESAETRDYKSMHHPHNWDKT 613
           +S   ++  S       D S   R  +    S+ K  ++S SAE +     HH ++ +  
Sbjct: 848 KSEHQKKTPSKSKSGQFDGSGPLRGNYKEDDSKGKSPSDSGSAEVK-----HHLNDGESA 902

Query: 614 EGELNASL------------KDPTVMEDDGFLSSKQKNYDLKKSMENVSAHENHGIKSTD 661
             E N+ L            KD  ++ D+G L+S   NY  + S EN  A +N G  S +
Sbjct: 903 TSEENSKLFGDVFQEPIINAKDSAILNDNGTLTSVNGNYKSEGSSENAGADDNPGWISVE 962

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30687254|ref|NP_189032.2| RNA recognition motif (RRM)-containing protein [Arabidopsis thaliana] gi|334185580|ref|NP_001189958.1| RNA recognition motif (RRM)-containing protein [Arabidopsis thaliana] gi|332643307|gb|AEE76828.1| RNA recognition motif (RRM)-containing protein [Arabidopsis thaliana] gi|332643309|gb|AEE76830.1| RNA recognition motif (RRM)-containing protein [Arabidopsis thaliana]

 Score =  268 bits (684), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 338/675 (50%), Positives = 412/675 (61%), Gaps = 102/675 (15%)

Query: 1   MTALAATTTMGTLSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQ-QSAKDLSGSPDK 59
           MTA+AATT+MG LSQVPMAPSAAAMAAAQAIVAAQALQAHA+Q+QAQ QS K   GSP+K
Sbjct: 284 MTAIAATTSMGNLSQVPMAPSAAAMAAAQAIVAAQALQAHASQMQAQAQSNKGSLGSPEK 343

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA 119
               D LKK LQVSNLSP LT EQLRQLFSFCGTVV+C+ITDSKH AYIEYS  EEATAA
Sbjct: 344 GENGD-LKKFLQVSNLSPSLTTEQLRQLFSFCGTVVDCSITDSKHIAYIEYSNSEEATAA 402

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
           LALNN +V GR LNVE+AKS P KPS  NSS +      MMQQAVAMQQMQFQQA+LMQQ
Sbjct: 403 LALNNTEVFGRALNVEIAKSLPHKPSSNNSSSSLPL---MMQQAVAMQQMQFQQAILMQQ 459

Query: 180 TLTAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRS 239
            +  QQAANRAA+MKSATELAAARAAEIS+KL+ DG+ +++KE  QKSRSPS        
Sbjct: 460 AVATQQAANRAATMKSATELAAARAAEISRKLRPDGVGNDEKEADQKSRSPS-------- 511

Query: 240 KSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYD 299
             +SP        ARSRSKS+SP+S+ RRRRS ++SPP+R  R HRSRSPLR +  S Y+
Sbjct: 512 --KSP--------ARSRSKSKSPISYRRRRRSPTYSPPFRRPRSHRSRSPLRYQRRSTYE 561

Query: 300 NERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDS---GSPKHRQE 356
             R S RD+RD ++  R      HHS     R+SRSVSP  RKS + DS      +    
Sbjct: 562 GRRRSYRDSRDISESRRYGRSDEHHSS--SSRRSRSVSPKKRKSGQEDSELSRLRRDSSS 619

Query: 357 SSARKSSRAHSKSPKRHRGNRNSPRNDDA-KPKYRHRSRSKSMERHDEEKDEARDGKSQH 415
              +KSSRA S+SP+R +  +++PR+D+  K K R RSRS+S+E   + KD++RD   + 
Sbjct: 620 RGEKKSSRAGSRSPRRRKEVKSTPRDDEENKVKRRTRSRSRSVEDSADIKDKSRD---EE 676

Query: 416 RERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRL 475
            +  + RS SR  E   + R  + N DE K K R RSRS S  +   S E  D ++D+ L
Sbjct: 677 LKHHKKRSRSRSREDRSKTRDTSRNSDEAKQKHRQRSRSRSLENDNGSHENVDVAQDNDL 736

Query: 476 RNRH-KRRSRS----------------------------------------------KSV 488
            +RH KRRS+S                                              KSV
Sbjct: 737 NSRHSKRRSKSLDEDYDMKERRGRSRSRSLETKNRSSRKNKLDEDRNTGSRRRRSRSKSV 796

Query: 489 EGKMGGG----SRDKKPKHHDRRRSRSISADGKHHRGSRSPRGL-DESRTKLGRRSRSKS 543
           EGK        SRDKK K    RRSRS S++GK  R  RS  G  DE +++  R SRS+S
Sbjct: 797 EGKRSYNKETRSRDKKSKRRSGRRSRSPSSEGKQGRDIRSSPGYSDEKKSRHKRHSRSRS 856

Query: 544 IERKL----------YRNRGRSRSADGRRRKSMLSPANLDRSESN--RRRHSASQS---K 588
           IE+K            R R  S   D RR    LSP +   SE +  ++RHS S+S   K
Sbjct: 857 IEKKNSSRDKRSKRHERLRSSSPGRDKRRGDRSLSPVS---SEDHKIKKRHSGSKSVKEK 913

Query: 589 DHANSESAETRDYKS 603
            H++ E  +  D  S
Sbjct: 914 PHSDYEKVDDGDANS 928

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	682
TAIR|locus:2076121	987	AT3G23900 [Arabidopsis thalian	0.790	0.546	0.307	9.7e-48
RGD|621696	494	Srek1 "splicing regulatory glu	0.151	0.208	0.293	1.3e-09
UNIPROTKB|Q9JKL7	494	Srek1 "Splicing regulatory glu	0.151	0.208	0.293	1.3e-09
UNIPROTKB|Q8WXA9	508	SREK1 "Splicing regulatory glu	0.151	0.202	0.293	6e-09
MGI|MGI:2145245	494	Srek1 "splicing regulatory glu	0.151	0.208	0.293	9.8e-08
UNIPROTKB|E2R749	510	SREK1 "Uncharacterized protein	0.151	0.201	0.293	1.1e-07
UNIPROTKB|J9P0H2	626	SREK1 "Uncharacterized protein	0.151	0.164	0.293	2.3e-07
TAIR|locus:2024842	314	CID8 "CTC-interacting domain 8	0.143	0.312	0.346	4.8e-07
TAIR|locus:2091657	327	CID9 "CTC-interacting domain 9	0.143	0.299	0.346	8.9e-07
TAIR|locus:2184022	320	CID13 "CTC-interacting domain	0.127	0.271	0.387	3.1e-06

TAIR|locus:2076121 AT3G23900 [Arabidopsis thaliana (taxid:3702)]

 Score = 508 (183.9 bits), Expect = 9.7e-48, P = 9.7e-48
 Identities = 183/595 (30%), Positives = 237/595 (39%)

Query:    55 GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPE 114
             GSP+K    D LKK LQVSNLSP LT EQLRQLFSFCGTVV+C+ITDSKH AYIEYS  E
Sbjct:   339 GSPEKGENGD-LKKFLQVSNLSPSLTTEQLRQLFSFCGTVVDCSITDSKHIAYIEYSNSE 397

Query:   115 EATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPXXXXXXXXXXXXXXXXX 174
             EATAALALNN +V GR LNVE+AKS P KPS  NSS   SSLP                 
Sbjct:   398 EATAALALNNTEVFGRALNVEIAKSLPHKPSSNNSS---SSLPLMMQQAVAMQQMQFQQA 454

Query:   175 XXXXXXXXXXXXXNRAASMKSATELXXXXXXEISKKLKADGLVDEDKETKQKXXXXXXXX 234
                          NRAA+MKSATEL      EIS+KL+ DG+ +++KE  QK        
Sbjct:   455 ILMQQAVATQQAANRAATMKSATELAAARAAEISRKLRPDGVGNDEKEADQKSRSPSKSP 514

Query:   235 XXXXXXXXXPVHYQRTYRARSRS---KXXXXXXXXXXXXXXXXXXXXXXXXGHR-SRSPL 290
                      P+ Y+R  R+ + S   +                         +R SR   
Sbjct:   515 ARSRSKSKSPISYRRRRRSPTYSPPFRRPRSHRSRSPLRYQRRSTYEGRRRSYRDSRDIS 574

Query:   291 RSRHYSKYDNERLST-RDTRDGADRSRRESDIXXXXXXXXXXXXXXXXXXXXXXYRSDSG 349
              SR Y + D    S+ R +R  + + R+                           R+ S 
Sbjct:   575 ESRRYGRSDEHHSSSSRRSRSVSPKKRKSGQEDSELSRLRRDSSSRGEKKSS---RAGSR 631

Query:   350 SPKHRQEXXXXXXXXXXXXXXXXXXGNRNSPRND-DAKPKYR------HRSRSKSMERHD 402
             SP+ R+E                      S  +  D K K R      H+ RS+S  R D
Sbjct:   632 SPRRRKEVKSTPRDDEENKVKRRTRSRSRSVEDSADIKDKSRDEELKHHKKRSRSRSRED 691

Query:   403 EEK--DEAR---DGKSQHXXXXXXXXXXXXXXHHGRGRSPAGNVDENKSKLRGRSRSVSA 457
               K  D +R   + K +H               H      A + D N    + RS+S+  
Sbjct:   692 RSKTRDTSRNSDEAKQKHRQRSRSRSLENDNGSH-ENVDVAQDNDLNSRHSKRRSKSLD- 749

Query:   458 LDKYKSSEIADDXXXXXXXXXXXXXXXXXXVEGKMGGGXXXXXXXXXXXXXXXXISADGK 517
              + Y   E                       E +  G                  S +GK
Sbjct:   750 -EDYDMKERRGRSRSRSLETKNRSSRKNKLDEDRNTGSRRRRSRSK---------SVEGK 799

Query:   518 HHRGSRSPRGLDE-SRTKLGRRSRSKSIERKLYXXXXXXXXXXXXXXKSMLSPANLDRSE 576
                 ++  R  D+ S+ + GRRSRS S E K                +S  SP   D  +
Sbjct:   800 RSY-NKETRSRDKKSKRRSGRRSRSPSSEGK-----------QGRDIRS--SPGYSDEKK 845

Query:   577 SNRRRHSASQSKDHANS--ESAETRDYKSMHHPHNWDKTEGELNASLKDPTVMED 629
             S  +RHS S+S +  NS  +    R  +        DK  G+ + S   P   ED
Sbjct:   846 SRHKRHSRSRSIEKKNSSRDKRSKRHERLRSSSPGRDKRRGDRSLS---PVSSED 897

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000226 "microtubule cytoskeleton organization" evidence=RCA

GO:0000911 "cytokinesis by cell plate formation" evidence=RCA

GO:0007155 "cell adhesion" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

GO:0009888 "tissue development" evidence=RCA

GO:0010090 "trichome morphogenesis" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010638 "positive regulation of organelle organization" evidence=RCA

GO:0016926 "protein desumoylation" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0045010 "actin nucleation" evidence=RCA

GO:0050665 "hydrogen peroxide biosynthetic process" evidence=RCA

RGD|621696 Srek1 "splicing regulatory glutamine/lysine-rich protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 112 (44.5 bits), Expect = 1.3e-09, Sum P(4) = 1.3e-09
 Identities = 32/109 (29%), Positives = 50/109 (45%)

Query:    53 LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
             L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct:    55 LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 113

Query:   108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSL 156
             +E++       ALA N +  G RPL +  + +   KP  +    A   L
Sbjct:   114 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKEL 162

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q9JKL7 Srek1 "Splicing regulatory glutamine/lysine-rich protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 112 (44.5 bits), Expect = 1.3e-09, Sum P(4) = 1.3e-09
 Identities = 32/109 (29%), Positives = 50/109 (45%)

Query:    53 LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
             L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct:    55 LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 113

Query:   108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSL 156
             +E++       ALA N +  G RPL +  + +   KP  +    A   L
Sbjct:   114 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKEL 162

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q8WXA9 SREK1 "Splicing regulatory glutamine/lysine-rich protein 1" [Homo sapiens (taxid:9606)]

 Score = 112 (44.5 bits), Expect = 6.0e-09, Sum P(4) = 6.0e-09
 Identities = 32/109 (29%), Positives = 50/109 (45%)

Query:    53 LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
             L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct:    52 LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 110

Query:   108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSL 156
             +E++       ALA N +  G RPL +  + +   KP  +    A   L
Sbjct:   111 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKEL 159

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

MGI|MGI:2145245 Srek1 "splicing regulatory glutamine/lysine-rich protein 1" [Mus musculus (taxid:10090)]

 Score = 112 (44.5 bits), Expect = 9.8e-08, Sum P(4) = 9.8e-08
 Identities = 32/109 (29%), Positives = 50/109 (45%)

Query:    53 LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
             L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct:    55 LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 113

Query:   108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSL 156
             +E++       ALA N +  G RPL +  + +   KP  +    A   L
Sbjct:   114 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKEL 162

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|E2R749 SREK1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 112 (44.5 bits), Expect = 1.1e-07, Sum P(3) = 1.1e-07
 Identities = 32/109 (29%), Positives = 50/109 (45%)

Query:    53 LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
             L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct:    52 LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 110

Query:   108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSL 156
             +E++       ALA N +  G RPL +  + +   KP  +    A   L
Sbjct:   111 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKEL 159

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|J9P0H2 SREK1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 112 (44.5 bits), Expect = 2.3e-07, Sum P(3) = 2.3e-07
 Identities = 32/109 (29%), Positives = 50/109 (45%)

Query:    53 LSGSPDKAGKADALKKTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAY 107
             L G+ D + K D +++T+ V NL S   T +QL + F   G V    +    T    FA+
Sbjct:   168 LMGNVDPS-KIDEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAF 226

Query:   108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSL 156
             +E++       ALA N +  G RPL +  + +   KP  +    A   L
Sbjct:   227 VEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIVKPPEMTPQAAAKEL 275

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

TAIR|locus:2024842 CID8 "CTC-interacting domain 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 36/104 (34%), Positives = 58/104 (55%)

Query:    53 LSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH----FAYI 108
             L G   KA + D++++T+ VS++   +T E L  LFS CG VV+C I    +    FA++
Sbjct:   113 LPGRASKAQREDSIRRTVYVSDIDQSVTEEGLAGLFSSCGQVVDCRICGDPNSVLRFAFV 172

Query:   109 EYSKPEEATAALALNNMDVGGRPLNVEMAKS--FPQKPSHLNSS 150
             E+S  + A +AL+L    +G  P+ V  +K+   P  P+ L  S
Sbjct:   173 EFSDDQGARSALSLGGTMIGYYPVRVLPSKTAILPVNPTFLPRS 216

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

TAIR|locus:2091657 CID9 "CTC-interacting domain 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 8.9e-07, P = 8.9e-07
 Identities = 36/104 (34%), Positives = 58/104 (55%)

Query:    53 LSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH----FAYI 108
             L+G   KA + D++++T+ VS++   +T E L  LFS CG VV+C I    H    FA++
Sbjct:   126 LTGRISKAQREDSIRRTVYVSDIDQSVTEEGLAGLFSNCGQVVDCRICGDPHSVLRFAFV 185

Query:   109 EYSKPEEATAALALNNMDVGGRPLNVEMAKS--FPQKPSHLNSS 150
             E++  + A  AL+L    +G  P+ V  +K+   P  P+ L  S
Sbjct:   186 EFADDQGAHEALSLGGTMLGFYPVRVLPSKTAILPVNPTFLPRS 229

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2184022 CID13 "CTC-interacting domain 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 136 (52.9 bits), Expect = 3.1e-06, P = 3.1e-06
 Identities = 36/93 (38%), Positives = 52/93 (55%)

Query:    64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSK---HFAYIEYSKPEEATAA 119
             D +K+T+ VS++   +T EQL  LF  CG VV+C +  D K    FA+IE++  E A +A
Sbjct:   133 DMIKRTVYVSDIDNQVTEEQLASLFLSCGQVVDCRMCGDYKSILRFAFIEFTDAEGARSA 192

Query:   120 LALNNMDVGGRPLNVEMAKSF--PQKPSHLNSS 150
             L  +    G  P+ V M+K+   P  PS L  S
Sbjct:   193 LRKSGTMFGSHPIRVFMSKTAIAPVNPSFLPQS 225

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_880014 hypothetical protein (950 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	682
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-16
smart00360	73	smart00360, RRM, RNA recognition motif	3e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-13
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	3e-13
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	7e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-10
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-10
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-09
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	6e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	9e-09
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	2e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-08
PRK12678	672	PRK12678, PRK12678, transcription termination fact	7e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-07
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-07
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	4e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	8e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	9e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	4e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	9e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	9e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-05
cd12432	90	cd12432, RRM_ACINU, RNA recognition motif in apopt	4e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	4e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	5e-05
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	5e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	5e-05
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12441	73	cd12441, RRM_Nup53_like, RNA recognition motif in	3e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-04
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	5e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	6e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	6e-04
TIGR00934	800	TIGR00934, 2a38euk, potassium uptake protein, Trk	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-04
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	7e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	8e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-04
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	8e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	9e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.001
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.001
cd12519	80	cd12519, RRM1_SREK1, RNA recognition motif 1 in sp	0.001
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.001
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.001
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.001
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.002
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.002
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	0.002
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.002
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.002
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.002
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.002
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	0.002
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.003
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.003
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.003
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.003
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.003
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.003
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	0.003
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.004
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.004
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.004
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.004

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

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 31/72 (43%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TDSKHFAYIEYSKPEEATAAL-ALN 123
           L V NL P  T E LR+LFS  G +    I       SK FA++E+  PE+A  AL ALN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 124 NMDVGGRPLNVE 135
             ++ GR L V 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 70.7 bits (174), Expect = 3e-15
 Identities = 33/73 (45%), Positives = 42/73 (57%), Gaps = 7/73 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-A 121
           TL V NL P  T E+LR+LFS  G V    +  D     SK FA++E+   E+A  AL A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 122 LNNMDVGGRPLNV 134
           LN  ++ GRPL V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 29/67 (43%), Positives = 37/67 (55%), Gaps = 6/67 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYIEYSKPEEATAAL-ALNNM 125
           V NL P  T E L+ LFS  G +    I  D    SK FA++E+   E+A  AL ALN  
Sbjct: 3   VGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGK 62

Query: 126 DVGGRPL 132
           ++GGR L
Sbjct: 63  ELGGREL 69

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

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

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 4/85 (4%)

Query: 64  DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAYIEYSKPEEATAA 119
           + +++T+ V NL P  T +QL + FS  G V    +    T    +A++E+++      A
Sbjct: 1   EEIRRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINA 60

Query: 120 LALNNMDVGGRPLNVEMAKSFPQKP 144
           L LN    GGRPL V  + +   KP
Sbjct: 61  LKLNGAMFGGRPLKVNHSNNAIVKP 85

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 58.1 bits (141), Expect = 7e-11
 Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVEC----TITDSKHF----AYIEYSKPEEATAAL 120
            +QV+N+SP  T EQ+R LF F G + E     +  D         +++Y  PE+   AL
Sbjct: 1   VVQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVAL 60

Query: 121 ALNN 124
            L N
Sbjct: 61  HLTN 64

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 31/77 (40%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-A 121
            L V NL   +T E L+ LF   G V     ITD     S+ F ++E    EEA AA+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 122 LNNMDVGGRPLNVEMAK 138
           LN  D GGR L V  A+
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 56.7 bits (137), Expect = 3e-10
 Identities = 30/78 (38%), Positives = 48/78 (61%), Gaps = 4/78 (5%)

Query: 66  LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKH---FAYIEYSKPEEATAALA 121
           +++T+ VS++   +T EQL  LFS CG VV+C +  D      FA+IE++  E A AAL+
Sbjct: 1   IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS 60

Query: 122 LNNMDVGGRPLNVEMAKS 139
           L+   +G  P+ V  +K+
Sbjct: 61  LSGTMLGFYPVRVLPSKT 78

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 56.2 bits (136), Expect = 4e-10
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAALALN 123
           TL V NLS     + L + F  CG VV+  I       SK F ++E++  E A  AL  +
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 124 NMDVGGRPLNVEMAKS 139
             ++ GR + V++A  
Sbjct: 61  GEELLGREIRVDLATE 76

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|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 = 55.7 bits (135), Expect = 5e-10
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-A 121
            L VS LS   T ++L  LFS  G V E  +       +S+ F ++ +   E+A AA+  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 122 LNNMDVGGRPLNVEMAK 138
           LN  ++ GR + VE AK
Sbjct: 63  LNGKELEGRVIKVEKAK 79

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

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

 Score = 55.3 bits (134), Expect = 6e-10
 Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 3/65 (4%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
           V NL    T E+LR LF   GTV EC +   K++ ++   + E+A  A+ ALN  +  G+
Sbjct: 4   VGNLPDATTSEELRALFEKYGTVTECDVV--KNYGFVHMEEEEDAEDAIKALNGYEFMGK 61

Query: 131 PLNVE 135
            +NVE
Sbjct: 62  RINVE 66

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

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

 Score = 54.9 bits (133), Expect = 8e-10
 Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAYIEYSKPEEATAALA-LNN 124
           L V NL P +T E LR+ FS  G V    +       + FA++E++ PE+A AAL  LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 125 MDVGGRPLN 133
           + + GR L 
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TDSKHFAYIEYSKPEEATAALA-LN 123
           L V NL   +  E+LR+ FS  GT+    +       SK F ++ +S PEEAT A+  +N
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 124 NMDVGGRPLNVEMA 137
              +GG+PL V +A
Sbjct: 64  GRIIGGKPLYVALA 77

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

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 9/74 (12%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKH---FAYIEYSKPEEATAALAL 122
           V NL   L  + LR +FS  G V    I         +    FA++ +     A  AL L
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQL 64

Query: 123 NNMDVGGRPLNVEM 136
           N  ++GGR ++V +
Sbjct: 65  NGTELGGRKISVSL 78

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

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 84  LRQLFSFCGTVVECTITDSK-HFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA 137
           L +LFS  G V +  +   K  FA++E+S  E A  A+  LN +  GGRPL V+ +
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 53.8 bits (130), Expect = 3e-09
 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           V N+    T E+L++ F  CGT+   TI  D      K FAYIE+        AL LN  
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNES 63

Query: 126 DVGGRPLNV 134
           +  GR + V
Sbjct: 64  EFRGRQIKV 72

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

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

 Score = 52.6 bits (126), Expect = 6e-09
 Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 3/66 (4%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
           V N+S   T ++LR LF   G VVEC     K +A++   + EEA AA+ ALN  +V GR
Sbjct: 5   VGNVSATCTSDELRGLFEEFGRVVECDKV--KDYAFVHMEREEEALAAIEALNGKEVKGR 62

Query: 131 PLNVEM 136
            +NVE+
Sbjct: 63  RINVEL 68

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

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

 Score = 58.7 bits (142), Expect = 7e-09
 Identities = 35/127 (27%), Positives = 55/127 (43%), Gaps = 7/127 (5%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALA-LN 123
           L V NL   +T E+LR+LFS CG +    +       S+ F ++ +S PEEA  A+  ++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMH 347

Query: 124 NMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQTLTA 183
              +GG+PL V +A+   Q+ +HL         P M Q  +                   
Sbjct: 348 GRMLGGKPLYVALAQRKEQRRAHL-QDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQ 406

Query: 184 QQAANRA 190
           QQ   + 
Sbjct: 407 QQFNGQP 413

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

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

 Score = 52.3 bits (126), Expect = 8e-09
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 7/72 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALA-L 122
           L V NL   +T + LR +F   G +    +        SK + +I+++  E+A  AL  L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 123 NNMDVGGRPLNV 134
           N  ++ GRP+ V
Sbjct: 61  NGFELAGRPIKV 72

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

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 52.2 bits (126), Expect = 9e-09
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA-LALNNMDV 127
           T+ V NL   LT E+L++ FS  G + E  +   K +A++ +   E A  A +A+N   +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTSI 61

Query: 128 GGRPL 132
            G+ +
Sbjct: 62  NGQTV 66

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

>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 11/76 (14%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFC-----------GTVVECTITDSKHFAYIEYSKPEEATA 118
           L V NL P +T E+L   F+               V+   I   K+FA++E+   EEATA
Sbjct: 4   LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEATA 63

Query: 119 ALALNNMDVGGRPLNV 134
           ALAL+ +   G+PL +
Sbjct: 64  ALALDGIIFKGQPLKI 79

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 27/77 (35%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITDSKH-----FAYIEYSKPEEATAALA- 121
           TL V NL    T EQL + FS  G +  C  + D        F Y+ ++  E+A  AL  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 122 LNNMDVGGRPLNVEMAK 138
                 GGR ++VE AK
Sbjct: 61  KKKTKFGGRKIHVEFAK 77

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

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

 Score = 55.7 bits (135), Expect = 7e-08
 Identities = 44/238 (18%), Positives = 77/238 (32%), Gaps = 30/238 (12%)

Query: 324 HSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRND 383
            +   RR    + +    +   +++ + K     +AR ++ A +++       +   R +
Sbjct: 73  PAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRE 132

Query: 384 DAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDE 443
             +   R  +  K+ E  ++   EAR   ++  E +      R  +   R          
Sbjct: 133 RGEAARR-GAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERG 191

Query: 444 NKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPKH 503
                R                      DDR R   + +   +   G+  GG R      
Sbjct: 192 R----REERG---------------RDGDDRDRRDRREQGDRREERGRRDGGDRRG---- 228

Query: 504 HDRRRSRSISADGKHHRGSRSPRGLDESRTKLGRRSRSKSIERKLYRNRGRSRSADGR 561
             RRR     A G  +R  R  R  D+   + GRR R     R   R+R   R  DG 
Sbjct: 229 -RRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGR-----RFRDRDRRGRRGGDGG 280

Length = 672

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

 Score = 49.6 bits (119), Expect = 7e-08
 Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAA-LA 121
            L V NL    T EQ R+L S  G V  C +       +SK + ++EY+    A  A   
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 122 LNNMDVGGRPLNV 134
           L+   +GGR L V
Sbjct: 61  LDGKQIGGRKLQV 73

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALN 123
           T+ VSNL   +  ++LR+LFS CG + +  +       SK +AY+E+   E    AL L+
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLD 60

Query: 124 NMDVGGRPLNV 134
              + GRP+ V
Sbjct: 61  RELIKGRPMFV 71

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 7/76 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD-----SKHFAYIEYSKPEEATAAL-A 121
           TL V NLS  +  E L+  F   GTVV    ITD     S+ F Y+++  PE+A  A+ A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 122 LNNMDVGGRPLNVEMA 137
           ++  ++ GRP+NV+ +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAALAL 122
           T+ V  LS  +    L + FS  G V +   I D     SK  AY+E+   E    AL L
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 123 NNMDVGGRPLNV 134
               + G+P+ V
Sbjct: 61  TGQRLLGQPIMV 72

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 53.4 bits (128), Expect = 3e-07
 Identities = 40/150 (26%), Positives = 56/150 (37%), Gaps = 15/150 (10%)

Query: 476 RNRHKRRSRSKSVEGKMGGGSRDK-KPKHHDRRRSRSISADGKHHRGSRSPRGLDESRTK 534
           R+    R R KS         RD+ +     RRRSR  S     HR SR     ++SR +
Sbjct: 1   RDEEPDREREKSRG-------RDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPR 53

Query: 535 LGRRSRSKSIERKLYRNRGRSRSADGRRRKSMLSPANLDRSESNRRRHSASQSKDHANSE 594
             RR  S+S     Y +  RSR    RR +S+       RS    RR    +S  +   +
Sbjct: 54  DRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV-------RSIEQHRRRLRDRSPSNQWRK 106

Query: 595 SAETRDYKSMHHPHNWDKTEGELNASLKDP 624
             + R    +  P     T  +  AS    
Sbjct: 107 DDKKRSLWDIKPPGYELVTADQAKASQVFS 136

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|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHF--AYIEYSKPEEATAALALNNMDVGG 129
           VSN+SP  T +Q+   FSFCG +    +T+      A I + KP  A  AL L+N  +GG
Sbjct: 3   VSNISPKTTEKQISDFFSFCGKISNLDLTNDGESQTATITFEKPSAAKTALLLDNALLGG 62

Query: 130 RPLNV 134
           + + V
Sbjct: 63  KVIQV 67

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TDSKHFAYIEYSKPEEATAALAL 122
           +TL V NL   +T E L +LF   G +    I        K FA++ +        A+ L
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 123 -NNMDVGGRPLNVE 135
            N + + GR L ++
Sbjct: 62  LNGIRLFGRELRIK 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|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           V N+    T EQL ++FS  G VV   + TD      K + + E+   E A +A+  LN 
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 125 MDVGGRPLNVEMA 137
            +  GR L V+ A
Sbjct: 63  YEFNGRALRVDFA 75

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

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 47.5 bits (114), Expect = 4e-07
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 6/64 (9%)

Query: 67  KKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA---- 121
             TL+V N+ P L  + +L + FS  GT+V   +  +   A +++S  EEA  A      
Sbjct: 1   NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYRSPEA 60

Query: 122 -LNN 124
             NN
Sbjct: 61  VFNN 64

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

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

 Score = 47.2 bits (113), Expect = 5e-07
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 11/74 (14%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKH--FAYIEYSKPEEATAALALN 123
           L V  L+  +  + L   F   G + +  I       KH  FA++E+ +PE+A A  A++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAA--AID 58

Query: 124 NMDVG---GRPLNV 134
           NM+     GR + V
Sbjct: 59  NMNESELFGRTIRV 72

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

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

 Score = 47.0 bits (112), Expect = 6e-07
 Identities = 26/66 (39%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKHFAYIEYSKPEEATAAL-A 121
           T+ V  L    T E L+ +FS  GTVV  ++       D K FA+IE+  PEEA  A   
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 122 LNNMDV 127
           LNN   
Sbjct: 61  LNNPPE 66

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

 Score = 46.8 bits (112), Expect = 8e-07
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYIEYSKPEEATAAL-ALNNM 125
           V NL   +  E+L++LF   G +    +  D    SK F ++ +   E A  A+  LN  
Sbjct: 6   VKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGK 65

Query: 126 DVGGRPLNV 134
           +V G+ L V
Sbjct: 66  EVNGKKLYV 74

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

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

 Score = 51.4 bits (123), Expect = 9e-07
 Identities = 32/115 (27%), Positives = 46/115 (40%), Gaps = 13/115 (11%)

Query: 399 ERHDEEKDEARDG-KSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSA 457
              + EK   RD  +S  R R+RSR  SR  + H R R  +   D      R R R    
Sbjct: 5   PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDS-----RPRDRR--- 56

Query: 458 LDKYKSSEIADDSRDDRLRNRHKRRSRSKSV--EGKMGGGSRDKKPKHHDRRRSR 510
             +Y S            R+R + R RS+SV    +     RD+ P +  R+  +
Sbjct: 57  --RYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDK 109

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

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

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 7/70 (10%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKH--FAYIEYSKPEEATAALA-LNN 124
           V+++ P L+ + ++ +F   G +  C++       KH  + +IEY  P+ A  A+A +N 
Sbjct: 5   VASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64

Query: 125 MDVGGRPLNV 134
            D+GG+ L V
Sbjct: 65  FDLGGQQLRV 74

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

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 26/72 (36%), Positives = 34/72 (47%), Gaps = 7/72 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVEC-----TITD-SKHFAYIEYSKPEEATAAL-AL 122
           L V NL    T E+LR+LF   G + E        T  SK FA++ +  PE A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 123 NNMDVGGRPLNV 134
           +     GR L+V
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALA-L 122
            L+VSNL   +T E L +LF   G V +  I       S+  A + + K E+A  A+   
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 123 NNMDVGGRPLNVEM 136
           N + + G+P+ VE+
Sbjct: 62  NGVLLDGQPMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 11/75 (14%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVEC------TITDSKHFAYIEYSKPEEATAALALN 123
           L V  L+  +  + L+++FS  GTV +        +   + +AY+E+  PE+  A  A+ 
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPED--AEKAIK 58

Query: 124 NMDVG---GRPLNVE 135
           +MD G   G+ + VE
Sbjct: 59  HMDGGQIDGQEVTVE 73

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

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

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVEC-----TITDSKHFAYIEYSKPEEATAALAL- 122
           TL V+N  P      +R LF   G ++           ++ F Y++++ PE A AA+AL 
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALL 61

Query: 123 NNMDVGGRPLNVEM 136
           N     G  L V++
Sbjct: 62  NGKLGEGYKLVVKI 75

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKH---FAYIEYSKPEEATAALALN 123
           +T+ V  +   L+ + L++ FS CG V    +  D +H   FA++E++  E A +AL L+
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNLS 60

Query: 124 NMDVGGRPLNVEMAKS 139
              +GG PL V  +K+
Sbjct: 61  GTLLGGHPLRVSPSKT 76

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITDSKH--FAYIEYSKPEEATAAL-ALNNM 125
           L V NL   +T + L +LFS  G +  C  I +  +  +A++EY     A AAL  +N  
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 126 DVGGRPLNVEMA 137
            + G+ + V  A
Sbjct: 61  LILGQEIKVNWA 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 6/62 (9%)

Query: 82  EQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVE 135
             L + FS CG +   +I TD     SK FAYIE+   +    AL L+  D+GG  L V+
Sbjct: 18  RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVVD 77

Query: 136 MA 137
            A
Sbjct: 78  EA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           K L V NL    T EQLR+LFS  G V     I D   +A++ + + ++A  A+  +N  
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD---YAFVHFEERDDAVKAMEEMNGK 58

Query: 126 DVGGRPLNVEMAK 138
           ++ G P+ V +AK
Sbjct: 59  ELEGSPIEVSLAK 71

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

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

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH-----FAYIEYSKPEEATAALA-LNNM 125
           V NL    T   L++LFS  G V E TI          FA+++++   +A  A+  +N  
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGK 63

Query: 126 DVGGRPLNVEMA 137
            + GRP+ V+ A
Sbjct: 64  KIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

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

 Score = 43.8 bits (104), Expect = 7e-06
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA-LALNNMDVG 128
           L V NL   +T E+ ++LFS  G V E  +   K F +I       A  A   L+ +   
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMRK 63

Query: 129 GRPLNV 134
           GR L V
Sbjct: 64  GRQLRV 69

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

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

 Score = 48.4 bits (115), Expect = 9e-06
 Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 352 KHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDG 411
           + R  SS R   R+  +S  R R  R+  R+     + R R R  S           R  
Sbjct: 15  RDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVR-- 72

Query: 412 KSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSK 447
           +S+ R R+RSRS+   ++H  R R  + +    K  
Sbjct: 73  RSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDD 108

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

 Score = 43.7 bits (104), Expect = 9e-06
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEEATAALA-L 122
           L V NLS   T EQ+ +LFS CG +    +   +       F ++EY   E+A  A+  L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 123 NNMDVGGRPLNVEM 136
           N   +  R + V+ 
Sbjct: 61  NGTKLDDRIIRVDW 74

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

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 82  EQLRQLFSFCGTVVECTIT-DS-----KHFAYIEYSKPEEATAALALNNMDVGGRPLNVE 135
           E+LR+ F  CG V    I  D      K F Y+ +   +    AL LN + + GR + V+
Sbjct: 14  EELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIKLKGRKIRVK 73

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

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCG-----TVVECTIT-DSKHFAYIEYSKPEEATAALA-L 122
           + +  L   L+ +Q+++L    G      +V+ + T  SK +A+ EY  P     A+A L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 123 NNMDVGGRPLNVEMA 137
           N M +G + L V+ A
Sbjct: 63  NGMQLGDKKLTVQRA 77

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

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH--FAYIEYSKPEEATAALALNNMD 126
           T++V NL    T  ++RQ F  CG + E  I +S+    A IE+   +EA AAL  ++  
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTKDHKR 61

Query: 127 VGGRPLNVE 135
           +GG  ++V 
Sbjct: 62  LGGNEISVS 70

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 6/62 (9%)

Query: 80  TVEQLRQLFSFCGTV--VEC-TITDSKHF---AYIEYSKPEEATAALALNNMDVGGRPLN 133
           T +++R  FS+CG +  ++  T  D+  F   A+I +   E A  ALAL+  D+GGR L 
Sbjct: 11  TEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFLK 70

Query: 134 VE 135
           VE
Sbjct: 71  VE 72

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|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TDSKHF-AYIEYSKPEEATAA-LALNN 124
           + +SNL   +TV+ L Q+FS  G V +  I   +    A +++   E A  A  ALN 
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNG 61

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

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 30/78 (38%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL 120
           K T+ VSNL   LT   L ++FS  G VV+ TI        SK  A+I +   E+A   +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 121 -ALNNMDVGGRPLNVEMA 137
            ALNN ++ GR L   +A
Sbjct: 61  KALNNKELFGRTLKCSIA 78

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

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 6/76 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD-----SKHFAYIEYSKPEEATAALA 121
             + V  L    T + LR+ FS  G + E   ITD     S+ + ++ +   E A  A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 122 LNNMDVGGRPLNVEMA 137
             N  + GR  NV +A
Sbjct: 61  DPNPIIDGRKANVNLA 76

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 28/86 (32%), Positives = 39/86 (45%), Gaps = 13/86 (15%)

Query: 68  KTLQVSNLSPLLT-VEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEA-TAAL 120
           + L V  L      V  LR+LFS  G    C +        + FA++EY+  E+A  A  
Sbjct: 3   RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQ 62

Query: 121 ALNNMDVGGRPLNVEMAKSF--PQKP 144
           ALN   + G P+ V    SF  P +P
Sbjct: 63  ALNGHSLQGSPIRV----SFGNPGRP 84

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

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

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 6/72 (8%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK-----HFAYIEYSKPEEATAALA-LN 123
           L V NL   +  ++LR+LF   GT+ +  +  +K      F ++ Y   EEA  AL   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 124 NMDVGGRPLNVE 135
           N  +    + VE
Sbjct: 63  NSFIDTSKITVE 74

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

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

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMD 126
           TL V NL P ++ + L Q+F   G + E   T + +H  +IE+     A AAL ALN  +
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 127 VGGRPLNVE 135
           + G+ + +E
Sbjct: 63  IAGKRIKLE 71

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

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

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITDS-----KHFAYIEYSKPEEATAAL- 120
            T+ V N+   ++ + +R+L   CG V+    + D      K F + E+  PE A  AL 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 121 ALNNMDVGGRPLNV 134
            LN +++GG+ L V
Sbjct: 61  LLNGLELGGKKLLV 74

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

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

 Score = 46.4 bits (110), Expect = 4e-05
 Identities = 37/144 (25%), Positives = 47/144 (32%), Gaps = 27/144 (18%)

Query: 251 YRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLST---RD 307
              R R KSR       R RS       R RR  R RS  R RH    +         RD
Sbjct: 4   EPDREREKSRG----RDRDRSSE-----RPRRRSRDRSRFRDRHRRSRERSYREDSRPRD 54

Query: 308 TRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRAHS 367
            R    RS R    S        R+SR      R+S    S   +HR+    R  S ++ 
Sbjct: 55  RRRYDSRSPRSLRYSSV------RRSRD--RPRRRSRSVRSIE-QHRRRL--RDRSPSNQ 103

Query: 368 KSPKRHRGNRNSPRNDDAKPKYRH 391
                 + ++     D   P Y  
Sbjct: 104 WR----KDDKKRSLWDIKPPGYEL 123

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

 Score = 46.0 bits (109), Expect = 4e-05
 Identities = 41/153 (26%), Positives = 53/153 (34%), Gaps = 36/153 (23%)

Query: 219 EDKETKQKSRSPSTSRARSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPY 278
           E    ++KSR     R+  R + RS        R RSR + R     HRR R RS+    
Sbjct: 4   EPDREREKSRGRDRDRSSERPRRRS--------RDRSRFRDR-----HRRSRERSYREDS 50

Query: 279 RHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSP 338
           R R   R  S       S       S R +RD                   RR+SRSV  
Sbjct: 51  RPRDRRRYDS------RSPRSLRYSSVRRSRD-----------------RPRRRSRSVRS 87

Query: 339 HSRKSYRSDSGSPKHRQESSARKSSRAHSKSPK 371
             +   R    SP ++     +K S    K P 
Sbjct: 88  IEQHRRRLRDRSPSNQWRKDDKKRSLWDIKPPG 120

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|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins

 Score = 42.6 bits (101), Expect = 4e-05
 Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECT--ITDSKHFAYIEYSKPEEATAAL-ALNNM 125
            L + NL    T+ QL++L S  GT V     +   K   Y+ YS  EEA A   AL+ +
Sbjct: 3   ALHIDNLVRPFTLNQLKELLSETGTGVIEGFWMDKIKSHCYVTYSTVEEAVATREALHGL 62

Query: 126 ---DVGGRPLNVE 135
                  + L V+
Sbjct: 63  QWPSSNPKRLKVD 75

This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity. . Length = 90

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGG 129
           L V NL P  T +++R LF   G V+EC I  +  F +++  K     A   L++  + G
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFVHMD-DKTAADEAIRNLHHYKLHG 61

Query: 130 RPLNVE 135
             +NVE
Sbjct: 62  VAINVE 67

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEEAT-AALAL 122
           L VS LS       L+QLFS  G VV   I  +        F ++  +  EEA      L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 123 NNMDVGGRPLNVE 135
           +  ++ GR ++VE
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV 127
           T+ V N+ P  T   L  LF   G ++E      + FA+++    E+A  A+  L    V
Sbjct: 2   TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPV 61

Query: 128 GGRPL 132
            GRPL
Sbjct: 62  HGRPL 66

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDVG 128
           L V N+S   T ++LR  F   G V+EC I   K +A++   + E+A  A+  L+N +  
Sbjct: 3   LHVGNISSSCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQ 60

Query: 129 GRPLNVE 135
           G+ ++V+
Sbjct: 61  GKRMHVQ 67

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 4/71 (5%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAY---IEYSKPEEATAALA-LNNM 125
           +Q+SN+ P +  E L  L S  GTV  C    +K       + Y  PE+A  A+  LN  
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNGH 62

Query: 126 DVGGRPLNVEM 136
           +  G  L V  
Sbjct: 63  EYEGSKLKVSY 73

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 25/78 (32%), Positives = 33/78 (42%), Gaps = 21/78 (26%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVV-----------ECTITDSKHF----------A 106
           +TL V N+ P  T E L++LFS CG V            E     SK F          A
Sbjct: 1   RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVA 60

Query: 107 YIEYSKPEEATAALALNN 124
           Y+ + KP   + AL L +
Sbjct: 61  YVVFKKPSSLSRALKLKS 78

This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. . Length = 102

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

 Score = 45.3 bits (107), Expect = 1e-04
 Identities = 34/124 (27%), Positives = 50/124 (40%), Gaps = 14/124 (11%)

Query: 416 RERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRL 475
            E  R R  SR      R RS        + + R R RS    D+++ S       D R 
Sbjct: 3   EEPDREREKSRG---RDRDRS------SERPRRRSRDRSRFR-DRHRRSRERSYREDSRP 52

Query: 476 RNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADGKHHRGSRSPRGLDESRTKL 535
           R+R +  SRS          S  ++ +   RRRSRS+ +  +H R  R     ++ R   
Sbjct: 53  RDRRRYDSRSPRSLRY----SSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDD 108

Query: 536 GRRS 539
            +RS
Sbjct: 109 KKRS 112

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

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVG 128
           L V  L P  ++ +L + F   G +        +++AYIEY   E A AA  AL    +G
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60

Query: 129 --GRPLNVEMAK 138
             GR L V+ A 
Sbjct: 61  GPGRRLRVDFAD 72

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

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 28/72 (38%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 69  TLQVSNLSPLLTVEQ-LRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMD 126
           TL V    P  T E+ + +LF   G +V C I   K FA++E+   E+AT AL AL+   
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--RKTFAFVEFEDSEDATKALEALHGSR 58

Query: 127 VGGRPLNVEMAK 138
           + G  L VE  K
Sbjct: 59  IDGSVLTVEFVK 70

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

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

 Score = 40.6 bits (96), Expect = 1e-04
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 15/81 (18%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALAL 122
           T++V+NLS     + LR+LF   G +    +  D     S+ FA++ +   E+A  A+  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 123 NNMDVGGRP-----LNVEMAK 138
            N    G       L+VE AK
Sbjct: 61  LN----GFGYDNLILSVEWAK 77

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

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

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAA-LA 121
            L V  L+P+ T E L  +FS  G +  C +       DS  +A+IE+   E+   A   
Sbjct: 5   VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 122 LNNMDVGGRPLNVEMAKS 139
           ++N+ +  R ++V+ ++S
Sbjct: 65  MDNVLIDDRRIHVDFSQS 82

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

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

 Score = 44.1 bits (105), Expect = 2e-04
 Identities = 32/206 (15%), Positives = 62/206 (30%), Gaps = 6/206 (2%)

Query: 281 RRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVP--RRRKSRSVSP 338
                +R+   +R   +   E  + +     A R+   +     S     + R+ R    
Sbjct: 76  AARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGE 135

Query: 339 HSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSM 398
            +R+     +G    +  + AR  +   ++  +R    R   R D      R     +  
Sbjct: 136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREE 195

Query: 399 ERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSAL 458
              D +  + RD + Q   R+        D    R R    +   + ++     R     
Sbjct: 196 RGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDG 255

Query: 459 DKYKSSEIADDSRDDRLRNRHKRRSR 484
           +           R  R R+R  RR  
Sbjct: 256 E----GRGGRRGRRFRDRDRRGRRGG 277

Length = 672

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALA- 121
           +TL V NL P +T E + +LF   G V++  I        K FA++ +        A+  
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 122 LNNMDVGGRPLNVE 135
           LN + + GRPLN++
Sbjct: 62  LNGIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALA-LNNM 125
           V NL   +T ++LR+ F   G V +  +       S+ F ++ +   E+A  A+   N  
Sbjct: 5   VKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKT 64

Query: 126 DVGGRPLNVEMA 137
            +    ++VE+A
Sbjct: 65  FIDTSKISVELA 76

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

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

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 28/73 (38%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNM 125
           V N+    T E+L   F  CG+V   TI         K FAYIE+S  E    ALAL+  
Sbjct: 4   VGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDES 63

Query: 126 DVGGRPLNVEMAK 138
              GR + V M K
Sbjct: 64  LFRGRQIKV-MPK 75

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

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNM 125
           V  L P +T E+ ++ FS  G VV+  +        S+ F ++ +          +   +
Sbjct: 4   VGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGML 63

Query: 126 DVGGRPLNVEMA 137
           ++GG+ + V+ A
Sbjct: 64  ELGGKQVEVKRA 75

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

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

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALA-LNNM 125
           V+NL   +  ++L+++F   G VV   I       S+    +++  P EA  A++  N  
Sbjct: 3   VANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQ 62

Query: 126 DVGGRPLNVEM 136
            +  RP+ V+M
Sbjct: 63  MLFDRPMRVKM 73

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

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

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEAT-AAL 120
           K  L VS L   +T E+L +LF   G V    +        K  AY+EY     A+ A L
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVL 61

Query: 121 ALNNMDVGGRPLNV 134
            ++  ++  + ++V
Sbjct: 62  KMDGTEIKEKTISV 75

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

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-AL 122
           L VS L   +T ++L  LFS  G ++   I  D     S+   +I + K  EA  A+ AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 123 NNMDVGG--RPLNVEMA 137
           N     G   P+ V+ A
Sbjct: 63  NGTIPPGATEPITVKFA 79

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

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

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 12/81 (14%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----------TDSKHFAYIEYSKPEEA 116
            TL V NL+   T E L++ F  CG V   TI             S  + ++E+   E A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 117 TAAL-ALNNMDVGGRPLNVEM 136
             AL  L    + G  L +++
Sbjct: 61  QKALKRLQGTVLDGHALELKL 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|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 84  LRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGR 130
           LR+ FS CGT++E       ++ +++YS   EA  AL+ N   + G 
Sbjct: 18  LRE-FSSCGTILEVRYPPGANWIHLKYSSRLEAERALSKNGTIINGG 63

This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. Length = 73

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TDS-----KHFAYIEYSKPEEATAALA-L 122
           L + NL+   T E L +LFS  G + E  +  D      K FA++ Y  PE A  A A L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 123 NNMDVGGRPLNV 134
           +     GR L++
Sbjct: 65  DGTVFQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 28/82 (34%), Positives = 39/82 (47%), Gaps = 12/82 (14%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TD-SKHFAYIEYSKPEEATAAL- 120
           +T+ + NL    T E+L++LFS  G V    I     T  SK  A++++   E A   L 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 121 -ALNNMDVG----GRPLNVEMA 137
            A N  D G    GR L V +A
Sbjct: 61  AADNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family proteins

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 74  NLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAA-LALNNMDVGGRPL 132
           NL+P +    LR L    G ++   +      A I YS  EEA  A  ALNN  +G   L
Sbjct: 8   NLTPQIDGSTLRTLCMQHGPLLTFHLNLRHGNALIRYSSKEEAAKAQSALNNCVLGNTTL 67

Query: 133 NVE 135
             E
Sbjct: 68  LAE 70

This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. . Length = 71

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKH--FAYIEYSKPEEATAAL-A 121
             L V N+    T ++LR+LFS  G V    +    D  H  FA++E+   +EA  A+ A
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 122 LNNMDVGGRPLNVEMA 137
           L +  + GR L +E A
Sbjct: 61  LKSTHLYGRHLVLEYA 76

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

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

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 8/78 (10%)

Query: 69  TLQVSNLSPLLTVEQLRQ----LFSFCGTVVECTITDSKHF---AYIEYSKPEEATAAL- 120
           TL ++NL+  +  ++L++    LFS  G V++   + +      A++ +   E AT AL 
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 121 ALNNMDVGGRPLNVEMAK 138
           AL       +P+ ++ AK
Sbjct: 61  ALQGFPFYDKPMRIQYAK 78

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|130009 TIGR00934, 2a38euk, potassium uptake protein, Trk family

 Score = 43.0 bits (101), Expect = 6e-04
 Identities = 49/286 (17%), Positives = 72/286 (25%), Gaps = 32/286 (11%)

Query: 302 RLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSD---SGSPKHRQESS 358
           R  T   R+  DR            V     S        K +  +      P       
Sbjct: 149 RTKTLLQRELEDRPETGV----AGRVTVPHGSAKRRDFQDKLFSGEFVKRDEPDQNSPDV 204

Query: 359 ARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRER 418
              +    S S            + D  P+  +RS       H+  ++     KS    R
Sbjct: 205 KSDTRADESISDLEFEKFAKRRGSRDVDPEDLYRSIMMLQGIHERIRE-----KSSANSR 259

Query: 419 KRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNR 478
              RS     E   R  S         S +   S+S++     KS + A   R  +  +R
Sbjct: 260 SDERSSESIQEQVERRPST--------SDIERNSQSLTRRYDDKSFDKAVRLRRSKTIDR 311

Query: 479 HKRRSRS---------KSVEGKMGGGSRDKKPKHHDRRRSRSISAD--GKHHRGSRSPRG 527
            +              K          R KK         +   A    K    +    G
Sbjct: 312 AEACDLEELDRAKDFEKMTYDNWKAHHRKKKNFRPRGWNLKFRKASRFPKDSDRNYEDNG 371

Query: 528 LDESRTK-LGRRSRSKSIERKLYRNRGRSRSADGRRRKSMLSPANL 572
              S +   G    S S E  LY    + R          +S   L
Sbjct: 372 NHLSASSSFGSEEPSLSSEENLYPTYNKKREDSRHTLSKTMSTNYL 417

The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system [Transport and binding proteins, Cations and iron carrying compounds]. Length = 800

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

 Score = 42.6 bits (100), Expect = 7e-04
 Identities = 32/154 (20%), Positives = 51/154 (33%), Gaps = 37/154 (24%)

Query: 352 KHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDG 411
           +  +    R+ SR   +     R            P+ R R RS+  +RH   ++ +   
Sbjct: 1   RDEEPDREREKSRGRDRDRSSER------------PRRRSRDRSRFRDRHRRSRERSYRE 48

Query: 412 KSQHRERKRSRSLSR---EDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIAD 468
            S+ R+R+R  S S          R R             R RSRSV ++++        
Sbjct: 49  DSRPRDRRRYDSRSPRSLRYSSVRRSRDR----------PRRRSRSVRSIEQ-------- 90

Query: 469 DSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPK 502
                R R R +  S     + K       K P 
Sbjct: 91  ----HRRRLRDRSPSNQWRKDDKKRSLWDIKPPG 120

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

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK------HFAYIEYSKPEEATAAL-AL 122
           L V+NL   LT ++LR++F   G +V+C +   K        A++ Y K EEA AA+ +L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 123 NNMDVGGR--PLNVEMA 137
           N     G   PL+V  A
Sbjct: 63  NGTIPPGSTMPLSVRYA 79

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

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-------TDSKHFAYIEYSKPEEATAAL-A 121
           L + NL P +  + L   FS  G +++           +SK FA+I Y   E + AA+ A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 122 LNNMDVGGRPLNVEMA 137
           +N   +  RP+ V  A
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

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

 Score = 42.2 bits (100), Expect = 8e-04
 Identities = 35/237 (14%), Positives = 65/237 (27%), Gaps = 15/237 (6%)

Query: 282 RGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVS--PH 339
           +  R      +                   A R   +      +       +   +    
Sbjct: 56  KEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA 115

Query: 340 SRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSME 399
           +  +   ++   + R+E        A  K+ +         R D A+         +   
Sbjct: 116 AEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRR 175

Query: 400 RHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALD 459
              E++    +   + R  +R R     D    R R   G+  E + +  G  R      
Sbjct: 176 GDREDRQAEAERGERGRREERGRDGDDRD---RRDRREQGDRREERGRRDGGDRRGRRRR 232

Query: 460 KYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADG 516
                    D RD R  +  + R      +G+  GG R ++    DR R      DG
Sbjct: 233 --------RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRR--FRDRDRRGRRGGDG 279

Length = 672

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 23/59 (38%), Positives = 32/59 (54%), Gaps = 7/59 (11%)

Query: 84  LRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE 135
           L QLF+  G V+   +  D     SK F ++ Y  PE A AA+ A+N   VGG+ L V+
Sbjct: 15  LYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

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

 Score = 38.3 bits (90), Expect = 8e-04
 Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 18/85 (21%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----------SKHFAYIEYSKPEEA 116
            TL +  L  L T E + Q  S   +V    I D           S+ FA++E+   E+A
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASV---PIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59

Query: 117 TAAL-ALNNMD---VGGRPLNVEMA 137
           T  + ALNN+D   + GR + V  A
Sbjct: 60  TQWMDALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 38.2 bits (89), Expect = 8e-04
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 69  TLQVSNLSPLLTVEQLR----QLFSFCG-TVVECTITDSKHFAYIEYSKPEEATAALALN 123
           +L V NL+P    ++L+    + FS     V +  I  SK F Y+++   E+   AL L 
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALELT 61

Query: 124 NMDVGGRPLNVEMA 137
              + G  + +E A
Sbjct: 62  GKKLLGNEIKLEKA 75

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

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

 Score = 38.1 bits (89), Expect = 9e-04
 Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 11/76 (14%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVV------ECTITDSKHFAYIEYSKPEEATAALA-LNN 124
           V NL P      L QLFS  G V       + T    K + ++  +  EEA +A+A LN 
Sbjct: 6   VYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNG 65

Query: 125 MDVGGRPLNVEMAKSF 140
             +GGR L V    SF
Sbjct: 66  YRLGGRVLQV----SF 77

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

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYIEYSKPEEATAAL-ALNNM 125
           V NL   +T + L+ LF  CG V+   + TD    SK F  + +  PE+A  A+   N  
Sbjct: 3   VRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGY 62

Query: 126 DVGGRPLNV 134
           D+ GR L V
Sbjct: 63  DLEGRELEV 71

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

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

 Score = 42.2 bits (100), Expect = 0.001
 Identities = 35/252 (13%), Positives = 72/252 (28%), Gaps = 13/252 (5%)

Query: 198 ELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRSKSRSPVHYQRTYRARSRS 257
           EL AA          A            +  + + + AR   +  +     +   A +  
Sbjct: 50  ELIAAIKEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAAR 109

Query: 258 KSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRR 317
            + +  +        + +   R R     R   R            +  D  +  +   R
Sbjct: 110 AAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEER 169

Query: 318 ESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNR 377
           +          R+ ++        +  R + G     ++   R+          +     
Sbjct: 170 DERRRRGDREDRQAEAER----GERGRREERGRDGDDRDRRDRRE---------QGDRRE 216

Query: 378 NSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSP 437
              R D    + R R R +   R D+ +++  D      E +  R   R  +   RGR  
Sbjct: 217 ERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRG 276

Query: 438 AGNVDENKSKLR 449
               +E + +LR
Sbjct: 277 GDGGNEREPELR 288

Length = 672

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDV 127
            L VSNL P +T + + +LFS  G +    +      A + Y + ++A  A+   NN ++
Sbjct: 2   RLVVSNLHPSVTEDDIVELFSAIGALKRARLV-RPGVAEVVYVRKDDALTAIDKYNNREL 60

Query: 128 GGRPLNVEM 136
            G+P+  ++
Sbjct: 61  DGQPMKCKL 69

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240963 cd12519, RRM1_SREK1, RNA recognition motif 1 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 8/63 (12%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVE--------CTITDSKHFAYIEYSKPEEATAALA 121
           +QV+NLS  +T +Q+R LF F G + E          +  S    YI+Y +P     A  
Sbjct: 2   IQVTNLSAAVTSDQMRTLFGFLGDIEELRLYPPDNAPLAFSSKVCYIKYREPSSVGVAQH 61

Query: 122 LNN 124
           L N
Sbjct: 62  LTN 64

This subgroup corresponds to the RRM1 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), and is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 generally contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1; plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 80

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 3/70 (4%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH--FAYIEYSKPEEATAALA-LNNM 125
           T+          +  +++LF  CG V + T+        A+I +   E A  A+  LN  
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 126 DVGGRPLNVE 135
            V G  + V+
Sbjct: 61  SVDGNCIKVQ 70

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

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

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 5/56 (8%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHF-----AYIEYSKPEEATAAL 120
           L V NL P +T + L+Q+F   G V    I   K+       ++EY +  +A  AL
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIAL 56

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSK----H--FAYIEYSKPEEATAALA-LNN 124
           V NL   +T E L +LF   G VV   I   +    H  + ++E+   E+A  A+  +N 
Sbjct: 3   VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62

Query: 125 MDVGGRPLNV 134
           + + G+P+ V
Sbjct: 63  IKLYGKPIRV 72

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

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

 Score = 41.0 bits (97), Expect = 0.002
 Identities = 30/196 (15%), Positives = 56/196 (28%), Gaps = 10/196 (5%)

Query: 405 KDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSS 464
                   +  R   R+ + +R+ E      + A             +   +A    +++
Sbjct: 67  AATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAA-------PAARAAAAAAAEAA 119

Query: 465 EIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADGKHHRGSRS 524
              + ++    R R +   R  + +   GG     + +     R+     D +  RG R 
Sbjct: 120 SAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDRE 179

Query: 525 PRGLDESRTKLGRRSRSKSIERKLYRNRGRSRSADGRRRKSMLSPANLDRSESNRRRHSA 584
            R  +  R + GRR           R   R +      R         DR    RRR   
Sbjct: 180 DRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERG---RRDGGDRRGRRRRRDRR 236

Query: 585 SQSKDHANSESAETRD 600
               D    +  +   
Sbjct: 237 DARGDDNREDRGDRDG 252

Length = 672

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 6/64 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGG 129
           L V    P  +   +R++FS  G V E  +    +FA++E+   E A  A       V G
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--SNFAFVEFESLESAIRAKD----SVHG 55

Query: 130 RPLN 133
           + LN
Sbjct: 56  KVLN 59

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

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

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVEC---TITDS---KHFAYIEYSKPEEATAALALNNM 125
           V NLS   T ++LR  F   G +      T  DS   K FA++++   E   A  AL   
Sbjct: 3   VGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF--EEIEFATNALKGK 60

Query: 126 DVGGRPLNVEMA 137
            + GR L VE  
Sbjct: 61  HLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDV 127
           T+ V  L P +T ++LR LF   G +V   I   K   ++++     A AA+  L    +
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTII 62

Query: 128 GGRP 131
           GG  
Sbjct: 63  GGSR 66

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

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

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK-HFAYIEYSKPEEATAAL-ALNNMD 126
           TL + NL P ++ E LR +F   G V E   T  K    ++E+    +A  AL A+N  +
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKE 62

Query: 127 VGGRPLNVE 135
           + G+P+ +E
Sbjct: 63  ISGKPVVIE 71

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

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

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALA- 121
           TL V NL+  +T E L   FS    +    +       +S+ + ++ ++  E+A  ALA 
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 122 LNNMDVGGRPLNVEMAK 138
           L N  + GR L +++A+
Sbjct: 61  LKNKKLHGRILRLDIAE 77

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

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDVGGR 130
           V N+    + E+LR LF   G V+ C +   + FA++       A  A+  LN  ++ GR
Sbjct: 5   VGNVDEDTSQEELRALFEAYGAVLSCAVM--RQFAFVHLRGEAAADRAIEELNGRELHGR 62

Query: 131 PLNVEMA 137
            L VE +
Sbjct: 63  KLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 34/125 (27%), Positives = 60/125 (48%), Gaps = 19/125 (15%)

Query: 41  AAQVQAQQSAKDLSG----------SPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSF 90
            ++  +Q++ K+L+G          S  + G        L V+NL   +T +QL  +F  
Sbjct: 157 GSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGK 216

Query: 91  CGTVVECTITDSKH------FAYIEYSKPEEATAAL-ALNNM--DVGGRPLNVEMAKSFP 141
            G +V+  I   K        A++ ++K EEA  A+ ALNN+  + G +PL V +A+   
Sbjct: 217 YGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG 276

Query: 142 QKPSH 146
           +  +H
Sbjct: 277 KAKAH 281

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

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           +  LS   T E LR+ FS  G VV+C I  D     S+ F ++ ++ P      LA    
Sbjct: 3   IGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPH 62

Query: 126 DVGGR 130
            + GR
Sbjct: 63  VLDGR 67

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

>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 11/68 (16%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHF------AYIEYSKPEEATAAL-A 121
           TL +SN+ P +T E L++LF+  G     T+   K F      A I+    EEA  AL A
Sbjct: 1   TLHLSNIPPSVTEEDLKELFTQTG----GTVKAFKFFPKDRKMALIQMGSVEEAIEALIA 56

Query: 122 LNNMDVGG 129
           L+N  +  
Sbjct: 57  LHNYQLSE 64

This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 7/68 (10%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALA-LNN 124
           V +LSP +  E LR  F+  G + +  +        SK + ++ + K E+A  A+  +N 
Sbjct: 4   VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

Query: 125 MDVGGRPL 132
             +GGR +
Sbjct: 64  QWLGGRAI 71

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

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

 Score = 39.9 bits (92), Expect = 0.003
 Identities = 33/96 (34%), Positives = 46/96 (47%), Gaps = 7/96 (7%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAY 107
           S SP    K+     TL V NL   +T E LR+LF   G V    +        S+ FA+
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAF 161

Query: 108 IEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ 142
           +E+   E A  A+  LN  ++ GRPL V+ A+   Q
Sbjct: 162 VEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ 197

Length = 306

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

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGG 129
           V NL P  T  +L   F   G +    +  +   FA++E+  P +A  A+ AL+   + G
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRICG 63

Query: 130 RPLNVEMAKS 139
             + VE+++ 
Sbjct: 64  NRVRVELSRG 73

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 26/79 (32%), Positives = 33/79 (41%), Gaps = 15/79 (18%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK----------HFAYIEYSKPEEATAA 119
           L V NL   LT  +L++ FS  G      ITD K            A+I Y   EEA  A
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGG----EITDVKLLRTEDGKSRRIAFIGYKTEEEAQKA 58

Query: 120 LA-LNNMDVGGRPLNVEMA 137
               NN  +    ++VE A
Sbjct: 59  KDYFNNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 36.9 bits (85), Expect = 0.003
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALA- 121
           +TL V NL   +  E L +LF   G + + TI        K F ++ +   E    A+A 
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIAL 61

Query: 122 LNNMDVGGRPLNV 134
           LN + + GRP+ V
Sbjct: 62  LNGIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALAL 122
            L V NL    T E L   F   G      + TD     SK  A++E+   E  T AL L
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 123 NNMDVGGRPLNVE 135
           ++  + GR +NVE
Sbjct: 62  HHTLLKGRKINVE 74

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFS-FCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           K L + NL    T E L  LF+ F G   E  +   +  A++E+   E+AT AL AL   
Sbjct: 3   KILFLQNLPEETTKEMLEMLFNQFPG-FKEVRLVPRRGIAFVEFETEEQATVALQALQGF 61

Query: 126 DV 127
            +
Sbjct: 62  KI 63

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAALAL 122
           ++V+NLSP  T   +   FSF G +    I    +    AY+ +  P+    AL L
Sbjct: 1   VEVTNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQTAYVTFKDPQAQETALLL 56

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

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

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 7/60 (11%)

Query: 82  EQLRQLFSFCGTVVECTIT-DS---KH--FAYIEYSKPEEATAAL-ALNNMDVGGRPLNV 134
           + +RQ FS  G +    ++ D    KH  FA++EY  PE A  AL  +N + +GGR + V
Sbjct: 15  DTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 81  VEQLRQLFSFCGTVVE-----CTITDSKHFAYIEYSKPEEATAALA-LNNMDV-GGRPLN 133
            ++L  LF   G + E          ++ +A++ Y+  E A  A+  L+N ++  G+ L 
Sbjct: 15  EDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLG 74

Query: 134 VEM 136
           V +
Sbjct: 75  VCI 77

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITDSKH---FAYIEYSKPEEATAAL-A 121
           K ++ V  LSP +T E+L + FS  G ++E   I  + H   FA+I++ + + A  A+ +
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62

Query: 122 LNNMDVGGRPLNVE 135
            N+  +  + ++V+
Sbjct: 63  ENHSMLKNKTMHVQ 76

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 22/80 (27%), Positives = 31/80 (38%), Gaps = 10/80 (12%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH---------FAYIEYSKPEEATAA 119
            L + NL   LT   L +LFS  G + +      K          + ++ +   EEA  A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 120 LA-LNNMDVGGRPLNVEMAK 138
           L  LN     G+ L V  A 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	682
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.68
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.64
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.6
PLN03120	260	nucleic acid binding protein; Provisional	99.6
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.54
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.52
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.46
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.44
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.38
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.37
PLN03213	759	repressor of silencing 3; Provisional	99.36
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.36
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.35
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.34
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.33
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.31
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.3
smart00362	72	RRM_2 RNA recognition motif.	99.3
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.29
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.28
KOG0122	270	consensus Translation initiation factor 3, subunit	99.28
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.26
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.26
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.25
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.25
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.24
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.24
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.24
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.22
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.22
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.21
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.21
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.21
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.2
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.19
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.18
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.18
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.18
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.18
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.17
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.16
smart00360	71	RRM RNA recognition motif.	99.14
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.13
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.09
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.06
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.06
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.05
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.04
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.03
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.02
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.99
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.96
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.96
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.95
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.94
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.93
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.93
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.89
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.85
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.85
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.8
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.79
smart00361	70	RRM_1 RNA recognition motif.	98.78
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.76
KOG0151	877	consensus Predicted splicing regulator, contains R	98.74
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.73
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.72
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.68
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.67
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.66
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.55
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.49
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.49
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.46
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.45
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.44
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.44
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.43
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.42
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.38
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.37
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.19
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.14
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.99
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.98
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.94
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.82
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.79
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.78
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.77
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.7
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.64
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.61
KOG0226	290	consensus RNA-binding proteins [General function p	97.59
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.58
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.55
KOG3152	278	consensus TBP-binding protein, activator of basal	97.46
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.41
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.38
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.34
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.29
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.29
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.28
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.24
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.21
KOG4210	285	consensus Nuclear localization sequence binding pr	97.18
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.13
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.07
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.93
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.83
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.82
KOG2314	698	consensus Translation initiation factor 3, subunit	96.75
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.65
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.58
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.54
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.47
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.42
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.37
KOG2135	526	consensus Proteins containing the RNA recognition	96.16
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.79
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.77
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.7
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.56
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.37
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.93
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.9
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.88
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.74
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.64
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.62
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.19
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.11
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	94.04
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	93.94
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.3
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.23
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	90.64
KOG4210	285	consensus Nuclear localization sequence binding pr	90.28
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	89.72
KOG2318	650	consensus Uncharacterized conserved protein [Funct	89.2
KOG4368	757	consensus Predicted RNA binding protein, contains	88.37
KOG4660	549	consensus Protein Mei2, essential for commitment t	86.21
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	86.06
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	85.92
KOG2146	354	consensus Splicing coactivator SRm160/300, subunit	83.48
KOG2891	445	consensus Surface glycoprotein [General function p	81.4
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	80.02

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=6.7e-16  Score=147.04  Aligned_cols=78  Identities=26%  Similarity=0.448  Sum_probs=72.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ...+.||||||+..+++.||+.+|..||.|..|+|. .+.|||||+|++..+|+.|+ .|||..|+|..|.|+++.....
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            347899999999999999999999999999999997 67899999999999999999 8999999999999999986544

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.64  E-value=7.3e-15  Score=143.04  Aligned_cols=77  Identities=30%  Similarity=0.452  Sum_probs=72.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...+|.|-||.+.++.++|..+|++||.|.+|.|.      +.+|||||-|.+..+|+.|| +|+|.+|+|+.|.|++|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            46799999999999999999999999999999997      58999999999999999999 899999999999999998


Q ss_pred             cCCC
Q 005698          139 SFPQ  142 (682)
Q Consensus       139 ~~~~  142 (682)
                      ....
T Consensus        92 ygr~   95 (256)
T KOG4207|consen   92 YGRP   95 (256)
T ss_pred             cCCC
Confidence            6543

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

Probab=99.60  E-value=5.9e-15  Score=140.76  Aligned_cols=82  Identities=24%  Similarity=0.419  Sum_probs=73.8

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ..-...++|||+|||+.+||++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|
T Consensus        29 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V  108 (144)
T PLN03134         29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV  108 (144)
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            334567899999999999999999999999999999997      36899999999999999999 79999999999999


Q ss_pred             EecccCCCC
Q 005698          135 EMAKSFPQK  143 (682)
Q Consensus       135 ~~a~~~~~~  143 (682)
                      .|+......
T Consensus       109 ~~a~~~~~~  117 (144)
T PLN03134        109 NPANDRPSA  117 (144)
T ss_pred             EeCCcCCCC
Confidence            999865443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.60  E-value=2e-14  Score=147.21  Aligned_cols=134  Identities=19%  Similarity=0.361  Sum_probs=98.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccCCCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      .++|||+||++.+|+++|++||+.||.|..|.|+   ...|||||+|.+.++|+.||.|||..|.|+.|.|.++......
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~~~p   83 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDYQLP   83 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCCCCC
Confidence            5799999999999999999999999999999997   3579999999999999999999999999999999998755433


Q ss_pred             CCCCCCCccCCchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHH
Q 005698          144 PSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQTLTAQQAANRAASMKSATELAAA  202 (682)
Q Consensus       144 ~~~~~~~~~~~~~P~~~~~~~~~qq~~~~q~~~~q~~~~~qq~a~~aa~~~~a~~~Aaa  202 (682)
                      +..+.........+  .......+.+.....++..+.++.+.+++.|..+..--+..+.
T Consensus        84 ~~~~~~~~~~~~~~--~~~~~~~~a~~vva~mLAkGy~l~~dA~~kAk~fDekH~~ss~  140 (260)
T PLN03120         84 PEALAPLSSNSPAS--GAESAVKKAEDVVSSMLAKGFILGKDAVNKAKAFDEKHQLTST  140 (260)
T ss_pred             cccccccccccCCC--CccchhhHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhhchHHH
Confidence            22111100000000  0001112234566777888888888888888877665444433

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.55  E-value=2.2e-14  Score=148.08  Aligned_cols=77  Identities=30%  Similarity=0.420  Sum_probs=72.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...+.|||.|||+.+.+.||..+|.+||.|.+|.|+    .+||||||+|++.++|+.|- +|||++|.|++|.|..|..
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            446899999999999999999999999999999998    68999999999999999999 8999999999999999886


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ..
T Consensus       174 rV  175 (376)
T KOG0125|consen  174 RV  175 (376)
T ss_pred             hh
Confidence            53

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.54  E-value=1.1e-13  Score=139.84  Aligned_cols=145  Identities=19%  Similarity=0.259  Sum_probs=99.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccCCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ...+|||+||++.+|+++|++||+.||+|.+|.|+   ...+||||+|.+.++|+.||.|||..|.|..|.|..+.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~y~~   83 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQYED   83 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCccccc
Confidence            35799999999999999999999999999999998   356899999999999999999999999999999987664333


Q ss_pred             CCCCCCCCcc-C-------Cch-hhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHH---HHHHHHHHHHh
Q 005698          143 KPSHLNSSLA-G-------SSL-PMM-MQQAVAMQQMQFQQALLMQQTLTAQQAANRAASMKSATE---LAAARAAEISK  209 (682)
Q Consensus       143 ~~~~~~~~~~-~-------~~~-P~~-~~~~~~~qq~~~~q~~~~q~~~~~qq~a~~aa~~~~a~~---~Aaa~aa~~a~  209 (682)
                      .+..+..... .       ... ... .........+.....++..+.++.+.+++.|.++..--+   .|++..+++.+
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~a~~~aq~Vv~tmLAkGyvLgkda~~KAkafDE~h~lss~a~a~v~~~d~  163 (243)
T PLN03121         84 EFDFWNRPSWDTEDISTHNYETNQFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAKVAELSK  163 (243)
T ss_pred             CcccccCccccccccccccccccccCCCchhhHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhcCccHhhhhhhhhhhh
Confidence            2221111100 0       000 000 000111122345667777788888888888877765433   33444444443


Q ss_pred             h
Q 005698          210 K  210 (682)
Q Consensus       210 k  210 (682)
                      .
T Consensus       164 ~  164 (243)
T PLN03121        164 R  164 (243)
T ss_pred             h
Confidence            3

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

Probab=99.52  E-value=8.7e-13  Score=134.95  Aligned_cols=79  Identities=25%  Similarity=0.383  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ...+-+||||+-|+++++|..|+..|..||.|..|.|+      .++|||||+|.+.-++..|. +.+|..|+|+.|.|.
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            44678999999999999999999999999999999997      58999999999999999999 899999999999999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      +-....
T Consensus       177 vERgRT  182 (335)
T KOG0113|consen  177 VERGRT  182 (335)
T ss_pred             eccccc
Confidence            876543

>PF00076 RRM_1: RNA recognition motif

Probab=99.47  E-value=1.2e-13  Score=113.47  Aligned_cols=64  Identities=38%  Similarity=0.624  Sum_probs=60.4

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      |||+|||+.+|+++|.++|.+||.|..|.|..     ..+||||+|.+.++|+.|| .|||..|.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            89999999999999999999999999999873     5799999999999999999 7999999999885

(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=99.47  E-value=1.6e-13  Score=148.55  Aligned_cols=76  Identities=29%  Similarity=0.391  Sum_probs=70.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...+|||+|||+.+++++|.++|.+||.|+.|.|+      .++|||||+|.+.++|..|| .|||..|+|+.|.|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999997      36899999999999999999 899999999999999987


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      .+.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            654

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.46  E-value=2.8e-13  Score=146.77  Aligned_cols=99  Identities=22%  Similarity=0.357  Sum_probs=81.8

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+++|+++|++||..||.|+.|.|+      ..+|||||+|.+.++|+.|| .|||++|.++.|.|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            345567899999999999999999999999999999996      35699999999999999999 89999999999999


Q ss_pred             EecccCCCCCCCCCCCccCCchhhhhHH
Q 005698          135 EMAKSFPQKPSHLNSSLAGSSLPMMMQQ  162 (682)
Q Consensus       135 ~~a~~~~~~~~~~~~~~~~~~~P~~~~~  162 (682)
                      .|+.+.....  ....+.+.+||..+..
T Consensus       182 ~~a~p~~~~~--~~~~lfV~nLp~~vte  207 (346)
T TIGR01659       182 SYARPGGESI--KDTNLYVTNLPRTITD  207 (346)
T ss_pred             eccccccccc--ccceeEEeCCCCcccH
Confidence            9987543221  2334566677665443

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.44  E-value=4.2e-13  Score=145.24  Aligned_cols=95  Identities=28%  Similarity=0.504  Sum_probs=79.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|++||..||+|..|.|+      .++|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.
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            36899999999999999999999999999999997      35699999999999999999 899999999999999987


Q ss_pred             cCCCCCCCCCCCccCCchhhhhHH
Q 005698          139 SFPQKPSHLNSSLAGSSLPMMMQQ  162 (682)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~P~~~~~  162 (682)
                      +.....  ....+...++|..+..
T Consensus        82 ~~~~~~--~~~~l~v~~l~~~~~~  103 (352)
T TIGR01661        82 PSSDSI--KGANLYVSGLPKTMTQ  103 (352)
T ss_pred             cccccc--ccceEEECCccccCCH
Confidence            643321  2334556666655443

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=99.38  E-value=6.7e-13  Score=120.65  Aligned_cols=75  Identities=29%  Similarity=0.488  Sum_probs=69.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..+|||||||++.++|++|.+||..+|+|..|.|-      .+.|||||+|...++|+.|| .++|+.|+.+.|.|.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            37899999999999999999999999999999874      47899999999999999999 899999999999999987


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      ..
T Consensus       115 GF  116 (153)
T KOG0121|consen  115 GF  116 (153)
T ss_pred             cc
Confidence            54

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.37  E-value=1.6e-12  Score=131.36  Aligned_cols=82  Identities=23%  Similarity=0.418  Sum_probs=76.1

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ++..+..++||||||+..+||++|++.|..||.|.+|+|.+.+|||||.|.+.|.|..|| .|||++|.|..++|.|.+.
T Consensus       158 NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  158 NQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             ccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            345667899999999999999999999999999999999999999999999999999999 8999999999999999886


Q ss_pred             CCC
Q 005698          140 FPQ  142 (682)
Q Consensus       140 ~~~  142 (682)
                      ...
T Consensus       238 ~~~  240 (321)
T KOG0148|consen  238 GDD  240 (321)
T ss_pred             CCC
Confidence            543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.36  E-value=1.8e-12  Score=139.35  Aligned_cols=76  Identities=28%  Similarity=0.357  Sum_probs=69.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCH--HHHHHHH-HcCCceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKP--EEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~--e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ......||||||++.||+++|..+|..||.|..|.|+  ..+|||||+|...  .++..|| .|||..|.|+.|+|+.|+
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            3456799999999999999999999999999999998  4689999999987  7899999 899999999999999987


Q ss_pred             c
Q 005698          139 S  139 (682)
Q Consensus       139 ~  139 (682)
                      +
T Consensus        87 P   87 (759)
T PLN03213         87 E   87 (759)
T ss_pred             H
Confidence            4

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.36  E-value=3.1e-12  Score=146.17  Aligned_cols=74  Identities=30%  Similarity=0.478  Sum_probs=68.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+||++.+++++|+++|..||.|..|.|+      .++|||||+|.+.++|+.|| .|||..|.|+.|.|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            356899999999999999999999999999999986      47899999999999999999 89999999999999865


Q ss_pred             c
Q 005698          138 K  138 (682)
Q Consensus       138 ~  138 (682)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

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.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.35  E-value=6e-12  Score=132.51  Aligned_cols=72  Identities=26%  Similarity=0.331  Sum_probs=64.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec---------CCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD---------SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~---------~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ...|.|.||.+.+|.++|+.||+.+|+|.++.|+.         ....|||.|.+...+..|.+|.+++|.|+.|.|..+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            34899999999999999999999999999998872         345899999999999999999999999999988754


Q ss_pred             c
Q 005698          138 K  138 (682)
Q Consensus       138 ~  138 (682)
                      .
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            3

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=1.3e-12  Score=125.39  Aligned_cols=75  Identities=24%  Similarity=0.426  Sum_probs=70.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..++|||||||.+|.+.+|++||-+||.|..|.|.   ....||||+|++.-+|+.|| .-||+.|+|..|.|+|+...
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            47899999999999999999999999999999997   35689999999999999999 89999999999999998765

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.33  E-value=8.8e-12  Score=142.48  Aligned_cols=75  Identities=25%  Similarity=0.550  Sum_probs=70.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..+|||+||++.+++++|+++|..||.|+.|.|.      ..+|||||+|.+.++|..|| .|||+.|+|+.|.|.++..
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            4689999999999999999999999999999997      36899999999999999999 8999999999999999886


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      .+
T Consensus       284 pP  285 (612)
T TIGR01645       284 PP  285 (612)
T ss_pred             Cc
Confidence            43

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=99.31  E-value=5.9e-12  Score=104.34  Aligned_cols=64  Identities=39%  Similarity=0.640  Sum_probs=57.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecC-----CCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS-----KHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~-----kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      |||+|||+.+++++|.++|..||.|..|.|...     +++|||+|.+.++|..|| .++|..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999833     699999999999999999 6888999999874

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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.30  E-value=7.7e-12  Score=135.58  Aligned_cols=77  Identities=34%  Similarity=0.514  Sum_probs=69.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVE  135 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~  135 (682)
                      ...++|||+|||..|||++|+++|.+||+|+.|.|+      ..+|||||+|.+.++|+.|| .||++.|.|  +.|.|.
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~  270 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR  270 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            346789999999999999999999999999999987      24689999999999999999 899999876  689999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      |+....
T Consensus       271 ~a~~~~  276 (346)
T TIGR01659       271 LAEEHG  276 (346)
T ss_pred             ECCccc
Confidence            987643

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=99.30  E-value=1.3e-11  Score=100.17  Aligned_cols=66  Identities=45%  Similarity=0.727  Sum_probs=61.8

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecC----CCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS----KHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~----kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      +|||+|||..+++++|.++|..||.|..|.+...    .|+|||+|.+.++|+.|+ .|+|..|.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            5899999999999999999999999999998844    499999999999999999 79999999999887

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=9.6e-12  Score=109.31  Aligned_cols=75  Identities=25%  Similarity=0.350  Sum_probs=69.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      +....|||.|||+.+|.+++.+||+.||.|..|.|-   ..+|.|||.|++..+|..|+ +|+|+.++++.|.|-+..+
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            457899999999999999999999999999999996   57899999999999999999 9999999999999987554

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.28  E-value=9.6e-12  Score=139.65  Aligned_cols=73  Identities=34%  Similarity=0.571  Sum_probs=69.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..+|||+|||+.+|+++|++||..||.|..|.|+      ..+|||||+|.+.++|..|| .|||+.|.|+.|.|.|+..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            6899999999999999999999999999999987      35799999999999999999 8999999999999999873

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.

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

Probab=99.28  E-value=9.1e-12  Score=124.56  Aligned_cols=75  Identities=28%  Similarity=0.405  Sum_probs=71.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|-|.||+.++++++|.+||..||.|..|.|.      .++|||||.|.+.++|++|| .|||+-++.-.|.|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            57899999999999999999999999999999987      48999999999999999999 899999999999999998


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            74

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.26  E-value=2.2e-11  Score=138.50  Aligned_cols=75  Identities=29%  Similarity=0.420  Sum_probs=69.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|.+||..||.|..|.|+      ..+|||||+|.+.++|..|| .|||+.|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45799999999999999999999999999999886      26899999999999999999 899999999999999987


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      ..
T Consensus       374 ~~  375 (509)
T TIGR01642       374 VG  375 (509)
T ss_pred             cC
Confidence            54

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.26  E-value=6.7e-12  Score=128.05  Aligned_cols=74  Identities=31%  Similarity=0.499  Sum_probs=69.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      -.|||||||..+++.+|+.||++||+|++|+|+  ++||||..++...|+.|| .|||+.|+|..|+|+-++.+...
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk~   77 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSKA   77 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee--cccceEEeecccccHHHHhhcccceecceEEEEEeccccCCC
Confidence            479999999999999999999999999999999  999999999999999999 79999999999999998876433

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

Probab=99.25  E-value=2.2e-11  Score=140.54  Aligned_cols=94  Identities=23%  Similarity=0.412  Sum_probs=76.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      +|||+|||+.+||++|.++|..||.|..|.|+      .+.|||||+|.+.++|+.|| .||+..|.|+.|.|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            79999999999999999999999999999997      35689999999999999999 899999999999999986443


Q ss_pred             CCCCCCCCCccCCchhhhhHH
Q 005698          142 QKPSHLNSSLAGSSLPMMMQQ  162 (682)
Q Consensus       142 ~~~~~~~~~~~~~~~P~~~~~  162 (682)
                      .........+.+.+||..+..
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~  102 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDN  102 (562)
T ss_pred             cccccCCCceEEcCCCccCCH
Confidence            322222233555666654433

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.25  E-value=2e-11  Score=137.02  Aligned_cols=77  Identities=30%  Similarity=0.373  Sum_probs=70.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .+...++|||+|||+.+++++|++||..||.|..|.|+      ..+|||||+|.+.++|..||.|+|..|.|+.|.|.+
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQS  164 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEee
Confidence            34457899999999999999999999999999999997      358999999999999999999999999999999988


Q ss_pred             ccc
Q 005698          137 AKS  139 (682)
Q Consensus       137 a~~  139 (682)
                      +..
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            654

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.

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=1e-11  Score=123.84  Aligned_cols=77  Identities=27%  Similarity=0.355  Sum_probs=70.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .|..-++||||||++.++.+.|+.+|++||+|+++.|+      .++|||||+|.+.+.|..|++--+-+|+|++..|++
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnl   87 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNL   87 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccch
Confidence            34456899999999999999999999999999998887      589999999999999999997777899999999998


Q ss_pred             ccc
Q 005698          137 AKS  139 (682)
Q Consensus       137 a~~  139 (682)
                      |--
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            865

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=1.2e-12  Score=125.56  Aligned_cols=76  Identities=24%  Similarity=0.399  Sum_probs=70.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ....-|||||||+.+||.||.-+|++||+|+.|.|+      .++||||++|++.-....|+ .|||+.|.|+.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            346789999999999999999999999999999998      58999999999999999999 99999999999999876


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      ...
T Consensus       113 ~~Y  115 (219)
T KOG0126|consen  113 SNY  115 (219)
T ss_pred             ccc
Confidence            544

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.24  E-value=2.3e-11  Score=138.87  Aligned_cols=73  Identities=29%  Similarity=0.434  Sum_probs=69.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFC--GTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~--G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .++|||+||+..+++++|+++|..|  |.|+.|.++  ++||||+|.+.++|+.|| .|||.+|.|+.|.|.|+++..
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            5789999999999999999999999  999999887  789999999999999999 799999999999999998753

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.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.22  E-value=7.6e-12  Score=123.01  Aligned_cols=80  Identities=29%  Similarity=0.450  Sum_probs=74.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...+|||||+|...||+.-|...|-.||.|..|.|+      +.+|||||+|...++|..|| .||+.+|.|+.|+|++|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            357899999999999999999999999999999997      57899999999999999999 89999999999999999


Q ss_pred             ccCCCCC
Q 005698          138 KSFPQKP  144 (682)
Q Consensus       138 ~~~~~~~  144 (682)
                      ++...+.
T Consensus        88 kP~kike   94 (298)
T KOG0111|consen   88 KPEKIKE   94 (298)
T ss_pred             CCccccC
Confidence            9765544

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.22  E-value=3.5e-11  Score=136.37  Aligned_cols=74  Identities=20%  Similarity=0.223  Sum_probs=69.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-H--cCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-A--LNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~--Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+..++||||+|.+.++|+.|| .  +++..|.|+.|.|.|+...
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            679999999999999999999999999999999988999999999999999999 4  5889999999999998754

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).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.21  E-value=4.3e-11  Score=135.68  Aligned_cols=77  Identities=31%  Similarity=0.402  Sum_probs=70.6

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           64 DALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..+.++|||+||++ .+|+++|.++|+.||.|..|.|+ ..+|||||+|.+.++|..|| .|||..|.|+.|.|.+++..
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            44678999999997 69999999999999999999987 45799999999999999999 89999999999999998653

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).

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.21  E-value=4.2e-11  Score=124.73  Aligned_cols=80  Identities=29%  Similarity=0.542  Sum_probs=73.2

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ...++.++|||+.|.+.+|.+||..||+.||.|..|.|+      ....||||+|++.++|++|+ .|+++.|+++.|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            345678999999999999999999999999999999998      46689999999999999999 89999999999999


Q ss_pred             EecccCC
Q 005698          135 EMAKSFP  141 (682)
Q Consensus       135 ~~a~~~~  141 (682)
                      .|++...
T Consensus       314 DFSQSVs  320 (479)
T KOG0415|consen  314 DFSQSVS  320 (479)
T ss_pred             ehhhhhh
Confidence            9987643

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.21  E-value=3.1e-11  Score=116.09  Aligned_cols=74  Identities=32%  Similarity=0.477  Sum_probs=69.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ....|||||||+..++++.|.++|-++|.|+.|.|+      ...|||||+|.++++|+-|| .||.+.|.|++|+|..+
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            346799999999999999999999999999999997      37899999999999999999 89999999999999987


Q ss_pred             c
Q 005698          138 K  138 (682)
Q Consensus       138 ~  138 (682)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.20  E-value=5.7e-11  Score=135.13  Aligned_cols=78  Identities=26%  Similarity=0.366  Sum_probs=68.1

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcC------------CCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceec
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFC------------GTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVG  128 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~------------G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~  128 (682)
                      ...+...++|||||||+.+|+++|.+||..|            +.|..|.+...+|||||+|.+.++|..||.|||+.|.
T Consensus       169 ~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~  248 (509)
T TIGR01642       169 QQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYS  248 (509)
T ss_pred             ccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCeEee
Confidence            3455667899999999999999999999974            4566777778899999999999999999999999999


Q ss_pred             CceEEEEecc
Q 005698          129 GRPLNVEMAK  138 (682)
Q Consensus       129 Gr~L~V~~a~  138 (682)
                      |..|.|....
T Consensus       249 g~~l~v~r~~  258 (509)
T TIGR01642       249 NVFLKIRRPH  258 (509)
T ss_pred             CceeEecCcc
Confidence            9999997543

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.19  E-value=2.4e-11  Score=111.47  Aligned_cols=77  Identities=23%  Similarity=0.283  Sum_probs=70.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...-.|||.|+.+.+|+++|.+.|..||+|..|.|.      -.+|||+|+|++.++|+.|| +|||..|.|..|.|.||
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            345689999999999999999999999999999986      36899999999999999999 89999999999999999


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      -...
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            7543

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.18  E-value=1.1e-10  Score=95.14  Aligned_cols=68  Identities=51%  Similarity=0.760  Sum_probs=63.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      +|||+|||..+++++|.++|..||.|..+.+..     ..++|||+|.+.++|..|+ .|++..|.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            589999999999999999999999999999983     3799999999999999999 8999999999999864

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).

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

Probab=99.18  E-value=6.5e-11  Score=136.59  Aligned_cols=75  Identities=37%  Similarity=0.629  Sum_probs=69.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ....+|||+||++.+|+++|+++|..||.|+.|.|+     ..+|||||+|.+.++|..|| .|||..|+|+.|.|.|+.
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            346789999999999999999999999999999997     35799999999999999999 899999999999999987


Q ss_pred             c
Q 005698          139 S  139 (682)
Q Consensus       139 ~  139 (682)
                      .
T Consensus       363 ~  363 (562)
T TIGR01628       363 R  363 (562)
T ss_pred             C
Confidence            4

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.18  E-value=1.1e-11  Score=135.92  Aligned_cols=71  Identities=32%  Similarity=0.507  Sum_probs=66.4

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ||||||.+++++++|..+|..||.|..|.++      ..+|||||+|.+.++|..|+ .|||++|.|+.|+|......
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            9999999999999999999999999999987      47899999999999999999 89999999999999776544

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.18  E-value=8.4e-11  Score=134.26  Aligned_cols=75  Identities=25%  Similarity=0.402  Sum_probs=67.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceec-CceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~V~~  136 (682)
                      ....++|||+|||.+++|++|.++|.+||.|..|.|+     .++|||||+|.+.++|+.|| .||+.+|. |+.|.|.+
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            3457899999999999999999999999999999986     47899999999999999999 89999985 78888876


Q ss_pred             cc
Q 005698          137 AK  138 (682)
Q Consensus       137 a~  138 (682)
                      +.
T Consensus       135 S~  136 (578)
T TIGR01648       135 SV  136 (578)
T ss_pred             cc
Confidence            53

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.17  E-value=1.3e-10  Score=117.00  Aligned_cols=103  Identities=27%  Similarity=0.466  Sum_probs=87.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .++..++|+|.-||.++|+++|+.||..+|+|+.|+|+      ++.|||||.|.++++|++|| .|||..|..+.|+|.
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            45667899999999999999999999999999999998      57899999999999999999 899999999999999


Q ss_pred             ecccCCCCCCCCCCCccCCchhhhhHHHHHHH
Q 005698          136 MAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQ  167 (682)
Q Consensus       136 ~a~~~~~~~~~~~~~~~~~~~P~~~~~~~~~q  167 (682)
                      ||.+....  +....+.+..+|..|.|....+
T Consensus       117 yARPSs~~--Ik~aNLYvSGlPktMtqkelE~  146 (360)
T KOG0145|consen  117 YARPSSDS--IKDANLYVSGLPKTMTQKELEQ  146 (360)
T ss_pred             eccCChhh--hcccceEEecCCccchHHHHHH
Confidence            99875433  3345667777887776654433

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.16  E-value=9.5e-11  Score=118.80  Aligned_cols=72  Identities=39%  Similarity=0.595  Sum_probs=68.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..+|||+|||..+|+++|.++|..||.|..|.|.      ..+|||||+|.+.++|..|| .|+|..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            6999999999999999999999999999988886      46799999999999999999 899999999999999965

>smart00360 RRM RNA recognition motif

Probab=99.14  E-value=1.4e-10  Score=93.50  Aligned_cols=63  Identities=46%  Similarity=0.734  Sum_probs=58.4

Q ss_pred             EeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           72 VSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        72 V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      |+|||..+++++|.++|..||.|..|.|..      ..|||||+|.+.++|..|+ .|++..|.|+.|.|
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            689999999999999999999999999873      2579999999999999999 89999999999887

>PF13893 RRM_5: RNA recognition motif

Probab=99.13  E-value=2e-10  Score=91.44  Aligned_cols=54  Identities=41%  Similarity=0.629  Sum_probs=50.1

Q ss_pred             HHHHHhcCCCeEEEEEecCC-CeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           84 LRQLFSFCGTVVECTITDSK-HFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        84 L~~~F~~~G~V~~v~i~~~k-g~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      |.++|++||+|..|.+.... ++|||+|.+.++|..|+ .|||..|.|+.|.|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            78999999999999998666 99999999999999999 89999999999999986

(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 ....

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=1.5e-10  Score=124.05  Aligned_cols=74  Identities=30%  Similarity=0.504  Sum_probs=69.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      -+.|||.||+..+|++.|+++|.+||.|+.|..+  +-||||.|.+.++|.+|| .|||++|+|..|.|.+|++...
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~--rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k  333 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP--RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDK  333 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecc--cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhh
Confidence            4789999999999999999999999999999887  779999999999999999 8999999999999999997543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.06  E-value=1.4e-10  Score=118.43  Aligned_cols=79  Identities=30%  Similarity=0.598  Sum_probs=73.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ....++|+||||.+.|+.++|+..|.+||.|++|+|+  ++|+||.|.-.++|..|| .|||++|.|++|+|+++.....
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee--cceeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence            4567899999999999999999999999999999999  999999999999999999 8999999999999999886544


Q ss_pred             CC
Q 005698          143 KP  144 (682)
Q Consensus       143 ~~  144 (682)
                      ..
T Consensus       153 ta  154 (346)
T KOG0109|consen  153 TA  154 (346)
T ss_pred             cC
Confidence            33

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.06  E-value=1.9e-10  Score=116.50  Aligned_cols=75  Identities=27%  Similarity=0.474  Sum_probs=70.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .--||||.|.+.|+-++|++.|.+||+|.+++|+      +++|||||.|.+.++|+.|| +|||.+|+++.|+..||.-
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            4579999999999999999999999999999997      68999999999999999999 8999999999999999986


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            65

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.05  E-value=5.8e-10  Score=119.70  Aligned_cols=77  Identities=23%  Similarity=0.390  Sum_probs=69.8

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceec-CceEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLN  133 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~  133 (682)
                      ......+-||||.||.++.|++|..||+..|+|-++.|+      .++|||||+|.+.++|+.|| .||+++|. |+.|.
T Consensus        78 ~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~ig  157 (506)
T KOG0117|consen   78 PPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLG  157 (506)
T ss_pred             CCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeE
Confidence            334668999999999999999999999999999999997      58999999999999999999 89999995 88888


Q ss_pred             EEecc
Q 005698          134 VEMAK  138 (682)
Q Consensus       134 V~~a~  138 (682)
                      |..+.
T Consensus       158 vc~Sv  162 (506)
T KOG0117|consen  158 VCVSV  162 (506)
T ss_pred             EEEee
Confidence            87654

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.04  E-value=5.1e-10  Score=117.03  Aligned_cols=80  Identities=21%  Similarity=0.333  Sum_probs=74.3

Q ss_pred             cCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH--HcCCceecCceEEEEec
Q 005698           60 AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL--ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        60 ~~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al--~Lng~~l~Gr~L~V~~a  137 (682)
                      +..+|...++|||+||...+++.+|.++|.+||+|..|.+...+++|||+|.+.+.|+.|.  .+|.++|+|.+|.|.|+
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            4456777899999999999999999999999999999999988999999999999999999  48989999999999999


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            87

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.03  E-value=6e-10  Score=121.86  Aligned_cols=82  Identities=29%  Similarity=0.397  Sum_probs=73.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      +.+.-.|+|.|||+.|...+|+.+|+.||.|.+|.|+     ...|||||+|....+|..|| .|||..|+|++|-|.||
T Consensus       114 ~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  114 DLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             cCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeee
Confidence            3346789999999999999999999999999999998     35699999999999999999 89999999999999999


Q ss_pred             ccCCCCCC
Q 005698          138 KSFPQKPS  145 (682)
Q Consensus       138 ~~~~~~~~  145 (682)
                      -.......
T Consensus       194 V~Kd~ye~  201 (678)
T KOG0127|consen  194 VDKDTYED  201 (678)
T ss_pred             cccccccc
Confidence            87655443

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.02  E-value=7.4e-10  Score=118.38  Aligned_cols=79  Identities=34%  Similarity=0.493  Sum_probs=71.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCc-eecC--ceEEEEe
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNM-DVGG--RPLNVEM  136 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~-~l~G--r~L~V~~  136 (682)
                      ...+||||-|+..+||.+|+++|.+||.|++|.|.     .++|||||+|.+.+.|..|| .|||. .+.|  .+|.|.|
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            36789999999999999999999999999999998     48999999999999999999 89994 5555  7899999


Q ss_pred             cccCCCCC
Q 005698          137 AKSFPQKP  144 (682)
Q Consensus       137 a~~~~~~~  144 (682)
                      |.+...+.
T Consensus       203 ADtqkdk~  210 (510)
T KOG0144|consen  203 ADTQKDKD  210 (510)
T ss_pred             cccCCCch
Confidence            99876554

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.00  E-value=6.2e-10  Score=122.90  Aligned_cols=73  Identities=30%  Similarity=0.432  Sum_probs=69.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..|||||||+.+++++|.++|..+|.|..++++      ..+|||||+|.+.++|..|| .|||.+|.|++|+|.|+...
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            899999999999999999999999999999997      57899999999999999999 89999999999999998643

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=98.99  E-value=1.4e-09  Score=109.56  Aligned_cols=74  Identities=30%  Similarity=0.400  Sum_probs=69.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..-+|||-||.+++.|.-|.++|++||.|..|+|+      +.+|||||.+.+.++|..|| .|||+.|+++.|.|.|..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            46789999999999999999999999999999997      58999999999999999999 899999999999999865


Q ss_pred             c
Q 005698          139 S  139 (682)
Q Consensus       139 ~  139 (682)
                      .
T Consensus       357 n  357 (360)
T KOG0145|consen  357 N  357 (360)
T ss_pred             C
Confidence            3

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.96  E-value=9.8e-10  Score=124.37  Aligned_cols=78  Identities=23%  Similarity=0.358  Sum_probs=74.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCCCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKP  144 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~~~  144 (682)
                      .+|||||+|+..|+++||..+|+.||+|..|.|+.+++||||++....+|+.|| +|.++.|.++.|+|.|+.....+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            589999999999999999999999999999999999999999999999999999 899999999999999998765554

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.96  E-value=1.2e-09  Score=109.63  Aligned_cols=70  Identities=20%  Similarity=0.425  Sum_probs=66.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..||||+||+.+.+.+|..||..||.|..|.|.  .||+||+|.+.-+|..|| .|||.+|+|-.|.|+|+..
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            469999999999999999999999999999998  799999999999999999 8999999998899999885

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.95  E-value=1.2e-09  Score=110.37  Aligned_cols=81  Identities=23%  Similarity=0.409  Sum_probs=73.7

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      ..+.+..++|||-.||..+.+.+|..+|-.||.|+..++.      .+++||||.|.+...++.|| +|||+.|+-++|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            4556778999999999999999999999999999988875      68999999999999999999 8999999999999


Q ss_pred             EEecccCC
Q 005698          134 VEMAKSFP  141 (682)
Q Consensus       134 V~~a~~~~  141 (682)
                      |.+..++.
T Consensus       359 VQLKRPkd  366 (371)
T KOG0146|consen  359 VQLKRPKD  366 (371)
T ss_pred             hhhcCccc
Confidence            98876653

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.94  E-value=2.2e-09  Score=117.61  Aligned_cols=76  Identities=30%  Similarity=0.327  Sum_probs=67.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-Hc-----CC-ceecCc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-AL-----NN-MDVGGR  130 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~L-----ng-~~l~Gr  130 (682)
                      .....||||.|||+++|+++|.++|.+||+|.++.|+      .++|+|||.|.+..+|+.|| ..     .| +.|.|+
T Consensus       289 ~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR  368 (678)
T KOG0127|consen  289 ITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGR  368 (678)
T ss_pred             ccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEecc
Confidence            3446899999999999999999999999999999987      58999999999999999999 33     34 789999


Q ss_pred             eEEEEeccc
Q 005698          131 PLNVEMAKS  139 (682)
Q Consensus       131 ~L~V~~a~~  139 (682)
                      .|.|..|.+
T Consensus       369 ~Lkv~~Av~  377 (678)
T KOG0127|consen  369 LLKVTLAVT  377 (678)
T ss_pred             EEeeeeccc
Confidence            999998864

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.93  E-value=2.7e-09  Score=112.88  Aligned_cols=74  Identities=22%  Similarity=0.243  Sum_probs=57.7

Q ss_pred             CCCCCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           61 GKADALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      ...+....++||++|.. .|+.+++..+|-.++.++-|..+    .+--||||.|.+...+..+|..+|+.+...+|..
T Consensus        46 ~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~  124 (479)
T KOG4676|consen   46 SKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTK  124 (479)
T ss_pred             ccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecCCCCCccHHHHHhcCcccccccccCCCCccCCCCcccc
Confidence            34566789999999975 55667888888888877666554    3456799999999988888888998888887754

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.93  E-value=6e-09  Score=105.42  Aligned_cols=77  Identities=31%  Similarity=0.472  Sum_probs=68.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCC-ceecC--ceEEEEe
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNN-MDVGG--RPLNVEM  136 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng-~~l~G--r~L~V~~  136 (682)
                      ..++||||-|...-.|+|++.+|..||.|.+|.+.     ..+|||||.|.+..+|+.|| .|+| .++-|  -.|.|.|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            57899999999999999999999999999999987     58999999999999999999 8999 45555  5799999


Q ss_pred             cccCCC
Q 005698          137 AKSFPQ  142 (682)
Q Consensus       137 a~~~~~  142 (682)
                      +.....
T Consensus        98 ADTdkE  103 (371)
T KOG0146|consen   98 ADTDKE  103 (371)
T ss_pred             ccchHH
Confidence            876543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.89  E-value=3e-09  Score=113.63  Aligned_cols=72  Identities=25%  Similarity=0.404  Sum_probs=67.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFS-FCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~-~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      .+.|||.|||+++.|++|++||. +.|+|++|.|.     +.+|||+|+|+++|.+++|+ .||.+.|.|+.|.|....
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            45699999999999999999998 78999999997     68899999999999999999 899999999999998754

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.85  E-value=5.7e-09  Score=109.32  Aligned_cols=70  Identities=30%  Similarity=0.500  Sum_probs=66.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ..+.||||.|.+.+.|+.|+..|..||.|..|.|.      +.+|||||+|+-++.|+.|+ .|||..|+|+.|+|.
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            36899999999999999999999999999999985      68999999999999999999 899999999999996

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.85  E-value=6.8e-09  Score=103.59  Aligned_cols=74  Identities=30%  Similarity=0.504  Sum_probs=68.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHH----HHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQ----LFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~----~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..||||.||+..+..++|+.    ||++||+|+.|.+.   +.+|-|||.|.+.+.|-.|+ +|+|+.|.|+.++|+||+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            33999999999999999888    99999999999886   67899999999999999999 999999999999999997


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      ..
T Consensus        89 s~   90 (221)
T KOG4206|consen   89 SD   90 (221)
T ss_pred             Cc
Confidence            53

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=1.4e-08  Score=114.65  Aligned_cols=71  Identities=39%  Similarity=0.571  Sum_probs=66.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec---------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD---------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~---------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ++|||.||++.+|.++|..+|..+|.|..|.|..         +.|||||+|.+.++|+.|| .|+|++|+|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            3499999999999999999999999999998861         3499999999999999999 89999999999999998


Q ss_pred             c
Q 005698          138 K  138 (682)
Q Consensus       138 ~  138 (682)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.79  E-value=3e-09  Score=111.34  Aligned_cols=75  Identities=24%  Similarity=0.522  Sum_probs=68.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ..-..|||..+.++++++||+.+|+-||+|+.|.|.      ..+|||||+|.+......|| .||-+.|+|..|+|..+
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            345799999999999999999999999999999996      57899999999999999999 79999999999999766


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      ..
T Consensus       288 vT  289 (544)
T KOG0124|consen  288 VT  289 (544)
T ss_pred             cC
Confidence            54

>smart00361 RRM_1 RNA recognition motif

Probab=98.78  E-value=1.7e-08  Score=84.24  Aligned_cols=54  Identities=28%  Similarity=0.470  Sum_probs=48.1

Q ss_pred             HHHHHHHHh----cCCCeEEEE-Ee--------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           81 VEQLRQLFS----FCGTVVECT-IT--------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        81 eedL~~~F~----~~G~V~~v~-i~--------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      +++|.++|.    .||.|..|. |.        ..+|||||+|.+.++|..|| .|||..|.|+.|.|
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            578999999    999999885 32        24899999999999999999 89999999999986

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

Probab=98.76  E-value=1.2e-08  Score=111.67  Aligned_cols=76  Identities=32%  Similarity=0.484  Sum_probs=69.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||.+|...+...||+.||.+||.|+..+|+      ..++|+||++.+.++|..|| +|+-++|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            345799999999999999999999999999999887      35789999999999999999 89999999999999988


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      +..
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            743

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.74  E-value=2.2e-08  Score=112.51  Aligned_cols=85  Identities=21%  Similarity=0.348  Sum_probs=76.3

Q ss_pred             CCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---------cCCCeEEEEeCCHHHHHHHH-HcCC
Q 005698           55 GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---------DSKHFAYIEYSKPEEATAAL-ALNN  124 (682)
Q Consensus        55 ~~~~~~~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---------~~kg~aFVeF~s~e~A~~Al-~Lng  124 (682)
                      +.+...+..++..++|||+||++.|++++|...|+.||.|..|+|+         ....||||-|.+..+|+.|+ .|+|
T Consensus       162 ~~~gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg  241 (877)
T KOG0151|consen  162 GRPGSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQG  241 (877)
T ss_pred             CCCCcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcc
Confidence            3334455668889999999999999999999999999999999998         36789999999999999999 8999


Q ss_pred             ceecCceEEEEeccc
Q 005698          125 MDVGGRPLNVEMAKS  139 (682)
Q Consensus       125 ~~l~Gr~L~V~~a~~  139 (682)
                      ..|.+..|++.|++.
T Consensus       242 ~iv~~~e~K~gWgk~  256 (877)
T KOG0151|consen  242 IIVMEYEMKLGWGKA  256 (877)
T ss_pred             eeeeeeeeeeccccc
Confidence            999999999999964

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.73  E-value=2.1e-08  Score=107.38  Aligned_cols=76  Identities=25%  Similarity=0.303  Sum_probs=67.8

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      -.....++|||.|||+++||+.|++-|..||.|.+++|+ ..+..+.|.|.++++|+.|+ .|||..|.|+.|.|.+.
T Consensus       531 gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  531 GAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            344567899999999999999999999999999999997 34455699999999999999 89999999999999863

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.72  E-value=4.1e-09  Score=118.81  Aligned_cols=76  Identities=28%  Similarity=0.421  Sum_probs=70.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...+.|+|.|||+..+..+|+.||..||.|..|.|+      -.+|||||+|.++.+|..|+ +|.++-|.|+.|.++|+
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            346799999999999999999999999999999998      25899999999999999999 89999999999999999


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      ...
T Consensus       691 ~~d  693 (725)
T KOG0110|consen  691 KSD  693 (725)
T ss_pred             ccc
Confidence            853

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.68  E-value=3.4e-08  Score=108.05  Aligned_cols=73  Identities=23%  Similarity=0.458  Sum_probs=67.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      .|||.||++.++..+|.++|+.||+|+.|+|.    ..+|| ||+|.++++|..|| .|||..+.|+.|.|........
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            39999999999999999999999999999997    57899 99999999999999 8999999999999987765444

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.67  E-value=6.2e-08  Score=103.91  Aligned_cols=80  Identities=21%  Similarity=0.356  Sum_probs=71.1

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      ..+.+...+|||.+||..+-+.+|...|..||.|+..++.      -+++|+||.|++..+|..|| .|||+.|++++|+
T Consensus       418 q~eGpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~Krlk  497 (510)
T KOG0144|consen  418 QVEGPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLK  497 (510)
T ss_pred             cccCCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccce
Confidence            3455567889999999999999999999999999987764      36899999999999999999 8999999999999


Q ss_pred             EEecccC
Q 005698          134 VEMAKSF  140 (682)
Q Consensus       134 V~~a~~~  140 (682)
                      |.+....
T Consensus       498 VQlk~~~  504 (510)
T KOG0144|consen  498 VQLKRDR  504 (510)
T ss_pred             EEeeecc
Confidence            9987654

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.66  E-value=5.4e-08  Score=95.87  Aligned_cols=79  Identities=19%  Similarity=0.281  Sum_probs=69.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFC-GTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~-G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      ...+....+||..||..+.+.+|..+|.+| |.|..+.|.      .++|||||+|++.+.|.-|. .||++.|.|+.|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            344557789999999999999999999998 677777774      58999999999999999999 8999999999999


Q ss_pred             EEecccC
Q 005698          134 VEMAKSF  140 (682)
Q Consensus       134 V~~a~~~  140 (682)
                      |.+-.+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9876654

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.55  E-value=1.1e-07  Score=91.94  Aligned_cols=81  Identities=28%  Similarity=0.388  Sum_probs=69.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEE-EEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v-~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....+|||+||.+.+++..|.++|+.||.|... .|+      ..+|||||.|.+.+.+.+|| .|||..++.++|.|.
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            3445899999999999999999999999988763 332      46789999999999999999 899999999999999


Q ss_pred             ecccCCCCC
Q 005698          136 MAKSFPQKP  144 (682)
Q Consensus       136 ~a~~~~~~~  144 (682)
                      ++.....+.
T Consensus       173 ya~k~~~kg  181 (203)
T KOG0131|consen  173 YAFKKDTKG  181 (203)
T ss_pred             EEEecCCCc
Confidence            998655444

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.49  E-value=3.3e-07  Score=94.15  Aligned_cols=78  Identities=23%  Similarity=0.385  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .+....+|+|.|||+.|+++||++||..||.+..|.|+     .+.|.|-|.|...++|..|| .|||+.|+|+.|.|..
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            44456899999999999999999999999988888886     46799999999999999999 8999999999999987


Q ss_pred             cccC
Q 005698          137 AKSF  140 (682)
Q Consensus       137 a~~~  140 (682)
                      ....
T Consensus       159 i~~~  162 (243)
T KOG0533|consen  159 ISSP  162 (243)
T ss_pred             ecCc
Confidence            6543

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.49  E-value=1.9e-07  Score=102.94  Aligned_cols=74  Identities=27%  Similarity=0.460  Sum_probs=65.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..+|||.|||++++..+|+++|..||.|+...|.      ...+||||+|.+.++++.||..+...|+|++|.|+.-...
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecccc
Confidence            4569999999999999999999999999988775      2239999999999999999977799999999999976654

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.46  E-value=6.4e-08  Score=95.85  Aligned_cols=75  Identities=23%  Similarity=0.289  Sum_probs=67.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      +...||||+||...|+|+-|.++|-+.|.|+.|.|.    ....||||+|.++..+..|+ .|||..|.+..|.|.+-.+
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            357899999999999999999999999999999997    22349999999999999999 7999999999999876543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.45  E-value=4.3e-07  Score=93.24  Aligned_cols=80  Identities=24%  Similarity=0.433  Sum_probs=73.0

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      ...+.....|||+|+.+.+|.++|..+|..||.|..|.|.      +.+|||||+|.+.+.++.||.|||..|.|..|.|
T Consensus        95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEV  174 (231)
T ss_pred             hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCccccccccee
Confidence            4567778999999999999999999999999999877775      4789999999999999999999999999999999


Q ss_pred             EecccC
Q 005698          135 EMAKSF  140 (682)
Q Consensus       135 ~~a~~~  140 (682)
                      .+....
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            987765

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.44  E-value=2.2e-07  Score=102.92  Aligned_cols=79  Identities=27%  Similarity=0.436  Sum_probs=70.5

Q ss_pred             CCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceE
Q 005698           55 GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL  132 (682)
Q Consensus        55 ~~~~~~~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L  132 (682)
                      ..+++....+-...+|+|-|||..|++++|..+|+.||+|..|... ...|.+||+|.|.-+|+.|| +|++.+|.|+.|
T Consensus        63 ~~~~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   63 LRPDNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             CCcCCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            3335555567778999999999999999999999999999998876 56799999999999999999 899999999998


Q ss_pred             E
Q 005698          133 N  133 (682)
Q Consensus       133 ~  133 (682)
                      .
T Consensus       143 k  143 (549)
T KOG4660|consen  143 K  143 (549)
T ss_pred             c
Confidence            8

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.44  E-value=4.5e-07  Score=95.22  Aligned_cols=77  Identities=27%  Similarity=0.368  Sum_probs=68.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE--------EEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE--------CTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~--------v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      +...+.|||.|||.+||.+++.++|.+||.|..        |+|.     ..+|-|+|+|...+++..|| .|++..|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            344667999999999999999999999998863        5555     57899999999999999999 899999999


Q ss_pred             ceEEEEecccC
Q 005698          130 RPLNVEMAKSF  140 (682)
Q Consensus       130 r~L~V~~a~~~  140 (682)
                      +.|+|+.|+..
T Consensus       211 ~~~rVerAkfq  221 (382)
T KOG1548|consen  211 KKLRVERAKFQ  221 (382)
T ss_pred             cEEEEehhhhh
Confidence            99999998753

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.43  E-value=1e-06  Score=87.65  Aligned_cols=78  Identities=27%  Similarity=0.306  Sum_probs=66.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-------cCCCeEEEEeCCHHHHHHHH-HcCCceec---CceE
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-------DSKHFAYIEYSKPEEATAAL-ALNNMDVG---GRPL  132 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~---Gr~L  132 (682)
                      ...-+||||.+||.+|..-+|..||..|-.-+.+.|.       ..+-+|||+|.+..+|++|+ +|||+.|+   +..|
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            3447899999999999999999999999766665554       13469999999999999999 89999996   6889


Q ss_pred             EEEecccCC
Q 005698          133 NVEMAKSFP  141 (682)
Q Consensus       133 ~V~~a~~~~  141 (682)
                      +|++|+...
T Consensus       111 hiElAKSNt  119 (284)
T KOG1457|consen  111 HIELAKSNT  119 (284)
T ss_pred             EeeehhcCc
Confidence            999998643

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.42  E-value=4.5e-07  Score=99.32  Aligned_cols=71  Identities=28%  Similarity=0.465  Sum_probs=65.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..||||   +.+|+.+|.++|..+|.|+.|.|+   .+.|||||.|.++.+|+.|| +||...|.|+.|+|-|+...+
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            368999   899999999999999999999987   46799999999999999999 899999999999999987543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.38  E-value=3.2e-07  Score=97.70  Aligned_cols=77  Identities=29%  Similarity=0.437  Sum_probs=69.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..++||||+|++.++++.|+++|.+||+|.+|.|+      ..+||+||+|.+.+.+..+|....+.|+|+.|.+..|.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            57899999999999999999999999999999997      477999999999999998887778899999999988876


Q ss_pred             CCC
Q 005698          140 FPQ  142 (682)
Q Consensus       140 ~~~  142 (682)
                      ...
T Consensus        85 r~~   87 (311)
T KOG4205|consen   85 RED   87 (311)
T ss_pred             ccc
Confidence            543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.37  E-value=3.8e-07  Score=97.11  Aligned_cols=78  Identities=19%  Similarity=0.317  Sum_probs=70.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...+||||+||+.+++++|+++|.+||.|..+.|+      ..+||+||.|.+.+.+..++.+.-++|+|+.|.|..|.+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            35699999999999999999999999999888876      578999999999999999998899999999999998887


Q ss_pred             CCCC
Q 005698          140 FPQK  143 (682)
Q Consensus       140 ~~~~  143 (682)
                      ....
T Consensus       176 k~~~  179 (311)
T KOG4205|consen  176 KEVM  179 (311)
T ss_pred             hhhc
Confidence            6443

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.19  E-value=6.3e-06  Score=88.31  Aligned_cols=74  Identities=31%  Similarity=0.386  Sum_probs=68.0

Q ss_pred             CCEEEEeCCC-CCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLS-PLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp-~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..+|.|.||. ..||.+-|..+|+-||.|..|.|. ..+--|+|+|.+...|+.|+ +|+|..|.|+.|+|.+++..
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            5789999996 789999999999999999999998 45578999999999999999 89999999999999998754

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.14  E-value=1.8e-06  Score=85.85  Aligned_cols=63  Identities=27%  Similarity=0.299  Sum_probs=55.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceec
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVG  128 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~  128 (682)
                      ...||||.||.++|||++|+.+|..|-...-++|.  ..-.+|||+|++.+.|..|| .|+|..|.
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            46799999999999999999999999877777776  45578999999999999999 89998764

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.99  E-value=2e-05  Score=71.36  Aligned_cols=68  Identities=25%  Similarity=0.441  Sum_probs=44.1

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc--C---CceecCceEEEE
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL--N---NMDVGGRPLNVE  135 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L--n---g~~l~Gr~L~V~  135 (682)
                      ..|+|.||+..++.++|+++|..||.|.+|.+...-..|||-|.+.+.|+.|| .+  .   +..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57899999999999999999999999999999977789999999999999998 43  3   345666665554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.98  E-value=3.7e-06  Score=84.84  Aligned_cols=68  Identities=31%  Similarity=0.480  Sum_probs=62.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ...+.|+|.||+..+.|++|.++|..||.+.++.+  ..+++||+|...++|..|| .|+|..|.|+.|.|
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            34578999999999999999999999999976666  4899999999999999999 89999999999999

>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=97.94  E-value=3.7e-05  Score=65.94  Aligned_cols=68  Identities=29%  Similarity=0.356  Sum_probs=47.8

Q ss_pred             CEEEEeCCCCCCCHHH----HHHHHhcCC-CeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           68 KTLQVSNLSPLLTVEQ----LRQLFSFCG-TVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        68 ~tL~V~NLp~~vteed----L~~~F~~~G-~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..|||.|||.+.+...    |+.|+..|| .|..|.    .+.|+|.|.+.+.|..|+ .|+|..+.|..|.|.|...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            4799999999888754    567777886 666662    689999999999999999 7999999999999998753

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.82  E-value=1.7e-05  Score=88.87  Aligned_cols=79  Identities=28%  Similarity=0.424  Sum_probs=70.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .....|||+|||..+++.+|.+++..||.+....++      .++||||.+|.+......|+ .|||..+++..|.|+.|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            345789999999999999999999999999888776      47899999999999999999 89999999999999988


Q ss_pred             ccCCCC
Q 005698          138 KSFPQK  143 (682)
Q Consensus       138 ~~~~~~  143 (682)
                      ......
T Consensus       367 ~~g~~~  372 (500)
T KOG0120|consen  367 IVGASN  372 (500)
T ss_pred             hccchh
Confidence            765443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.79  E-value=0.00011  Score=65.48  Aligned_cols=72  Identities=18%  Similarity=0.236  Sum_probs=59.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhc--CCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceec----CceEEE
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSF--CGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVG----GRPLNV  134 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~--~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~----Gr~L~V  134 (682)
                      +||-|.|||..+|.++|.+++..  .|....+.|+      -+.|||||.|.+.+.|..-. .++|..|.    .+.+.|
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            69999999999999999999975  3666666665      36799999999999999888 89999886    366677


Q ss_pred             Eeccc
Q 005698          135 EMAKS  139 (682)
Q Consensus       135 ~~a~~  139 (682)
                      .||.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77663

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.78  E-value=6.9e-05  Score=82.37  Aligned_cols=74  Identities=23%  Similarity=0.323  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ....|-+.+||+.+|++||.+||..++ |..+.|.    ...|-|||+|.+.++++.||++|-..+..+-|.|..+...
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCc
Confidence            355677889999999999999999995 6666665    4679999999999999999999999999999999877543

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.77  E-value=9.5e-06  Score=90.00  Aligned_cols=77  Identities=25%  Similarity=0.398  Sum_probs=70.1

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVE  135 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~  135 (682)
                      ..+-...|||+--|...++.-+|.+||..+|.|..|.|+      ..+|.|||+|.+.+.+..||.|.|..+.|.+|.|.
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQ  253 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEec
Confidence            345557899999999999999999999999999999998      47899999999999999999999999999999997


Q ss_pred             ecc
Q 005698          136 MAK  138 (682)
Q Consensus       136 ~a~  138 (682)
                      ...
T Consensus       254 ~sE  256 (549)
T KOG0147|consen  254 LSE  256 (549)
T ss_pred             ccH
Confidence            654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.70  E-value=0.0001  Score=74.13  Aligned_cols=75  Identities=21%  Similarity=0.310  Sum_probs=66.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-CCCeEEEEeCCHHHHHHHH-HcCCceec-CceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-SKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~V~~a~  138 (682)
                      ..+..+||+.|||..++.+.|..+|.+|+....|.++. -.++|||+|.+...|..|. .|+|..|- ...|.|.++.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            45678999999999999999999999999999999884 5799999999999999999 89998886 7788887764

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.64  E-value=0.00011  Score=58.31  Aligned_cols=52  Identities=25%  Similarity=0.488  Sum_probs=45.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL  120 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al  120 (682)
                      +.|-|.|+++...+ +|..+|..||+|+.+.+.....+.||+|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            57889999977764 45569999999999999877899999999999999986

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.61  E-value=9.3e-05  Score=77.65  Aligned_cols=76  Identities=21%  Similarity=0.396  Sum_probs=62.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHH------HHHHhcCCCeEEEEEec--------CCCe-EEEEeCCHHHHHHHH-HcCCcee
Q 005698           64 DALKKTLQVSNLSPLLTVEQL------RQLFSFCGTVVECTITD--------SKHF-AYIEYSKPEEATAAL-ALNNMDV  127 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL------~~~F~~~G~V~~v~i~~--------~kg~-aFVeF~s~e~A~~Al-~Lng~~l  127 (682)
                      .....-|||-+|++.+-.+++      .+||++||.|..|.|..        ...+ .||+|...++|..|| +++|..+
T Consensus       111 VvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         111 VVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             eeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            344678999999988877762      48999999999998861        1113 499999999999999 8999999


Q ss_pred             cCceEEEEeccc
Q 005698          128 GGRPLNVEMAKS  139 (682)
Q Consensus       128 ~Gr~L~V~~a~~  139 (682)
                      +|+.|++.+...
T Consensus       191 DGr~lkatYGTT  202 (480)
T COG5175         191 DGRVLKATYGTT  202 (480)
T ss_pred             cCceEeeecCch
Confidence            999999988653

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.59  E-value=6.4e-05  Score=76.49  Aligned_cols=76  Identities=17%  Similarity=0.337  Sum_probs=65.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .+...-.||+|.|...++.+.|-..|.+|-......++      +.+||+||.|.+..++..|+ +|||..++.+.|.+.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            34556789999999999999999999999766655554      68999999999999999999 999999999998885


Q ss_pred             ecc
Q 005698          136 MAK  138 (682)
Q Consensus       136 ~a~  138 (682)
                      -..
T Consensus       266 kS~  268 (290)
T KOG0226|consen  266 KSE  268 (290)
T ss_pred             hhh
Confidence            433

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.58  E-value=6.2e-05  Score=80.09  Aligned_cols=78  Identities=22%  Similarity=0.290  Sum_probs=67.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE--------EEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE--------CTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVG  128 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~--------v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~  128 (682)
                      .....+|||-+|+..+++++|.+||.+||.|..        |.|.      ..++-|.|.|.+...|+.|| -|++..|+
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            455779999999999999999999999998853        3332      47899999999999999999 79999999


Q ss_pred             CceEEEEecccCC
Q 005698          129 GRPLNVEMAKSFP  141 (682)
Q Consensus       129 Gr~L~V~~a~~~~  141 (682)
                      |..|.|.+|....
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998886543

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.55  E-value=0.00035  Score=62.68  Aligned_cols=71  Identities=25%  Similarity=0.330  Sum_probs=54.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEE-------------EecCCCeEEEEeCCHHHHHHHHHcCCceecCce-E
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-------------ITDSKHFAYIEYSKPEEATAALALNNMDVGGRP-L  132 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~-------------i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~-L  132 (682)
                      ..-|.|-++|+. ....|..+|.+||+|++..             +....++..|.|.+..+|..||..||..|.|.. |
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            567888899987 4577889999999998885             446778999999999999999999999999864 4


Q ss_pred             EEEecc
Q 005698          133 NVEMAK  138 (682)
Q Consensus       133 ~V~~a~  138 (682)
                      -|.+++
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            466664

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.46  E-value=0.00051  Score=70.16  Aligned_cols=65  Identities=25%  Similarity=0.395  Sum_probs=56.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec---C---------C------CeEEEEeCCHHHHHHHH-HcCCcee
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD---S---------K------HFAYIEYSKPEEATAAL-ALNNMDV  127 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~---~---------k------g~aFVeF~s~e~A~~Al-~Lng~~l  127 (682)
                      .-.|||+|||+.+...-|++||..||+|-.|.|..   .         .      -.|+|+|.+...|..+. .|||..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            35899999999999999999999999999999861   0         1      13889999999998887 8999999


Q ss_pred             cCce
Q 005698          128 GGRP  131 (682)
Q Consensus       128 ~Gr~  131 (682)
                      +|+.
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9975

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.41  E-value=9.2e-05  Score=82.73  Aligned_cols=75  Identities=29%  Similarity=0.418  Sum_probs=65.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCcee---cCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFS-FCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV---GGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~-~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l---~Gr~L~V~~a~~  139 (682)
                      ...+.|||.||---+|.-+|+.|++ .+|.|+.++|-+.+..|||.|.+.++|...+ +|||+.|   +++.|.|.|+..
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~  521 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRA  521 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecch
Confidence            4578999999999999999999999 6777888866577889999999999999999 8999887   458899988764

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.38  E-value=0.00028  Score=77.77  Aligned_cols=74  Identities=19%  Similarity=0.237  Sum_probs=60.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-EEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~-v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...-+|-+.+||+.||++||.+||.-.-.|.. |.|+     ...|.|||+|++.+.|+.||.-|...|.-+-|.|..+.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            34568889999999999999999997755544 3333     46789999999999999999778888888888886553

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.34  E-value=0.00016  Score=84.25  Aligned_cols=82  Identities=28%  Similarity=0.452  Sum_probs=73.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~a~~  139 (682)
                      .....+.|||++|.+++....|...|..||.|..|.+-+..-||||.|++...++.|+ .|-|+.|+|  +.|.|.|+..
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            4556789999999999999999999999999999999888899999999999999999 899999997  7899999886


Q ss_pred             CCCCC
Q 005698          140 FPQKP  144 (682)
Q Consensus       140 ~~~~~  144 (682)
                      ....+
T Consensus       531 ~~~~P  535 (975)
T KOG0112|consen  531 PGATP  535 (975)
T ss_pred             CCCCh
Confidence            54443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.29  E-value=0.00095  Score=71.24  Aligned_cols=76  Identities=25%  Similarity=0.298  Sum_probs=67.7

Q ss_pred             CCCCCEEEEeCCC-CCCCHHHHHHHHhcCCCeEEEEEec-CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           64 DALKKTLQVSNLS-PLLTVEQLRQLFSFCGTVVECTITD-SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        64 ~~~~~tL~V~NLp-~~vteedL~~~F~~~G~V~~v~i~~-~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ......+.|-+|. ..+..+.|..+|..||.|..|.+++ ..|.|+|++.+..+++.|| +|||..|-|.+|.|.+++.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence            3457889999998 4677789999999999999999984 4599999999999999999 8999999999999988774

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.29  E-value=0.001  Score=70.58  Aligned_cols=77  Identities=16%  Similarity=0.187  Sum_probs=64.2

Q ss_pred             CCCCCEEEEeCCC----CCCCH-------HHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           64 DALKKTLQVSNLS----PLLTV-------EQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        64 ~~~~~tL~V~NLp----~~vte-------edL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      ....+||+|.||-    +..+.       ++|.+-+.+||.|..|.|.  ++.|.+.|.|.+.++|..|| .|+|.+|+|
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdg  341 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDG  341 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecc
Confidence            3457899999984    23342       4556668899999999998  78999999999999999999 899999999


Q ss_pred             ceEEEEecccC
Q 005698          130 RPLNVEMAKSF  140 (682)
Q Consensus       130 r~L~V~~a~~~  140 (682)
                      +.|...+....
T Consensus       342 Rql~A~i~DG~  352 (382)
T KOG1548|consen  342 RQLTASIWDGK  352 (382)
T ss_pred             eEEEEEEeCCc
Confidence            99999876544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=97.28  E-value=0.00077  Score=65.81  Aligned_cols=62  Identities=19%  Similarity=0.287  Sum_probs=55.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      ...|.|.+||+..+|+||++++...|.|+...+.. -|+++|+|...++++-|| .|+.+.|.-
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r-Dg~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR-DGVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeec-ccceeeeeeehhhHHHHHHhhccccccC
Confidence            35799999999999999999999999999999873 479999999999999999 888877653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.24  E-value=0.00024  Score=76.89  Aligned_cols=64  Identities=27%  Similarity=0.342  Sum_probs=55.0

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecC-------------------CCeEEEEeCCHHHHHHHHHc
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS-------------------KHFAYIEYSKPEEATAALAL  122 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~-------------------kg~aFVeF~s~e~A~~Al~L  122 (682)
                      .++.+.+||.|.|||.+-.-+-|.+||+.||.|..|.|+++                   +-+|||+|...+.|.+|.+|
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34457899999999998888999999999999999999832                   45799999999999999965


Q ss_pred             CCc
Q 005698          123 NNM  125 (682)
Q Consensus       123 ng~  125 (682)
                      .+.
T Consensus       306 ~~~  308 (484)
T KOG1855|consen  306 LNP  308 (484)
T ss_pred             hch
Confidence            543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.21  E-value=0.00053  Score=74.05  Aligned_cols=74  Identities=22%  Similarity=0.362  Sum_probs=59.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCC-ceecCceEEEEecccCCCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFC--GTVVECTITDSKHFAYIEYSKPEEATAAL-ALNN-MDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~--G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng-~~l~Gr~L~V~~a~~~~~~  143 (682)
                      ..||||||.+.++..+|..+|...  |.-..+-|  ..||+||.+.+...|..|+ .|+| .++.|.++.|...-+....
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~--k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr   79 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV--KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR   79 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee--ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH
Confidence            469999999999999999999854  22222223  3799999999999999999 7888 6789999999877655443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.18  E-value=0.00027  Score=75.01  Aligned_cols=77  Identities=31%  Similarity=0.507  Sum_probs=66.7

Q ss_pred             CCCEEE-EeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           66 LKKTLQ-VSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~-V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...++| |+||++.+++++|+.+|..+|.|..|.+.      ..+|||||+|.+..++..||..+...|.|+.|.|.+..
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDE  262 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCC
Confidence            345555 99999999999999999999999999987      47899999999999999998447888899999999887


Q ss_pred             cCCC
Q 005698          139 SFPQ  142 (682)
Q Consensus       139 ~~~~  142 (682)
                      ....
T Consensus       263 ~~~~  266 (285)
T KOG4210|consen  263 PRPK  266 (285)
T ss_pred             CCcc
Confidence            6543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.13  E-value=0.00089  Score=72.25  Aligned_cols=75  Identities=32%  Similarity=0.403  Sum_probs=64.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCc-eEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGR-PLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr-~L~V~~a~~  139 (682)
                      ++..+|.+.|||+.++|++|+.+|..-|.++.....  +...+|++.|.+.++|..|+ .|+++.+++. .|+|.|++.
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            455799999999999999999999999876554433  56789999999999999999 8999999874 899999874

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.07  E-value=0.0024  Score=60.77  Aligned_cols=57  Identities=26%  Similarity=0.441  Sum_probs=47.8

Q ss_pred             HHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           82 EQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        82 edL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .+|.+.|..||+|+-|++.  .+.-+|+|.+-..|.+||.|+|+.|+|+.|.|.+-.+.
T Consensus        51 ~~ll~~~~~~GevvLvRfv--~~~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFV--GDTMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEE--TTCEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEe--CCeEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            3788899999999999998  46889999999999999999999999999999876543

; PDB: 1UFW_A 2DNR_A.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.93  E-value=0.00036  Score=71.38  Aligned_cols=63  Identities=25%  Similarity=0.356  Sum_probs=52.6

Q ss_pred             HHHHHHHh-cCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCCCC
Q 005698           82 EQLRQLFS-FCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKP  144 (682)
Q Consensus        82 edL~~~F~-~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~~~  144 (682)
                      ++|...|. +||+|+.+.|.     +..|-+||.|...++|+.|+ .|||-+|.|++|.+++........
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~re  152 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFRE  152 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchhh
Confidence            45555556 89999999876     46788999999999999999 899999999999999987654443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.83  E-value=0.0039  Score=66.72  Aligned_cols=76  Identities=30%  Similarity=0.310  Sum_probs=63.0

Q ss_pred             CCCCEEEEeCCC--CCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceec-C-ceEEEEecc
Q 005698           65 ALKKTLQVSNLS--PLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVG-G-RPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp--~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-G-r~L~V~~a~  138 (682)
                      .+...|.+.=|.  +.||.+.|..++...|.|..|.|. +.---|.|||++.+.|++|. .|||..|. | ..|+|+||+
T Consensus       118 ~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAk  197 (494)
T KOG1456|consen  118 TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAK  197 (494)
T ss_pred             CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecC
Confidence            345566666554  689999999999999999999987 44456999999999999999 89998876 4 789999998


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      +.
T Consensus       198 P~  199 (494)
T KOG1456|consen  198 PT  199 (494)
T ss_pred             cc
Confidence            64

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.82  E-value=0.00013  Score=85.16  Aligned_cols=76  Identities=20%  Similarity=0.286  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ......|||+|||+..+++.+|...|..||.|..|.|.     ....||||.|.+...+..|+ .|.+..|..-.+.+.+
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            34456899999999999999999999999999999986     34569999999999999999 8888877765666655


Q ss_pred             cc
Q 005698          137 AK  138 (682)
Q Consensus       137 a~  138 (682)
                      ..
T Consensus       448 G~  449 (975)
T KOG0112|consen  448 GQ  449 (975)
T ss_pred             cc
Confidence            54

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.75  E-value=0.0039  Score=69.79  Aligned_cols=73  Identities=19%  Similarity=0.377  Sum_probs=58.9

Q ss_pred             CCCCCEEEEeCCCCCCC--H----HHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceec-Cc
Q 005698           64 DALKKTLQVSNLSPLLT--V----EQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVG-GR  130 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vt--e----edL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr  130 (682)
                      +.....|+|.|+|.--.  .    .-|..+|++||+|+.+.++     ..+||.|++|.+..+|+.|+ .|||+.|+ .+
T Consensus        55 eg~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   55 EGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            35578999999983221  1    3466889999999999987     57899999999999999999 89999887 46


Q ss_pred             eEEEEe
Q 005698          131 PLNVEM  136 (682)
Q Consensus       131 ~L~V~~  136 (682)
                      .+.|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            677754

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=96.65  E-value=0.0038  Score=70.37  Aligned_cols=57  Identities=16%  Similarity=0.277  Sum_probs=48.2

Q ss_pred             HHHHHHhcCCCeEEEEEe---------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           83 QLRQLFSFCGTVVECTIT---------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        83 dL~~~F~~~G~V~~v~i~---------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      +|+.-|..||.|..|.|.         ...|..||+|.+.++++.|+ +|+|..|.|+.|.+.|...
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            445556789999999987         24678999999999999999 8999999999988877543

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.58  E-value=0.0051  Score=68.49  Aligned_cols=59  Identities=22%  Similarity=0.280  Sum_probs=52.6

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFS-FCGTVVECTIT------DSKHFAYIEYSKPEEATAAL  120 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~-~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al  120 (682)
                      ..-.+.+|||||+||--++.++|..||. -||.|++|-|-      -++|-|=|+|.+...-.+||
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AI  430 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAI  430 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHH
Confidence            3445679999999999999999999999 89999999885      26889999999999999998

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.54  E-value=0.005  Score=70.34  Aligned_cols=70  Identities=17%  Similarity=0.237  Sum_probs=59.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeE-EEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVV-ECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~-~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .++|-|.|+|+.++-+||.+||..|-.+- +|.|.     ...|.|.|.|++.++|..|. .|++..|..+.|.|.+
T Consensus       867 p~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  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            45889999999999999999999996553 33333     35689999999999999999 7999999999988864

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.47  E-value=0.0052  Score=68.43  Aligned_cols=58  Identities=16%  Similarity=0.265  Sum_probs=47.6

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---------cCCC---eEEEEeCCHHHHHHHH
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---------DSKH---FAYIEYSKPEEATAAL  120 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---------~~kg---~aFVeF~s~e~A~~Al  120 (682)
                      ........||||+||++|+|++|...|..||.|. |++.         ..+|   |+|+.|+++..++.-|
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll  323 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLL  323 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHH
Confidence            3445578999999999999999999999999864 3332         3566   9999999998887766

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.42  E-value=0.0058  Score=63.56  Aligned_cols=57  Identities=21%  Similarity=0.310  Sum_probs=48.3

Q ss_pred             HHHHHHHhcCCCeEEEEEec-------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           82 EQLRQLFSFCGTVVECTITD-------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        82 edL~~~F~~~G~V~~v~i~~-------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      +++++-+.+||.|..|.|..       ..--.||+|...++|.+|+ .|||..|+|+.+...|..
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            57788899999999998862       2334799999999999999 899999999988877654

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.37  E-value=0.0049  Score=66.15  Aligned_cols=75  Identities=19%  Similarity=0.152  Sum_probs=61.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCC-eEE--EEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGT-VVE--CTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~-V~~--v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      .....+|-+.+||+..+.+||.+||..|.. |..  |.|+     ...|.|||+|.+.+.|..|. ..+++...++.|.|
T Consensus       277 ~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  277 TRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            334678999999999999999999999874 322  5554     56799999999999999998 68888888999999


Q ss_pred             Eecc
Q 005698          135 EMAK  138 (682)
Q Consensus       135 ~~a~  138 (682)
                      ..+.
T Consensus       357 fp~S  360 (508)
T KOG1365|consen  357 FPCS  360 (508)
T ss_pred             eecc
Confidence            7664

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.16  E-value=0.0028  Score=69.68  Aligned_cols=75  Identities=19%  Similarity=0.209  Sum_probs=63.0

Q ss_pred             CCEEEEeCCCCCC-CHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccCC
Q 005698           67 KKTLQVSNLSPLL-TVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        67 ~~tL~V~NLp~~v-teedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .+.|-|.-+++.+ |-++|..+|.+||+|..|.|-...--|+|+|.+..+|-.|...++..|+|+.|+|.|..+..
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhccccceecCceeEEEEecCCc
Confidence            4555555566544 44899999999999999999755677999999999999999999999999999999988744

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.79  E-value=0.032  Score=58.50  Aligned_cols=71  Identities=25%  Similarity=0.345  Sum_probs=57.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCc-eEEEEecc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGR-PLNVEMAK  138 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr-~L~V~~a~  138 (682)
                      ..-|-|-++++.-+ .-|..+|.+||+|+........+|-+|.|....+|++||..||+.|+|. .|-|..|.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecC
Confidence            44566667876543 5688899999999998877777899999999999999999999999984 45565544

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.77  E-value=0.01  Score=62.96  Aligned_cols=69  Identities=19%  Similarity=0.174  Sum_probs=55.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCC--eEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGT--VVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~--V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .-.+|||||-+++|++||.+.+...|.  |.++++.      +++|||+|...+...+++.+ .|--.+|.|..-.|.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            457999999999999999999988774  3333332      68999999999988888888 688889999765553

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.70  E-value=0.039  Score=52.19  Aligned_cols=74  Identities=16%  Similarity=0.227  Sum_probs=56.5

Q ss_pred             CCCCCCEEEEeCCCCCCC----HHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           63 ADALKKTLQVSNLSPLLT----VEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vt----eedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .+++-.||.|.=|..++.    ...|...+..||+|..|.+. .+.-|+|.|.+...|-.|+ +++. ..-|..+.|.|-
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            466678888875554443    34455667789999999987 4677999999999999999 7776 566778888775


Q ss_pred             c
Q 005698          138 K  138 (682)
Q Consensus       138 ~  138 (682)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            4

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.56  E-value=0.0021  Score=75.08  Aligned_cols=76  Identities=18%  Similarity=0.197  Sum_probs=67.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ...|||.|+|+..|.++|+.+|..+|.|..+.++     .++|.|||.|.+..++..++ .+++..+.-..+.|..+.+.
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~  815 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            4679999999999999999999999999998876     57899999999999999999 78888888888888876654


Q ss_pred             CC
Q 005698          141 PQ  142 (682)
Q Consensus       141 ~~  142 (682)
                      ..
T Consensus       816 ~~  817 (881)
T KOG0128|consen  816 RD  817 (881)
T ss_pred             cc
Confidence            33

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

Probab=95.37  E-value=0.012  Score=67.42  Aligned_cols=70  Identities=20%  Similarity=0.274  Sum_probs=62.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ++.-+|||+||...|..+-++.++..||-|..+....   |||++|.....+..|+ .|+-..++|..|.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            3577999999999999999999999999998887763   9999999999999999 78889999998888764

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.93  E-value=0.0077  Score=70.30  Aligned_cols=81  Identities=31%  Similarity=0.352  Sum_probs=67.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCcee--cCceEEEEecccCCCCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV--GGRPLNVEMAKSFPQKP  144 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l--~Gr~L~V~~a~~~~~~~  144 (682)
                      .+.++.|++-..+-.-|..+|..||.|..++....-+.|.|+|...+.|..|+ +|+|.++  .|-+.+|.+|+..+...
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~~e  378 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPMYE  378 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccccccc
Confidence            34455566667788889999999999999999878889999999999999999 8999765  57889999999877655


Q ss_pred             CCCC
Q 005698          145 SHLN  148 (682)
Q Consensus       145 ~~~~  148 (682)
                      ..++
T Consensus       379 p~ln  382 (1007)
T KOG4574|consen  379 PPLN  382 (1007)
T ss_pred             CCcC
Confidence            5444

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.90  E-value=0.0022  Score=74.88  Aligned_cols=63  Identities=38%  Similarity=0.484  Sum_probs=53.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCc
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGR  130 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr  130 (682)
                      .++||.||++.+.+.+|..+|..||.|..|.|.      +.+|+|||+|...+++.+||+++...|.|+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK  736 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK  736 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh
Confidence            468999999999999999999999988777664      578999999999999999996555555553

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.88  E-value=0.0094  Score=63.46  Aligned_cols=74  Identities=20%  Similarity=0.308  Sum_probs=59.6

Q ss_pred             CCEEEEeCCCCCCCHHHHH---HHHhcCCCeEEEEEec---------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           67 KKTLQVSNLSPLLTVEQLR---QLFSFCGTVVECTITD---------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~---~~F~~~G~V~~v~i~~---------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      ..-+||-+|++.+-.+.+.   ++|++||.|..|.+..         .-.-+||+|...++|..|| ..+|+.++|+.|.
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            4678999999877665553   7899999999998862         1123799999999999999 8999999999988


Q ss_pred             EEecccC
Q 005698          134 VEMAKSF  140 (682)
Q Consensus       134 V~~a~~~  140 (682)
                      ..+....
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7766543

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.74  E-value=0.044  Score=54.31  Aligned_cols=74  Identities=20%  Similarity=0.169  Sum_probs=48.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhc-CCCe---EEEEEe--------cCCCeEEEEeCCHHHHHHHH-HcCCceecCc--
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSF-CGTV---VECTIT--------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGR--  130 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~-~G~V---~~v~i~--------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr--  130 (682)
                      ....|.|.+||+.+||+++.+.+.. +|..   .++.-.        ..-.-|||.|.+.+++..-+ .++|+.|.+.  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4569999999999999999997776 6655   444421        12245999999999988888 8999888652  


Q ss_pred             ---eEEEEeccc
Q 005698          131 ---PLNVEMAKS  139 (682)
Q Consensus       131 ---~L~V~~a~~  139 (682)
                         ...|++|..
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence               345666654

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.64  E-value=0.024  Score=63.57  Aligned_cols=68  Identities=19%  Similarity=0.446  Sum_probs=53.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHh--cCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCC--ceecCceEEEE
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFS--FCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNN--MDVGGRPLNVE  135 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~--~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng--~~l~Gr~L~V~  135 (682)
                      .+.|+|.-||..+.+++|+.||.  .|-.++.|.+..+.+ =||+|++..||+.|+ .|..  .+|.|+.|...
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            36788889999999999999998  478899998874333 589999999999998 5543  45667665443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.62  E-value=0.15  Score=41.84  Aligned_cols=54  Identities=19%  Similarity=0.284  Sum_probs=43.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC---CCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFC---GTVVECTITDSKHFAYIEYSKPEEATAAL-AL  122 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~---G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L  122 (682)
                      ...|+|.||. .++.+||+.||..|   .....|.+++. .-|-|.|.+.+.|..|| +|
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            5689999997 68889999999988   23456777633 34889999999999999 54

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.19  E-value=0.098  Score=52.20  Aligned_cols=62  Identities=24%  Similarity=0.338  Sum_probs=47.4

Q ss_pred             CHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC--CceecCceEEEEecccCC
Q 005698           80 TVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN--NMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        80 teedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln--g~~l~Gr~L~V~~a~~~~  141 (682)
                      ..+.|..||..|+.+..+.+..+-+=.+|.|.+.++|..|. .|+  ++.|.|..|+|.|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            34789999999999998888877777899999999999999 788  999999999999986443

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=94.11  E-value=0.2  Score=42.35  Aligned_cols=66  Identities=23%  Similarity=0.281  Sum_probs=40.6

Q ss_pred             EEEEe-CCCCCCCHHHHHHHHhcCC-----CeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           69 TLQVS-NLSPLLTVEQLRQLFSFCG-----TVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~-NLp~~vteedL~~~F~~~G-----~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      +|||. +--..++..+|..+|...+     .|-.|.|.  ..|+||+-... .|..+| .|++..+.|+.|.|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45553 2236889999999999775     45677777  78999998654 677888 89999999999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=94.04  E-value=0.029  Score=64.42  Aligned_cols=70  Identities=17%  Similarity=0.185  Sum_probs=57.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-EEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~-v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ...+|||..||..+++.++.++|...-.|++ |.|.     ...+.|||.|..++++..|+ .-+-+.++.+.|+|.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            3578999999999999999999998888877 6664     35689999999988888888 455566666788885

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=93.94  E-value=0.043  Score=59.19  Aligned_cols=66  Identities=17%  Similarity=0.207  Sum_probs=48.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcC----CCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFC----GTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~----G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      .|-+.+||+++|+.||.+||..-    |.++.|-++     ...|-|||.|..+++|+.||.-|-..|+-+.|.|
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIEl  237 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIEL  237 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHH
Confidence            45566999999999999999732    233444433     3568999999999999999955555555555554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=93.30  E-value=0.08  Score=54.58  Aligned_cols=70  Identities=26%  Similarity=0.312  Sum_probs=56.1

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-Hc--CC--ceecCceEEEEec
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-AL--NN--MDVGGRPLNVEMA  137 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~L--ng--~~l~Gr~L~V~~a  137 (682)
                      ..|||.||...+.-+.|...|..||.|....++     ...+-++|+|...-.|..|+ .+  .|  .++.+....|...
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            789999999999999999999999999765554     46688999999999999998 44  22  3445666666543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.23  E-value=0.34  Score=41.97  Aligned_cols=54  Identities=17%  Similarity=0.311  Sum_probs=40.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN  123 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln  123 (682)
                      ...+||+ +|...-..||.++|..||.|.=-.|.  ..-|||.+.+.+.|..|+ .++
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~--dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN--DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEEC--TTEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc--CCcEEEEeecHHHHHHHHHHhc
Confidence            3466676 99999999999999999998644454  567999999999999988 564

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=90.64  E-value=0.22  Score=49.03  Aligned_cols=76  Identities=20%  Similarity=0.252  Sum_probs=61.8

Q ss_pred             CCCCEEEEeCCCCCCCH-----HHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCc-eEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTV-----EQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGR-PLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vte-----edL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr-~L~V~~a  137 (682)
                      ...++|++++|+..+-.     .....+|.+|.++..+.+..+.++.-|.|.+.+.|..|. .++++.|.|. .|.+.++
T Consensus         8 dlp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrsfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfa   87 (193)
T KOG4019|consen    8 DLPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRSFRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFA   87 (193)
T ss_pred             cccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHhhceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEc
Confidence            45678899999864433     345678888888887777777788889999999999999 8999999998 8999888


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      ...
T Consensus        88 Q~~   90 (193)
T KOG4019|consen   88 QPG   90 (193)
T ss_pred             cCC
Confidence            764

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=90.28  E-value=0.16  Score=54.06  Aligned_cols=75  Identities=17%  Similarity=0.106  Sum_probs=61.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCC-ceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNN-MDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng-~~l~Gr~L~V~~a~  138 (682)
                      ..+++||+++...+.+.++..+|..+|.+..+.+.      ..++|++|.|...+.+..||++.+ ..+.+..+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            47899999999999999999999999988877654      578999999999999999997777 46666666655544


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      ..
T Consensus       167 ~~  168 (285)
T KOG4210|consen  167 RR  168 (285)
T ss_pred             cc
Confidence            43

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=89.72  E-value=1.8  Score=39.59  Aligned_cols=63  Identities=10%  Similarity=0.047  Sum_probs=44.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC-CCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFC-GTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~-G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      ...+.+...|..++.++|..|...+ ..|..+.|+    .++-.++|.|.+.+.|..-. .+||..|+.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3444455555555556666555555 366778887    24447899999999999988 899998864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.20  E-value=1.3  Score=50.47  Aligned_cols=75  Identities=20%  Similarity=0.284  Sum_probs=59.3

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcC----CCeEEEEEe--------------c-C---------------------
Q 005698           64 DALKKTLQVSNLSP-LLTVEQLRQLFSFC----GTVVECTIT--------------D-S---------------------  102 (682)
Q Consensus        64 ~~~~~tL~V~NLp~-~vteedL~~~F~~~----G~V~~v~i~--------------~-~---------------------  102 (682)
                      ....+.|-|.||.+ .|...||..+|..|    |.|..|.|+              + +                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            45678999999995 67789999999976    689999986              0 1                     


Q ss_pred             -----------------CCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEEecc
Q 005698          103 -----------------KHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMAK  138 (682)
Q Consensus       103 -----------------kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~a~  138 (682)
                                       .-||+|+|.+.+.|...+ .++|++|..  ..|-+.|..
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIP  306 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIP  306 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecC
Confidence                             127999999999999888 899999974  555555543

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=88.37  E-value=0.81  Score=52.06  Aligned_cols=10  Identities=40%  Similarity=0.395  Sum_probs=4.2

Q ss_pred             cccCCCCCCC
Q 005698            7 TTTMGTLSQV   16 (682)
Q Consensus         7 ~~s~~~l~~~   16 (682)
                      .+++..+.+.
T Consensus        28 ~~~~pp~~q~   37 (757)
T KOG4368|consen   28 AATMPPLPQP   37 (757)
T ss_pred             ccCCCCCCCC
Confidence            3444444443

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=86.21  E-value=0.86  Score=51.77  Aligned_cols=72  Identities=19%  Similarity=0.191  Sum_probs=46.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceec---C-ceEEE
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFS-FCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVG---G-RPLNV  134 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~-~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~---G-r~L~V  134 (682)
                      .+|+-|.|++...|-..|...-. ..|.-..+.|+      -+.|||||.|.+.+++..+. ++||+.|.   + +.+.|
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            45666666666655555444422 24544445554      36799999999999999999 89998654   2 34445


Q ss_pred             Eecc
Q 005698          135 EMAK  138 (682)
Q Consensus       135 ~~a~  138 (682)
                      .||.
T Consensus       468 tYAr  471 (549)
T KOG4660|consen  468 TYAR  471 (549)
T ss_pred             ehhh
Confidence            5554

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=86.06  E-value=3.2  Score=46.25  Aligned_cols=64  Identities=11%  Similarity=0.188  Sum_probs=54.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC-CeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCG-TVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G-~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      ..+.|+|-.+|..+|..||..|+..|- .|..|.|+    .+.-.++|.|.+.++|..-. ++||..|+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            378999999999999999999999764 67888887    23446889999999999999 899998875

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=85.92  E-value=0.036  Score=60.34  Aligned_cols=72  Identities=26%  Similarity=0.434  Sum_probs=60.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--c-CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--D-SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~-~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      .+.|.|.|||+...|+.|..|+..||.|..|..+  + .....-|+|...+.+..|| .|+|..|....+.|.|-.
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            4569999999999999999999999999988765  2 2234457899999999999 899999999999987653

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

Probab=83.48  E-value=36  Score=36.12  Aligned_cols=12  Identities=0%  Similarity=0.376  Sum_probs=6.3

Q ss_pred             ceecCceEEEEe
Q 005698          125 MDVGGRPLNVEM  136 (682)
Q Consensus       125 ~~l~Gr~L~V~~  136 (682)
                      ..++-+.|.|++
T Consensus        76 k~ldpkkmQiNl   87 (354)
T KOG2146|consen   76 KNLDPKKMQINL   87 (354)
T ss_pred             cCCCchheeeee
Confidence            445555555554

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=81.40  E-value=0.66  Score=48.31  Aligned_cols=62  Identities=23%  Similarity=0.417  Sum_probs=44.4

Q ss_pred             CCCEEEEeCCCC------------CCCHHHHHHHHhcCCCeEEEEEe----------------cCCCe---------EEE
Q 005698           66 LKKTLQVSNLSP------------LLTVEQLRQLFSFCGTVVECTIT----------------DSKHF---------AYI  108 (682)
Q Consensus        66 ~~~tL~V~NLp~------------~vteedL~~~F~~~G~V~~v~i~----------------~~kg~---------aFV  108 (682)
                      -..|||+.+||-            .-+++-|...|..||.|..|.|+                +..||         |||
T Consensus       148 rpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayv  227 (445)
T KOG2891|consen  148 RPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYV  227 (445)
T ss_pred             CCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHH
Confidence            356888888883            24567899999999999998875                12333         456


Q ss_pred             EeCCHHHHHHHH-HcCCcee
Q 005698          109 EYSKPEEATAAL-ALNNMDV  127 (682)
Q Consensus       109 eF~s~e~A~~Al-~Lng~~l  127 (682)
                      +|........|+ .|.|..|
T Consensus       228 qfmeykgfa~amdalr~~k~  247 (445)
T KOG2891|consen  228 QFMEYKGFAQAMDALRGMKL  247 (445)
T ss_pred             HHHHHHhHHHHHHHHhcchH
Confidence            676666677777 7777554

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=80.02  E-value=4  Score=42.95  Aligned_cols=50  Identities=12%  Similarity=0.204  Sum_probs=41.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCe-EEEEEecCCCeEEEEeCCHH
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTV-VECTITDSKHFAYIEYSKPE  114 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V-~~v~i~~~kg~aFVeF~s~e  114 (682)
                      ...+-|||+||+.++...||+..+.+.|.+ ..|.+....|-||+.|.+..
T Consensus       328 ~~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg~~~k~flh~~~~~  378 (396)
T KOG4410|consen  328 GAKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKGHFGKCFLHFGNRK  378 (396)
T ss_pred             ccccceeeccCccccchHHHHHHHHhcCCCceeEeeecCCcceeEecCCcc
Confidence            345679999999999999999999988854 56666677899999998753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	682
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		2e-05
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		2e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-04

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDVG 128
           + V N+S   T ++LR LF   G V+EC +   K +A++   K  +A AA+A LN  +V 
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVK 69
Query: 129 GRPLNVEMA 137
           G+ +NVE++
Sbjct: 70  GKRINVELS 78

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 3/71 (4%)
Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVG 128
           L V N+SP  T ++LR  F   G V+EC I   K +A++   + E+A  A+  L+N +  
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQ 70
Query: 129 GRPLNVEMAKS 139
           G+ ++V+++ S
Sbjct: 71  GKRMHVQLSTS 81

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAALA-LNN 124
           L V NL   +  E+LR+ FS  GT+    +      SK F ++ +S PEEAT A+  +N 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 125 MDVGGRPLNVEMAK 138
             V  +PL V +A+
Sbjct: 78  RIVATKPLYVALAQ 91

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	682
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-17
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-17
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-16
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-15
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-15
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-15
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-14
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-14
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-14
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-14
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-13
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-12
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	9e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-11
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-11
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-10
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-10
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	8e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	9e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-09
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-08
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-07
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	7e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-07
2div_A	99	TRNA selenocysteine associated protein; structural	9e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-06
3eml_A	488	Human adenosine A2A receptor/T4 lysozyme chimera;	6e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	8e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-04
2rh1_A	500	Beta-2-adrenergic receptor/T4-lysozyme chimera; GP	4e-04
3pbl_A	481	D(3) dopamine receptor, lysozyme chimera; structur	5e-04

>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 = 81.1 bits (201), Expect = 5e-18
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIE 109
           GS    G        L + NL+P  +V +L+   S      +  + D     ++ F Y++
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 60

Query: 110 YSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           +   E+   AL L  + V G  + +E  K    K  
Sbjct: 61  FESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKV 96

>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 = 66.9 bits (164), Expect = 5e-13
 Identities = 22/109 (20%), Positives = 42/109 (38%), Gaps = 9/109 (8%)

Query: 39  AHAAQVQAQQSAKDLSGSPDKAGKADALKK-------TLQVSNLSPLLTVEQLRQLFSFC 91
           A   +   + +   + G+  K  K             TL   NLS  +T ++L+++F   
Sbjct: 64  AEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDA 123

Query: 92  GTVVECTITD-SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
             +   +    SK  AYIE+    +A   L      ++ GR +++    
Sbjct: 124 LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

>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 = 77.2 bits (191), Expect = 1e-17
 Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 8/87 (9%)

Query: 64  DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEAT 117
           +A  +++ V N+    T E+L   F  CG+V   TI  D      K FAYIE+S  E   
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 118 AALALNNMDVGGRPLNVEMAKSFPQKP 144
            +LAL+     GR + V   +    +P
Sbjct: 63  TSLALDESLFRGRQIKVIPKR--TNRP 87

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 78.2 bits (193), Expect = 1e-17
 Identities = 27/112 (24%), Positives = 50/112 (44%), Gaps = 6/112 (5%)

Query: 34  AQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGT 93
           A  +Q   +++ A    +          K +  K+++ V N+    T + L   FS CG+
Sbjct: 3   APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGS 62

Query: 94  VVECTI-TD-----SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS 139
           +   TI  D      K +AYIE+++     AA+A++     GR + V   ++
Sbjct: 63  INRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT 114

>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 = 74.2 bits (183), Expect = 2e-16
 Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 3/94 (3%)

Query: 55  GSPDKAGKADALK--KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSK 112
           GS   +G  D +   K L V NL    + E + + F+         +   + +A++ +S 
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSN 60

Query: 113 PEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
            E+A  A+ ALN   + G P+ V +AK   +  S
Sbjct: 61  REDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSS 94

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 73.2 bits (180), Expect = 6e-16
 Identities = 16/101 (15%), Positives = 35/101 (34%), Gaps = 7/101 (6%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL 120
            K +  + L+  +    L+ +    G V E  I            A + ++    A   +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 121 -ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMM 160
             L+   V G  ++ ++     Q+  +    + GS  P  +
Sbjct: 66  KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTV 106

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 72.7 bits (179), Expect = 7e-16
 Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 63  ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-A 121
           A     T  + N+    T   L  LF   G +++      K   +I+Y   E+A   + A
Sbjct: 23  APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVA 82

Query: 122 LNNMDVGGRPLNVEMAKS 139
           L N    GR L     K 
Sbjct: 83  LANFPFQGRNLRTGWGKE 100

>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 = 72.7 bits (179), Expect = 7e-16
 Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 5/104 (4%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPE 114
           GS   +G A    K L V NL+  +T E L + FS  G +        K +A+I + + +
Sbjct: 1   GSSGSSGMAKV--KVLFVRNLANTVTEEILEKAFSQFGKLERVKK--LKDYAFIHFDERD 56

Query: 115 EATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
            A  A+  +N  D+ G  + +  AK   QK     +    +S P
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 72.3 bits (178), Expect = 9e-16
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAALALN 123
            L + NL+P  +V +L+   S      +  + D     ++ F Y+++   E+   AL L 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78

Query: 124 NMDVGGRPLNVEMAKS 139
            + V G  + +E  K 
Sbjct: 79  GLKVFGNEIKLEKPKG 94

>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 = 71.9 bits (177), Expect = 1e-15
 Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 6/92 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYI 108
           SGS       +   +T+ V NL   +  E L +LF   G + + TI  D     K F ++
Sbjct: 3   SGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFV 62

Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS 139
            +  PE  + A+  LN + + GRP+NV    S
Sbjct: 63  CFKHPESVSYAIALLNGIRLYGRPINVSGPSS 94

>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 = 74.2 bits (183), Expect = 1e-15
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 11/92 (11%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----------SKHFAYIEYSKPEEA 116
           + L V N+   +T E +   F+    +   T               K+FA++E+   +E 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 117 TAALALNNMDVGGRPLNVEMAKSFPQKPSHLN 148
           T A+A + +   G+ L +     +   P    
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 = 68.0 bits (167), Expect = 2e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALA-LNN 124
           +  L   L  +Q+++L +  G +    +  D     SK +A+ EY        A+A LN 
Sbjct: 99  IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 158

Query: 125 MDVGGRPLNVEMA 137
           M +G + L V+ A
Sbjct: 159 MQLGDKKLLVQRA 171

>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 = 76.6 bits (189), Expect = 1e-15
 Identities = 24/98 (24%), Positives = 37/98 (37%), Gaps = 7/98 (7%)

Query: 68  KTLQVSNLSPLLT-VEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL- 120
           + L V  L P    V+ L +  S   +   C +        K FA +EY   E A  A  
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 244

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPM 158
             + + +GG  L V      P   S L + +A  +  +
Sbjct: 245 QADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATAL 282

>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 = 66.9 bits (164), Expect = 2e-12
 Identities = 15/91 (16%), Positives = 40/91 (43%), Gaps = 2/91 (2%)

Query: 51  KDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEY 110
           +++    +   +    ++ + +  L   +T +++  L S    +  C +   K  A++  
Sbjct: 6   EEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTL 64

Query: 111 SKPEEATAAL-ALNNMDVGGRPLNVEMAKSF 140
              E+A AA+ A +   +  R L+V++  + 
Sbjct: 65  LNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 66.5 bits (163), Expect = 3e-12
 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           V+NL P LT +Q  +L    G++  C +        SK + + EY K + A  A   L  
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159

Query: 125 MDVGGRPLNVEMAKSFPQKPSHLNS 149
             +G R L V    +    P+ L+S
Sbjct: 160 KPLGPRTLYVHWTDAGQLTPALLHS 184

>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 = 72.9 bits (179), Expect = 2e-15
 Identities = 30/144 (20%), Positives = 57/144 (39%), Gaps = 20/144 (13%)

Query: 13  LSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQV 72
           +SQ+P+             V+        AQ+Q  Q  +     P +      + + L V
Sbjct: 1   MSQIPL-------------VSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMV 47

Query: 73  SNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNNM 125
           + +   +   QLRQLF   G +     + D     S+ + ++++     A  A+  LN  
Sbjct: 48  NYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107

Query: 126 DVGGRPLNVEMAKSFPQKPSHLNS 149
           ++  + L V +A S  Q+P    +
Sbjct: 108 NILNKRLKVALAASGHQRPGIAGA 131

>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 = 74.3 bits (183), Expect = 2e-15
 Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 11/92 (11%)

Query: 65  ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----------SKHFAYIEYSKP 113
           A+ + L V N+   +T E +   F+    +   T               K+FA++E+   
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 114 EEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           +E T A+A + +   G+ L +     +   P 
Sbjct: 62  DETTQAMAFDGIIFQGQSLKIRRPHDYQPLPG 93

>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 = 73.5 bits (181), Expect = 4e-15
 Identities = 24/107 (22%), Positives = 38/107 (35%), Gaps = 8/107 (7%)

Query: 39  AHAAQVQAQQSAKDLSGSPDKAGKADALK-KTLQVSNLSPLLTVEQLRQLFSFCGTVVEC 97
            H  Q     S       P             L +  L   L  +Q+++L +  G +   
Sbjct: 85  PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 144

Query: 98  TI-TD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA 137
            +  D     SK +A+ EY        A+  LN M +G + L V+ A
Sbjct: 145 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>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 = 71.1 bits (175), Expect = 3e-15
 Identities = 28/93 (30%), Positives = 37/93 (39%), Gaps = 1/93 (1%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKP 113
           S       K    +  L V NL P +T E++R+LF   G   E  I   K F +I     
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETR 61

Query: 114 EEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
             A  A   L+NM + G+ L V  A       S
Sbjct: 62  TLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 70.4 bits (173), Expect = 4e-15
 Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYI 108
             S          K  L +S L    T E+L ++    GTV +  + T+     K  AY+
Sbjct: 4   GSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYV 63

Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK 143
           EY    +A+ A+  ++ M +    + V ++ S P  
Sbjct: 64  EYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>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 = 70.8 bits (174), Expect = 4e-15
 Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL- 120
           ++     T+    ++  LT + +RQ FS  G ++E  +   K ++++ +S  E A  A+ 
Sbjct: 20  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV 79

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPSHLNS 149
           ++N   + G  +     K  P   S  +S
Sbjct: 80  SVNGTTIEGHVVKCYWGKESPDMTSGPSS 108

>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 = 69.9 bits (172), Expect = 6e-15
 Identities = 31/91 (34%), Positives = 44/91 (48%), Gaps = 7/91 (7%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAY 107
           SGS   +G     K T+ VSNL   LT   L ++FS  G VV+ T + D     SK  A+
Sbjct: 3   SGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62

Query: 108 IEYSKPEEATAAL-ALNNMDVGGRPLNVEMA 137
           I +   + A     A+NN  + GR +   +A
Sbjct: 63  ILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 = 70.4 bits (173), Expect = 6e-15
 Identities = 28/110 (25%), Positives = 47/110 (42%), Gaps = 6/110 (5%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYI 108
           S     A +A  L  T+ V+NL   +  ++L+++FS  G VV   I  D    S+    +
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61

Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
            + +  EA  A+   N   +  RP++V+M +    K           S P
Sbjct: 62  TFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGP 111

>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 = 69.6 bits (171), Expect = 7e-15
 Identities = 30/93 (32%), Positives = 40/93 (43%), Gaps = 4/93 (4%)

Query: 54  SGSPDKAGKADAL-KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSK 112
           SGS  K G   A     L V  L P  ++  L + F   G++          FAYI+Y  
Sbjct: 3   SGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYES 62

Query: 113 PEEATAAL-ALNNMDVGG--RPLNVEMAKSFPQ 142
            + A AA   +    +GG  R L V+ AKS P 
Sbjct: 63  LDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 69.2 bits (170), Expect = 1e-14
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 5/83 (6%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD---SKHFAYIEYSKPEEATAAL-ALNNMD 126
           V NL   +  E+LR+ FS  GT+    +  +   SK F ++ +S PEEAT A+  +N   
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 127 VGGRPLNVEMAKSFPQKPSHLNS 149
           V  +PL V +A+   ++ S  +S
Sbjct: 80  VATKPLYVALAQRKEERQSGPSS 102

>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 = 69.7 bits (171), Expect = 1e-14
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAY 107
               D     +   +T+    L+  +    L   FS  G V +  I +D     SK  AY
Sbjct: 12  REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKS 139
           +E+ + +    A+ L    + G P+ V+ +++
Sbjct: 72  VEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA 103

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 69.6 bits (171), Expect = 1e-14
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD---SKHFAYIEYSKPEEATAAL-ALNNMD 126
           + NL   +  + L   FS  G ++ C  + D   SK + ++ +   E A  A+  +N M 
Sbjct: 10  IKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGML 69

Query: 127 VGGRPLNVEMAKSFPQKPSHLNSSLA 152
           +  R + V   KS  ++ + L +   
Sbjct: 70  LNDRKVFVGRFKSRKEREAELGARAK 95

>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 = 68.6 bits (168), Expect = 1e-14
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 11/78 (14%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGT-----------VVECTITDSKHFAYIEYSKPEEA 116
           + L V N+   +T E +   F+               V+   I   K+FA++E+   +E 
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 117 TAALALNNMDVGGRPLNV 134
           T A+A + +   G+ L +
Sbjct: 67  TQAMAFDGIIFQGQSLKI 84

>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 = 73.9 bits (182), Expect = 1e-14
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 11/96 (11%)

Query: 57  PDKAGKADALKKTLQVSNLSPLLTVEQ-LRQLFSFCGTVVECTIT-------DSKHFAYI 108
             +   A    + + + NLS  L  E  LR+ F   G++ +  I         +   A++
Sbjct: 200 SKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFM 259

Query: 109 EYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKP 144
            +   + A  AL +N   +G R ++V +A     KP
Sbjct: 260 VFENKDSAERALQMNRSLLGNREISVSLADK---KP 292

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 68.5 bits (168), Expect = 9e-13
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAALALNN 124
           T+ V NL       ++ + F  CG ++   + D    +  FA IE+++ + A AA+   +
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 125 MDVGGRPLNVEMAKS 139
             VG   + V     
Sbjct: 103 KVVGQNEIIVSHLTE 117

>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 = 66.2 bits (162), Expect = 5e-12
 Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 9/100 (9%)

Query: 51  KDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKH 104
           K +  +          + TL ++N  P  T   +R L      V             S+ 
Sbjct: 103 KVVGQNEIIVSHLT--ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 160

Query: 105 FAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK 143
           FAYI+ +  E+A   +  LN + + G  L  +++    + 
Sbjct: 161 FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS 200

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 69.4 bits (170), Expect = 2e-14
 Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 7/107 (6%)

Query: 38  QAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC 97
            A+      ++     SG    +G +   K+ L V  L+  +  + L   F   G + + 
Sbjct: 34  VAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 98  T-ITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA 137
               D      + FA++E+   E+A AA+  +N  ++ GR + V +A
Sbjct: 94  QIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 67.6 bits (166), Expect = 3e-14
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 7/85 (8%)

Query: 61  GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPE 114
           G     K+ L V  L+  +  + L   F   G + +     D      + FA++E+   E
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 115 EATAAL-ALNNMDVGGRPLNVEMAK 138
           +A AA+  +N  ++ GR + V +AK
Sbjct: 61  DAAAAIDNMNESELFGRTIRVNLAK 85

>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 = 68.1 bits (167), Expect = 3e-14
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYIEYSKPEEATAAL-AL 122
            L VSNL   ++   +++LF+  GT+ +  +  D    S   A + + +  +A  A+   
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90

Query: 123 NNMDVGGRPLNVEMAKS 139
           N + + GRP+N+++  S
Sbjct: 91  NGVPLDGRPMNIQLVTS 107

>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 = 67.3 bits (165), Expect = 3e-14
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPE 114
           GS   +   D    TL V  L   +T   LR  F   G +   T+   +  A+I+++  +
Sbjct: 1   GSSG-SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQ 59

Query: 115 EATAAL--ALNNMDVGGRPLNVEMAK 138
            A  A   + N + V GR LNV+  +
Sbjct: 60  AAEVAAEKSFNKLIVNGRRLNVKWGR 85

>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 = 68.1 bits (167), Expect = 4e-14
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           + +L      + L Q+F   G VV      D     SK F ++ Y  P  A AA+ ++N 
Sbjct: 30  IYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG 89

Query: 125 MDVGGRPLNVEMAKSFPQKPSHLNS 149
             +G + L V++ +S     S  +S
Sbjct: 90  FQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 68.2 bits (167), Expect = 5e-14
 Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 6/104 (5%)

Query: 51  KDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHF 105
            DL  S    G+       L VSNL   ++   +++LF+  GT+ +  +  D    S   
Sbjct: 19  HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 78

Query: 106 AYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSHLN 148
           A + + +  +A  A+     + + GRP+++++  S      H +
Sbjct: 79  ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 28/98 (28%), Positives = 44/98 (44%), Gaps = 5/98 (5%)

Query: 55  GSPDKAG--KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSK 112
           GS   +G  +A     TL V      +T   LR  FS  G +++ ++   ++ A++ Y K
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58

Query: 113 PEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSHLNS 149
            E A  A+  LN   V    L V +A+  P   S  +S
Sbjct: 59  MESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPSS 96

>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 = 66.9 bits (164), Expect = 6e-14
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 10/80 (12%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD--------SKHFAYIEYSKPEEATAA 119
            L + NL+   T E L+ +FS  G +  CTI           S  F ++EY KPE+A  A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 120 L-ALNNMDVGGRPLNVEMAK 138
           L  L    V G  L V +++
Sbjct: 67  LKQLQGHTVDGHKLEVRISE 86

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 67.0 bits (164), Expect = 1e-13
 Identities = 27/127 (21%), Positives = 45/127 (35%), Gaps = 16/127 (12%)

Query: 19  APSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPL 78
           A       +A A+  +       +   A  + K + G              L + +L   
Sbjct: 1   AAGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGC---------NLFIYHLPQE 51

Query: 79  LTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRP 131
            T   L   F   G V+      D     SK F ++ +  P+ A  A+ A+N   VG + 
Sbjct: 52  FTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKR 111

Query: 132 LNVEMAK 138
           L V++ K
Sbjct: 112 LKVQLKK 118

>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 = 66.1 bits (162), Expect = 1e-13
 Identities = 31/99 (31%), Positives = 47/99 (47%), Gaps = 10/99 (10%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAY 107
           SGS     +AD    T++V+NLS       L++LF   G++    +  D     SK FA+
Sbjct: 3   SGSSGPNRRADD-NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 108 IEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
           I + + E+A  A+  ++        LNVE AK  P   S
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAK--PSTNS 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 15/96 (15%)

Query: 57  PDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT---------ITD-----S 102
                 + +   T+ V  L   +T+E +   F   G +              TD      
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 103 KHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA 137
           K  A + +  P  A AA+   +  +  G P+ V  A
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 66.0 bits (161), Expect = 2e-13
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           K  +   NL       ++++ FS  G++    + +    A +E+ +P EA  A   L   
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69

Query: 126 DVGGRPLNVEMA--KSFPQKPS 145
                PL +E A    F   P 
Sbjct: 70  KFHHVPLYLEWAPIGVFGAAPQ 91

>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 = 65.3 bits (160), Expect = 2e-13
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD------SKHFAYIEYSKPEEATAAL- 120
            + +  L+  +T + + ++FS  G +       +      SK +AY+E+  P+EA  AL 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKP 144
            ++   + G+ +           P
Sbjct: 66  HMDGGQIDGQEITATAVL--APWP 87

>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 = 65.7 bits (161), Expect = 2e-13
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 7/96 (7%)

Query: 57  PDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEY 110
              +      K+ L V  L+  +  + L   F   G + +     D      + FA++E+
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 111 SKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
              E+A AA+  +N  ++ GR + V +AK    K S
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97

>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 = 64.8 bits (159), Expect = 3e-13
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           V +L+  +  E LR  F    + +    + D     S+ + ++ ++  ++A  A+ ++  
Sbjct: 6   VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 65

Query: 125 MDVGGRPLNVEMAKSFPQ 142
            D+ GRPL +  A     
Sbjct: 66  QDLNGRPLRINWAAKLEH 83

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 67.2 bits (165), Expect = 3e-13
 Identities = 29/101 (28%), Positives = 50/101 (49%), Gaps = 14/101 (13%)

Query: 51  KDLSGSPDKAGKADALKKTLQ-----VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD--- 101
             +     K   A    ++++     V+NL   +T +QL  +F   G++V+  I  D   
Sbjct: 68  ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLT 127

Query: 102 --SKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMA 137
              +  A++ Y+K EEA  A+ ALNN+   G  +PL+V +A
Sbjct: 128 GRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 64.1 bits (157), Expect = 3e-12
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL 120
              L V+ L   +T  +L  LF   G +  C  + D     S  +A+++++   ++  A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 121 -ALNNMDVGGRPLNVEMAKSFPQKPSHLN 148
             LN + V  + L V  A+   +     N
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGESIKDTN 91

>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 = 67.2 bits (165), Expect = 3e-13
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD----SKHFAYIEYSKPEEATAAL-A 121
           + L V NL   +T + L+Q F   G +     + D    + ++A++EY +  +A  AL  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
           LN   +    + +  A    Q  S
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSS 84

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 61.4 bits (150), Expect = 3e-11
 Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           V +L+  +  E LR  F    + +   +  D     S+ + ++ ++  ++A  A+ ++  
Sbjct: 92  VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 151

Query: 125 MDVGGRPLNVEMA 137
            D+ GRPL +  A
Sbjct: 152 QDLNGRPLRINWA 164

>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 = 65.0 bits (159), Expect = 3e-13
 Identities = 28/98 (28%), Positives = 43/98 (43%), Gaps = 8/98 (8%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYI 108
           GS   +G A    K L V  LS     + L Q+FS  G + E   + D     S+ F ++
Sbjct: 1   GSSGSSGMASDEGK-LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 59

Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
            +   ++A  A+ A+N   V GR + V+ A       S
Sbjct: 60  TFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>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 = 64.9 bits (159), Expect = 4e-13
 Identities = 25/98 (25%), Positives = 47/98 (47%), Gaps = 7/98 (7%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYI 108
           GS   +G       TL+V NL+   + + LR++F   G V +  I  +      + FA++
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
            +    +A  A  A++  ++ GR L V++A+   +  S
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLS 98

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 5/97 (5%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD---SKHFAYIE 109
           S       ++ +  K L VSN+        LRQ+F   G +++   I +   SK F ++ 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 110 YSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
           +    +A  A   L+   V GR + V  A +     S
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 64.4 bits (157), Expect = 5e-13
 Identities = 28/90 (31%), Positives = 36/90 (40%), Gaps = 5/90 (5%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI--TDS-KHFAYIEY 110
           SGS     K   ++K LQ+ N+ P L  E L  L    G V  C    TDS      + Y
Sbjct: 3   SGSSGSVPKRQRIRK-LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTY 61

Query: 111 SKPEEATAAL-ALNNMDVGGRPLNVEMAKS 139
           S  ++A  AL  LN   +    L V     
Sbjct: 62  SSKDQARQALDKLNGFQLENFTLKVAYIPD 91

>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 = 64.1 bits (157), Expect = 5e-13
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL- 120
             L V  LS   T   LR++FS  G + + +I  D     S+ FA++ +   ++A  A  
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 121 ALNNMDVGGRPLNVEMAKS 139
             N M++ GR + V    S
Sbjct: 76  RANGMELDGRRIRVSGPSS 94

>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 = 63.8 bits (156), Expect = 7e-13
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
           V N+S   T ++LR LF   G V+EC +   K +A++   K  +A AA+  LN  +V G+
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGK 71

Query: 131 PLNVEMAKSFPQKPS 145
            +NVE++    +K  
Sbjct: 72  RINVELSTKGQKKSG 86

>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 = 64.6 bits (158), Expect = 7e-13
 Identities = 17/104 (16%), Positives = 33/104 (31%), Gaps = 8/104 (7%)

Query: 41  AAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI- 99
            +   +   A  +     K  + D     L +SNL   +  ++L  +    G V+   I 
Sbjct: 1   GSSGSSGLKASGVQAQMAKQQEQDPTN--LYISNLPLSMDEQELENMLKPFGQVISTRIL 58

Query: 100 TD----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
            D    S+   +      E+  A +   N   +   P      +
Sbjct: 59  RDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>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 = 63.8 bits (156), Expect = 7e-13
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMD 126
             L V N+SP  T ++LR  F   G V+EC I   K +A++   + E+A  A+  L+N +
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTE 68

Query: 127 VGGRPLNVEMAKSFPQKPS 145
             G+ ++V+++ S  +  S
Sbjct: 69  FQGKRMHVQLSTSRLRTAS 87

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 64.4 bits (157), Expect = 7e-13
 Identities = 27/108 (25%), Positives = 38/108 (35%), Gaps = 17/108 (15%)

Query: 55  GSPDKAGKADALKK--TLQVSNLSPLLTVEQLRQLFSFCGTVVECT---------ITD-- 101
           GS   +G  D       + V  L+  +T++ L   F  CG V               D  
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 102 ---SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
               K  A + Y  P  A AA+   +  D  G  L V +A+  P   S
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 63.8 bits (156), Expect = 8e-13
 Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL- 120
             L V NLS   + E L +LFS  G + E     D      K FA++ +  PE A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPSHLNSS 150
            ++     GR L+V  +    +      SS
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 68.4 bits (166), Expect = 8e-13
 Identities = 20/146 (13%), Positives = 56/146 (38%), Gaps = 9/146 (6%)

Query: 68  KTLQVSNLSPLLTVEQLRQ----LFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL 120
            T+ ++NL+  +  ++L++    +FS  G +++  ++     +  A++ + +   AT AL
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69

Query: 121 -ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQ 179
            ++       +P+ ++ AK+     + +  +          ++    Q+    +  +   
Sbjct: 70  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERD-RKREKRKPKSQETPATKKAVQGG 128

Query: 180 TLTAQQAANRAASMKSATELAAARAA 205
             T    A +           A R  
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIM 154

>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 = 56.0 bits (134), Expect = 1e-08
 Identities = 19/125 (15%), Positives = 32/125 (25%), Gaps = 3/125 (2%)

Query: 17  PMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLS 76
                              A           Q        P +    +     L ++NL 
Sbjct: 157 MPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLP 216

Query: 77  PLLTVEQLRQLFSFCGTVVEC-TITDSKHFAYIEYSKPEEATAAL-ALNNMDV-GGRPLN 133
                  L  LF+      E   +      A++E+    +A AA  AL    +     + 
Sbjct: 217 EETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMK 276

Query: 134 VEMAK 138
           +  AK
Sbjct: 277 ISFAK 281

>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 = 63.4 bits (155), Expect = 8e-13
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
           + NL    T +++R LF   G V+EC I   K++ ++       A  A+  L++  + G 
Sbjct: 13  IGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70

Query: 131 PLNVEMAKSFPQKPS 145
            +NVE +K+  +  S
Sbjct: 71  NINVEASKNKSKASS 85

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 63.9 bits (156), Expect = 9e-13
 Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 10/101 (9%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYI 108
           GS   +G  D     L +  +   L  + L+ LF   G + E T+  D      K  A++
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 109 EYSKPEEATAAL-ALNN---MDVGGRPLNVEMAKSFPQKPS 145
            Y + E A  A  AL+    +    RP+ V+ A S  +  S
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101

>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 = 63.3 bits (155), Expect = 9e-13
 Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL- 120
             L V +L   +T + LR +F   G +     + D     SK + +I +S  E A  AL 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPS 145
            LN  ++ GRP+ V          S
Sbjct: 66  QLNGFELAGRPMRVGHVTERLDGGS 90

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 66.6 bits (163), Expect = 1e-12
 Identities = 29/125 (23%), Positives = 52/125 (41%), Gaps = 10/125 (8%)

Query: 38  QAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC 97
              A+    QQ  +    S  +   A A+   + V ++   L  + +RQ F+  G +   
Sbjct: 2   SHMASMTGGQQMGRG---SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSI 58

Query: 98  TI-TD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSHLNSS 150
            +  D      K FA++EY  PE A  AL  +N++ +GGR + V    +  Q    ++  
Sbjct: 59  DMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL 118

Query: 151 LAGSS 155
              + 
Sbjct: 119 AEEAR 123

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.4 bits (160), Expect = 3e-12
 Identities = 22/109 (20%), Positives = 46/109 (42%), Gaps = 7/109 (6%)

Query: 44  VQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD- 101
           V    +        D+  +       + V+++   L+ + ++ +F   G +   T+  D 
Sbjct: 102 VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP 161

Query: 102 ----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
                K + +IEY K + +  A+ ++N  D+GG+ L V  A + P    
Sbjct: 162 TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210

>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 = 63.1 bits (154), Expect = 1e-12
 Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 2/88 (2%)

Query: 59  KAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-SKHFAYIEYSKPEEAT 117
              K     +TL   NLS  +T ++L+++F     +   +    SK  AYIE+    +A 
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 118 AAL-ALNNMDVGGRPLNVEMAKSFPQKP 144
             L      ++ GR +++          
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 62.5 bits (153), Expect = 2e-12
 Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           +  L P  T + L +L    G +V    I D      K + ++++  P  A  A+ AL  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 125 MDVGGRPLNVEMAKS 139
             V  +        S
Sbjct: 70  SGVQAQMAKQSGPSS 84

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 8/86 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT--ITD-----SKHFAYIEYSKPEEATAAL-ALN 123
           + NL P +  + L   FS  G +++    + D     SK +A+I ++  + + AA+ A+N
Sbjct: 10  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69

Query: 124 NMDVGGRPLNVEMAKSFPQKPSHLNS 149
              +  RP+ V  A     K S  +S
Sbjct: 70  GQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 65.7 bits (160), Expect = 2e-12
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 68  KTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTI-TDSKHFAYIEYSKPEEATAAL-ALNN 124
             L VSNL+P  +T + L  LF   G V    I  + K  A ++ +   +A  A+  LN 
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 63

Query: 125 MDVGGRPLNVEMAKSFPQKPSHLNSSLAGSS 155
             + G+P+ + ++K    +         G +
Sbjct: 64  HKLHGKPIRITLSKHQNVQLPREGQEDQGLT 94

>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 = 64.9 bits (158), Expect = 3e-12
 Identities = 37/118 (31%), Positives = 50/118 (42%), Gaps = 13/118 (11%)

Query: 35  QALQAHAAQVQAQQSAKDLSGSPDKAGKADALK---------KTLQVSNLSPLLTVEQLR 85
           Q +Q      + Q   KD   SP    K    K          TL +SN+ P ++ E L+
Sbjct: 79  QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLK 138

Query: 86  QLFSFCGTVVECTI--TDSKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEMAKS 139
            LFS  G VV+        +  A I+    EEA  AL  L+N D+G    L V  +KS
Sbjct: 139 VLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL- 120
           + + + ++    T EQ+  L S  G V+    + D     SK +A+IE+   E + +A+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPS 145
            LN   +G R L    + +      
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDISGV 87

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 9/84 (10%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-A 121
           KTL +SNLS   T E L+++F     +    +       SK +A+IE++  E+A  AL +
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
            N  ++ GR + +E+        S
Sbjct: 73  CNKREIEGRAIRLELQGPRGSPNS 96

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL- 120
           +++ V N+    T EQL+ +FS  G VV    + D      K + + EY   E A +A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKP 144
            LN  +  GR L V+ A S   K 
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKE 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 = 61.9 bits (151), Expect = 4e-12
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN-NM 125
             L + NLSP +T + LRQLF      +   +     +A+++Y     A  A+  L+  +
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 126 DVGGRPLNVEMAKSFPQKPS 145
           ++ G+ + V+ + S   + S
Sbjct: 69  ELHGKIMEVDYSVSKKLRSS 88

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 64.2 bits (157), Expect = 4e-12
 Identities = 27/116 (23%), Positives = 50/116 (43%), Gaps = 12/116 (10%)

Query: 33  AAQALQA-HAAQVQAQQSAKDLSGSPDKAGKADALKKT-LQVSNLSPLLTVEQLRQLFSF 90
           A +A  A H  +V        +   P  + K +A++   L +  +S   T   +R +FS 
Sbjct: 60  ALEAQNALHNMKVLPGM-HHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSS 118

Query: 91  CGTVVECTI-TD----SKHFAYIEYSKPEEATAAL-ALNN---MDVGGRPLNVEMA 137
            G + EC I       S+  A++ ++    A  A+ A++    M+    P+ V+ A
Sbjct: 119 FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 52.2 bits (126), Expect = 4e-08
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI--------TDSKHFAYIEYSKPEEATAAL 120
            + V  +    + + LR+LF   G V E  +          SK   ++ +   + A  A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 121 -ALNNMDVGGRPLNVEMAK 138
            AL+NM V     +    K
Sbjct: 65  NALHNMKVLPGMHHPIQMK 83

>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 = 62.3 bits (152), Expect = 4e-12
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL 120
             T+ V  L   ++   L +LF   G VV   +  D      + + ++E+   E+A  A+
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74

Query: 121 -ALNNMDVGGRPLNVEMAKSFPQKPS 145
             ++ + + G+P+ V  A +  +  S
Sbjct: 75  KIMDMIKLYGKPIRVNKASAHNKNLS 100

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 61.8 bits (151), Expect = 4e-12
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD---SKHFAYIEYSKPEEATAAL-ALNNMD 126
           V NL    T + L+  F+ CG V+   I  +   SK    +++  PE A  A   +N M 
Sbjct: 13  VRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMK 72

Query: 127 VGGRPLNVEMAKSFPQKPS 145
           + GR ++V + ++     S
Sbjct: 73  LSGREIDVRIDRNASGPSS 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 62.0 bits (151), Expect = 4e-12
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 1/79 (1%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TDSKHFAYIEYSKPEEATAALALNNMD 126
           +++ VS     +   QL + F   G V    +  D   FA +E        A L+ +   
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHS 68

Query: 127 VGGRPLNVEMAKSFPQKPS 145
           +GG  L V   +    +  
Sbjct: 69  LGGHRLRVRPREQKEFQSP 87

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 62.4 bits (152), Expect = 4e-12
 Identities = 20/103 (19%), Positives = 32/103 (31%), Gaps = 15/103 (14%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECT---------ITD-----SKHFAYIEYSKP 113
            T+ V  L   +T+E +   F   G +              TD      K  A + +  P
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 114 EEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSS 155
             A AA+   +  +  G P+ V  A           +   G  
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLE 110

>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 = 61.9 bits (151), Expect = 5e-12
 Identities = 27/107 (25%), Positives = 42/107 (39%), Gaps = 11/107 (10%)

Query: 39  AHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT 98
            H     +  +A       +   K  A    L V +L   +T + LR +F   G +    
Sbjct: 2   GHHHHHHSHMAAA----MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQ 57

Query: 99  -ITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
            + D     SK + +I +S  E A  AL  LN  ++ GRP+ V    
Sbjct: 58  LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>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 = 61.1 bits (149), Expect = 7e-12
 Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 7/98 (7%)

Query: 55  GSPDKAGKA--DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD---SKHFAYI 108
           GS   +G    D   +TL V NLS  +T   + QLFS  G    C + T+   +  + ++
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60

Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
           E+ +  +A AAL A+N   + G+ + V  A +   + S
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>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 = 61.1 bits (149), Expect = 8e-12
 Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 9/99 (9%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TDSKHFAYI 108
           S     +       + L V  L+   + E + +LF   G + ECT+       SK  A++
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFV 61

Query: 109 EYSKPEEATAAL-ALNN---MDVGGRPLNVEMAKSFPQK 143
           ++S   EA AA+ AL+    M      L V+ A +  + 
Sbjct: 62  KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 60.8 bits (148), Expect = 9e-12
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 13/85 (15%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGT--VVECTI-TD-----SKHFAYIEYSKPEEATAA 119
            T+ + N++P   V+ +    S   +  V    +  D     ++ FA+++ S   +A+  
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 120 L-ALNNMD----VGGRPLNVEMAKS 139
           L  L ++     + G+ + V+ AKS
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKS 94

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 61.1 bits (149), Expect = 9e-12
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 9/83 (10%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-A 121
            L V+ +    T E +   F+  G +    +  D      K +  +EY   +EA AA+  
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 122 LNNMDVGGRPLNVEMAKSFPQKP 144
           LN  D+ G+P++V+    F + P
Sbjct: 85  LNGQDLMGQPISVDWC--FVRGP 105

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 60.7 bits (148), Expect = 1e-11
 Identities = 15/81 (18%), Positives = 42/81 (51%), Gaps = 8/81 (9%)

Query: 67  KKTLQVSNLSPLLTVEQLRQ----LFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAA 119
             T+ ++NL+  +  ++L++    +FS  G +++  ++     +  A++ + +   AT A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67

Query: 120 L-ALNNMDVGGRPLNVEMAKS 139
           L ++       +P+ ++ AK+
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKT 88

>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 = 60.3 bits (147), Expect = 1e-11
 Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 6/84 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAALA 121
           + + V NL    T EQ+++LFS  G V     I D      K F ++E  +   + A   
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
           L+N D  GR + V  A        
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEH 85

>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 = 60.8 bits (148), Expect = 1e-11
 Identities = 22/109 (20%), Positives = 46/109 (42%), Gaps = 11/109 (10%)

Query: 43  QVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD 101
             +  ++  D    P      +     L V+++      +++++ F   G +    +  D
Sbjct: 4   SYERVRNEDDDELEPGPQRSVEG--WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61

Query: 102 -----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKP 144
                SK +A +EY   ++A AA  ALN  ++ G+ + V+    F + P
Sbjct: 62  RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD--WCFVKGP 108

>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 = 62.1 bits (151), Expect = 1e-11
 Identities = 27/115 (23%), Positives = 50/115 (43%), Gaps = 7/115 (6%)

Query: 35  QALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTV 94
           +AL++ +    +Q   +   G  ++  K      TL V NLS   T EQ+ +LFS  G +
Sbjct: 7   KALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 95  VECTI-TD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ 142
            +  +  D     +  F ++EY    +A  A+  +N   +  R +  +    F +
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 121

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.4 bits (147), Expect = 2e-11
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 5/102 (4%)

Query: 42  AQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-IT 100
           +      S+  +        +  +  K L VSN+        LRQ+F   G +++   I 
Sbjct: 4   SHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF 63

Query: 101 D---SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
           +   SK F ++ +    +A  A   L+   V GR + V  A 
Sbjct: 64  NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105

>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 = 63.1 bits (154), Expect = 2e-11
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD---SKHFAYIEYSKPEEATAAL-ALNNMD 126
           + NL   +  + L   FS  G ++ C +  D   SK + ++ +   E A  A+  +N M 
Sbjct: 108 IKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGML 167

Query: 127 VGGRPLNVEMAKSFPQKPSHLNS 149
           +  R + V   KS  ++ + L +
Sbjct: 168 LNDRKVFVGRFKSRKEREAELGA 190

>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 = 58.1 bits (141), Expect = 1e-09
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD-----SKHFAYIEYSKPEEATAAL 120
             +L V +L P +T   L + FS  G ++      D     S  +AY+ + +P +A  AL
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74

Query: 121 -ALNNMDVGGRPLNVEMAKSFPQK 143
             +N   + G+P+ +  ++  P  
Sbjct: 75  DTMNFDVIKGKPVRIMWSQRDPSL 98

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.1 bits (146), Expect = 2e-11
 Identities = 9/87 (10%), Positives = 26/87 (29%), Gaps = 5/87 (5%)

Query: 59  KAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKP 113
              K D   +++ +       T++ +++     G V+   +        K   ++ +   
Sbjct: 3   WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSI 62

Query: 114 EEATAALALNNMDVGGRPLNVEMAKSF 140
           E A   +           L +     +
Sbjct: 63  ESAKKFVETPGQKYKETDLLILFKDDY 89

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 10/105 (9%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD------SKHFA 106
           SGS  +  K       + V N+       ++R+LFS  G +    +          + F 
Sbjct: 3   SGSSGQVPKKQT-TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 107 YIEYSKPEEATAAL-ALNNM-DVGGRPLNVEMAKSFPQKPSHLNS 149
           ++++   ++A  A  AL +   + GR L +E A S     S  +S
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 63.6 bits (155), Expect = 3e-11
 Identities = 20/70 (28%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV 127
            L V NL   +T E  ++LF   G   E  I   + F +I       A  A   L+   +
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83

Query: 128 GGRPLNVEMA 137
             RPL +  A
Sbjct: 84  KSRPLRIRFA 93

>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 = 60.5 bits (147), Expect = 2e-10
 Identities = 26/148 (17%), Positives = 48/148 (32%), Gaps = 14/148 (9%)

Query: 51  KDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHF 105
             L   P +   A      L V NLSP+++ E L Q FS  G V +  +  D    +   
Sbjct: 81  TILKSRPLRIRFATHGAA-LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGK 139

Query: 106 AYIEYSKPEEATAAL-ALNN----MDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMM 160
            ++E++    A  AL    +    +    RP+ VE  +                      
Sbjct: 140 GFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPME--QFDDEDGLPEKLMQKTQQYH 197

Query: 161 QQAVAMQQMQFQQALLMQQTLTAQQAAN 188
           ++     +         +   +  +A +
Sbjct: 198 KEREQPPRFAQPGTFEFEYA-SRWKALD 224

>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 = 60.0 bits (146), Expect = 3e-11
 Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL- 120
           K L + NLSP +T   L  LF+         I         +  A+I +   E A  AL 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPS 145
            +N   + G+ L +E  K+  Q+ S
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 61.0 bits (149), Expect = 4e-11
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-A 121
            L V+ L   +T E+ R LF   G +  C  + D     S  + ++ Y  P++A  A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPSHLN 148
           LN + +  + + V  A+         N
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDAN 90

>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 = 61.0 bits (149), Expect = 4e-11
 Identities = 28/113 (24%), Positives = 44/113 (38%), Gaps = 14/113 (12%)

Query: 39  AHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQ-----VSNLSPLLTVEQLRQLFSFCGT 93
             A +     +   L     K   A     +++     VS L   +T ++L QLFS  G 
Sbjct: 55  KDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGR 114

Query: 94  VVECTI-TD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMA 137
           ++   I  D     S+   +I + K  EA  A+  LN     G   P+ V+ A
Sbjct: 115 IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 = 62.0 bits (150), Expect = 4e-11
 Identities = 21/110 (19%), Positives = 39/110 (35%), Gaps = 3/110 (2%)

Query: 68  KTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNN 124
             L V  L    +  +++  +F   G V +          A +E +       A+  LNN
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64

Query: 125 MDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQA 174
             + G+ +NV ++K     P        GS       ++   +    +QA
Sbjct: 65  NFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

>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 = 60.5 bits (146), Expect = 1e-10
 Identities = 10/74 (13%), Positives = 22/74 (29%), Gaps = 7/74 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKHFAYIEYSKPEEATAALA- 121
            L   N    +T E   ++    G     ++      ++      +E+    +A   L  
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184

Query: 122 LNNMDVGGRPLNVE 135
           LN+  +        
Sbjct: 185 LNHYQMKNPNGPYP 198

>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 = 59.2 bits (144), Expect = 4e-11
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALA 121
            T  + NL   +T E +++ F            +       K F Y E+   +   +AL+
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
           LN   +G + + V++A     K S
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDS 99

>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 = 58.9 bits (143), Expect = 6e-11
 Identities = 22/105 (20%), Positives = 37/105 (35%), Gaps = 13/105 (12%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAY 107
           S             KT+ + NLS     E L ++    G +    +        SK  A+
Sbjct: 2   SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 108 IEYSKPEEATAALA-------LNNMDVGGRPLNVEMAKSFPQKPS 145
            ++   E A   LA          + + GR L V++A +  +  S
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 58.8 bits (143), Expect = 7e-11
 Identities = 18/105 (17%), Positives = 39/105 (37%), Gaps = 5/105 (4%)

Query: 42  AQVQAQQSAKDLS--GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI 99
           +      S+  +          + +     L V      +   +L ++F   G + E  I
Sbjct: 4   SHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

Query: 100 TDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK 143
                FA++E+ + E A  A+  ++      +PL V  +K   ++
Sbjct: 64  --LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>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 = 61.6 bits (149), Expect = 8e-11
 Identities = 28/76 (36%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI--TDSKHFAYIEYSKPEEATAAL-ALNN 124
            TL +SN+ P ++ E L+ LFS  G VV+        +  A I+    EEA  AL  L+N
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 211

Query: 125 MDVG-GRPLNVEMAKS 139
            D+G    L V  +KS
Sbjct: 212 HDLGENHHLRVSFSKS 227

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 58.9 bits (142), Expect = 7e-10
 Identities = 27/110 (24%), Positives = 49/110 (44%), Gaps = 6/110 (5%)

Query: 40  HAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECT 98
           H++ +  + S       P  AG  ++    L VSNL+P  +T + L  LF   G V    
Sbjct: 10  HSSGLVPRGSHMGRIAIPGLAGAGNS---VLLVSNLNPERVTPQSLFILFGVYGDVQRVK 66

Query: 99  I-TDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSH 146
           I  + K  A ++ +   +A  A+  LN   + G+P+ + ++K    +   
Sbjct: 67  ILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR 116

>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 = 57.6 bits (140), Expect = 9e-11
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           V +LSP +T   +   F+  G + +   + D     SK + ++ +    +A  A+  +  
Sbjct: 11  VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70

Query: 125 MDVGGRPLNVEMAKSFP 141
             +GGR +    A   P
Sbjct: 71  QWLGGRQIRTNWATRKP 87

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.9 bits (140), Expect = 1e-10
 Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 2/88 (2%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTV-VECTITDSKHFAYIEYSK 112
           SG     G+   L   + V NL     V  L++     G+V +  T    +  A++ Y  
Sbjct: 6   SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPD 65

Query: 113 PEEATAAL-ALNNMDVGGRPLNVEMAKS 139
              A  A+  L  + +G   L V +A+ 
Sbjct: 66  SAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>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 = 57.4 bits (139), Expect = 1e-10
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
              + V NL      +++  L      +  C +  +K  A++     E+A  A+   +  
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 126 DVGGRPLNVEMAKS 139
              G+ L V++  +
Sbjct: 64  SFRGKDLIVQLQPT 77

>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 = 58.1 bits (141), Expect = 1e-10
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD----SKHFAYIEYSKPEEATAAL-ALNNM 125
           +  L+     + L+ +F   G + E   I D    S+ FA+I +  P +A  A   +N  
Sbjct: 12  IGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGK 71

Query: 126 DVGGRPLNVEMAKSFPQKPSHLNSSLAGSS 155
            + G+ + VE AK    +        A S 
Sbjct: 72  SLHGKAIKVEQAKKPSFQSGGRRRPPASSR 101

>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 = 58.1 bits (141), Expect = 1e-10
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 7/93 (7%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNN 124
           V +LSP +T E ++  F+  G + +   + D     SK + ++ +    +A  A+  +  
Sbjct: 20  VGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 79

Query: 125 MDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
             +GGR +    A   P  P     S    S P
Sbjct: 80  QWLGGRQIRTNWATRKPPAPKSTYESNTKQSGP 112

>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 = 57.7 bits (140), Expect = 2e-10
 Identities = 23/96 (23%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI---TDSKHFAYIEY 110
           SG     G A      + V NL P +  + +  +F   G + +  +        FA++E+
Sbjct: 9   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 68

Query: 111 SKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
             P +A  A+   +  D  G  L VE  +S     S
Sbjct: 69  EDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 57.5 bits (139), Expect = 2e-10
 Identities = 11/75 (14%), Positives = 24/75 (32%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA---LNN 124
             + V  L   +    L +     GT+    +   K  A +E+   + A   +       
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 125 MDVGGRPLNVEMAKS 139
           + + G+      + S
Sbjct: 76  VYIAGQQAFFNYSTS 90

>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 = 56.4 bits (137), Expect = 3e-10
 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 9/84 (10%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGT--VVECT-ITD-----SKHFAYIEYSKPEEATAAL-AL 122
           + NL+   T E L +     G   ++E     +     SK FA +       +   +  L
Sbjct: 6   IGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLL 65

Query: 123 NNMDVGGRPLNVEMAKSFPQKPSH 146
              ++ G+   V  +        H
Sbjct: 66  PKRELHGQNPVVTPSNKLEHHHHH 89

>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 = 57.4 bits (139), Expect = 3e-10
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI---TDSKHFAYIEYSKPEEATAAL-ALN 123
           + L + NL   +T E++  +F   G + +  +    +++  AY+ Y    +A  A+  L+
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 124 NMDVGGRPLNVEMAKS 139
             +V  R L V    +
Sbjct: 69  GFNVSNRYLVVLYYNA 84

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TDSKHFAYIEYSKPEEATAAL-ALNNMDVGG 129
           V NL       +L + FS+ G +    I  +   FA++E+  P +A  A+  L+   + G
Sbjct: 5   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 64

Query: 130 RPLNVEMAKSFPQKPS 145
             + VE++   P++  
Sbjct: 65  SRVRVELSTGMPRRSR 80

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 58.7 bits (142), Expect = 3e-10
 Identities = 23/109 (21%), Positives = 47/109 (43%), Gaps = 6/109 (5%)

Query: 47  QQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD---- 101
            +   DL  S    G+       L VSNL   ++   +++LF+  GT+ +  +  D    
Sbjct: 68  DKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 127

Query: 102 SKHFAYIEYSKPEEATAALA-LNNMDVGGRPLNVEMAKSFPQKPSHLNS 149
           S   A + + +  +A  A+     + + GRP+++++  S      H + 
Sbjct: 128 SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 176

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 57.0 bits (138), Expect = 4e-10
 Identities = 22/96 (22%), Positives = 37/96 (38%), Gaps = 7/96 (7%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-A 121
            L V+ +    T E +   F+  G +    +  D      K +  +EY   +EA AA+  
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
           LN  D+ G+P++V+                  S  P
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSP 119

>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 = 56.1 bits (136), Expect = 4e-10
 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALA 121
            T  + NL   +T E +++ F            +       K F Y E+   +   +AL+
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 122 LNNMDVGGRPLNVEMAKS 139
           LN   +G R + V++A  
Sbjct: 80  LNEESLGNRRIRVDVADQ 97

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 56.4 bits (136), Expect = 4e-10
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA---LNN 124
           + + +  L   +T  ++  L    G V    +   K+ A+IE +  E A   +       
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76

Query: 125 MDVGGRPLNVEMAKS 139
             + G+P+ ++ +  
Sbjct: 77  PVLRGQPIYIQFSNH 91

>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 = 55.7 bits (135), Expect = 6e-10
 Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 8/84 (9%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-A 121
           KTL V  LS   T E L++ F          +TD     SK F +++++  E+A AA  A
Sbjct: 16  KTLFVKGLSEDTTEETLKESFDGSVRAR--IVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
           + + ++ G  + ++ AK   +  S
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGEGGS 97

>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 = 57.2 bits (138), Expect = 7e-10
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 7/85 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-A 121
           +L+V NL+   + + LR++F   G V +  I  D     S+ FA++ +    +A  A+ A
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPSH 146
           ++   + GR L V+MA+      SH
Sbjct: 132 MDGAVLDGRELRVQMARYGRPPDSH 156

>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 = 56.3 bits (136), Expect = 8e-10
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 9/84 (10%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL- 120
             L V  LS   T   LR++FS  G + + +I  D     S+ FA++ +   ++A  A  
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKP 144
             N M++ GR + V+ +    ++P
Sbjct: 107 RANGMELDGRRIRVDFSI--TKRP 128

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 55.1 bits (133), Expect = 9e-10
 Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL---ALNN 124
             + +  L   +    L +     G +    +   K  A +E+     A  A+   A N 
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQ 81

Query: 125 MDVGGRPLNVEMAKS 139
           + + G P  V  + S
Sbjct: 82  IYIAGHPAFVNYSTS 96

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 55.9 bits (135), Expect = 1e-09
 Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 7/115 (6%)

Query: 39  AHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT 98
           +H A +   Q     S S  +         +L+V NL+   + + LR++F   G V +  
Sbjct: 19  SHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY 78

Query: 99  I-TD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPSH 146
           I  D     S+ FA++ +    +A  A+ A++   + GR L V+MA+      SH
Sbjct: 79  IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 55.7 bits (134), Expect = 1e-09
 Identities = 22/108 (20%), Positives = 47/108 (43%), Gaps = 10/108 (9%)

Query: 42  AQVQAQQSAKDLSGSPDKAGKADALK--KTLQVSNLSPLLTVEQLRQ----LFSFCGTVV 95
            +  A +  +    SPD        +  + + ++N++P +  E+L+     L S  G ++
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 96  ECTI---TDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS 139
           +  +    D+   AYI ++  E A A + A       G PL +  +++
Sbjct: 62  DIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSET 109

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.8 bits (132), Expect = 1e-09
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL---ALNN 124
           + L +  L   +T  ++  L    G V    +   K+ A++E +  E A   +   +   
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75

Query: 125 MDVGGRPLNVEMAKS 139
             +  +P+ ++ +  
Sbjct: 76  PHLRNQPIYIQYSNH 90

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 15/94 (15%), Positives = 37/94 (39%), Gaps = 6/94 (6%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD----SKHFAYIEYSKPEEA 116
           +   +  T+ V  +   +   ++R  F+  G+V E  I TD    SK + ++ +    + 
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63

Query: 117 TAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSS 150
              +  + ++  G+ L +  A       ++    
Sbjct: 64  QKIVE-SQINFHGKKLKLGPAIRKQNLSTYHVQP 96

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALA 121
            T  V NL        +  +F     +    +  D      K F Y+E+ + +    AL 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
            +   +G R L V++A+   Q  S
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKS 98

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 54.7 bits (132), Expect = 2e-09
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 72  VSNLSPLLTVEQ-LRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGG 129
           + NL+  L  +  +  +FS  G V  C++   K +A+++YS    A AA+   N   + G
Sbjct: 32  IGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAG 89

Query: 130 RPLNVEMAKS 139
           + L++ MA  
Sbjct: 90  QTLDINMAGE 99

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 72  VSNLSPL-LTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGG 129
           + NL    ++ E L ++FS  G +++  I     F +I++  P+    A+   +     G
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIECESQEMNFG 72

Query: 130 RPLNVEMAKS 139
           + L +E++ S
Sbjct: 73  KKLILEVSSS 82

>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 = 56.0 bits (136), Expect = 2e-09
 Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           V  + P +  ++  + FS  GT+++  +  D     S+ F ++ Y   +          +
Sbjct: 92  VGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFI 151

Query: 126 DVGGRPLNVEMAKS 139
           D   R + ++ A+ 
Sbjct: 152 DFKDRKIEIKRAEP 165

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 53.7 bits (130), Expect = 1e-08
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           +  L+   T + LR+ F   GTV +  I  D     S+ F ++ + KP      +   ++
Sbjct: 8   IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHI 67

Query: 126 DVGGRPLNVEMAKS 139
            + G+ ++ + A  
Sbjct: 68  -LDGKVIDPKRAIP 80

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.5 bits (131), Expect = 3e-09
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL---ALNN 124
           + + +  L   +T  ++  L    G V    +   K+ A+IE +  E A   +       
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91

Query: 125 MDVGGRPLNVEMAKS 139
             + G+P+ ++ +  
Sbjct: 92  PVLRGQPIYIQFSNH 106

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 54.8 bits (132), Expect = 4e-09
 Identities = 18/84 (21%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----------SKHFAYIEYSKPEEA 116
             + V NL+  +  + L+ +F         T               K  A+I     + A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 117 TAAL-ALNNMDVGGRPLNVEMAKS 139
             AL   N   + G+P+ V+ A+S
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARS 129

>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 = 55.2 bits (133), Expect = 4e-09
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL- 120
             L V+++      +++++ F   G +    +  D     SK +A +EY   ++A AA  
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPS 145
           ALN  ++ G+ + V+       K  
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGPKRV 157

>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 = 56.6 bits (136), Expect = 4e-09
 Identities = 21/149 (14%), Positives = 40/149 (26%), Gaps = 9/149 (6%)

Query: 22  AAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTV 81
                +A    A +                    +P+        +  L + NL+   T 
Sbjct: 23  DVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTD 82

Query: 82  EQLRQLFSFCGT--VVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL 132
           E L +     G   ++E    +      SK FA +       +   +  L   ++ G+  
Sbjct: 83  EDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP 142

Query: 133 NVEMAKSFPQKPSHLNSSLAGSSLPMMMQ 161
            V            + S     S  M  +
Sbjct: 143 VVTPVNKQFLSQFEMQSRKTTQSGQMSGE 171

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 55.2 bits (132), Expect = 7e-09
 Identities = 8/81 (9%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TDSKHFAYIEYSKPEEATAALAL 122
           +++ +       T++ +++     G V+   +        K   ++ +   E A   +  
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169

Query: 123 NNMDVGGRPLNVEMAKSFPQK 143
                    L +     +  K
Sbjct: 170 PGQKYKETDLLILFKDDYFAK 190

>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 = 52.3 bits (126), Expect = 8e-09
 Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 9/94 (9%)

Query: 55  GSPDKAGKADAL--KKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD-----SKHFA 106
           GS   +G +        ++V N+   ++++++   F     +     +           A
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 107 YIEYSKPEEATAALA-LNNMDVGGRPLNVEMAKS 139
            + +   +EATAA+  LN+  +G R + + +   
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 27/110 (24%), Positives = 39/110 (35%), Gaps = 7/110 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-ITD-----SKHFAY 107
           S     + K     K + V  L    T   LR+ F   G + E   ITD     S+ + +
Sbjct: 5   SSGMHGSQKDTTFTK-IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
           +  +    A  A    N  + GR  NV +A    +  S       G S P
Sbjct: 64  VTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113

>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 = 54.6 bits (132), Expect = 1e-08
 Identities = 27/103 (26%), Positives = 41/103 (39%), Gaps = 13/103 (12%)

Query: 49  SAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----S 102
           S  +    P++  K       L +  LS   T E LR  F   GT+ +C +  D     S
Sbjct: 2   SKSESPKEPEQLRK-------LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRS 54

Query: 103 KHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           + F ++ Y+  EE  AA+      V GR +  + A S      
Sbjct: 55  RGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 97

>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 = 54.6 bits (132), Expect = 1e-08
 Identities = 19/95 (20%), Positives = 30/95 (31%), Gaps = 6/95 (6%)

Query: 61  GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPE 114
             A    K + V  +        LR  F   G +    I TD      + FA++ +   +
Sbjct: 98  PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157

Query: 115 EATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNS 149
                +      V G    V  A S  +  S  +S
Sbjct: 158 SVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS 192

>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 = 51.5 bits (124), Expect = 2e-08
 Identities = 15/93 (16%), Positives = 35/93 (37%), Gaps = 7/93 (7%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD-----SKHFAY 107
           S     +         ++V N+   ++++++   F     +     +           A 
Sbjct: 2   SSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 108 IEYSKPEEATAALA-LNNMDVGGRPLNVEMAKS 139
           + +   +EATAA+  LN+  +G R + +    S
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 7/67 (10%)

Query: 71  QVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAAL-ALN 123
            + +    +  + L  LFS  G VV      D     +K F ++E     +A   + + +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 124 NMDVGGR 130
              +  +
Sbjct: 76  GKRLDLK 82

>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 = 51.3 bits (123), Expect = 3e-08
 Identities = 18/111 (16%), Positives = 37/111 (33%), Gaps = 8/111 (7%)

Query: 55  GSPDKAGKADA--LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITDSKH-----FA 106
           GS   +G+ D    K    ++N+   +T   + Q             +    +      A
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 107 YIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
            +++   ++A  +  L+   + GR   V +      +    N    G S P
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGP 111

>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 = 50.9 bits (122), Expect = 3e-08
 Identities = 16/100 (16%), Positives = 36/100 (36%), Gaps = 11/100 (11%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI--------TDSKHFAYIEYSKPEEATA 118
              L +  +  +   E++ +  +     V   I          ++ FA++EY     A  
Sbjct: 8   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67

Query: 119 A---LALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSS 155
           A   L    + + G  + V+ A+        +  +++G S
Sbjct: 68  ARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPS 107

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKP 113
           +G + +    + V  +       +LR+ F   G V E  +  D      + F +I +   
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 114 EEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           +    A+ ++  D+ G+ + V+ A+    K S
Sbjct: 63  QSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSS 94

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 72  VSNLSPL-LTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDVGG 129
           + NL    ++ E L ++FS  G +++  I     F +I++  P+    A+   +     G
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIEXESQEMNFG 84

Query: 130 RPLNVEMAKS 139
           + L +E++ S
Sbjct: 85  KKLILEVSSS 94

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 51.8 bits (124), Expect = 5e-08
 Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TDSKHFAYIEYSKPEEATAAL-ALNNMDVGG 129
           V NL       +L + F + G +    +  +   FA++E+  P +A  A+  L+   + G
Sbjct: 78  VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 137

Query: 130 RPLNVEMAK 138
             + VE++ 
Sbjct: 138 CRVRVELSN 146

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 50.3 bits (120), Expect = 2e-07
 Identities = 23/119 (19%), Positives = 39/119 (32%), Gaps = 12/119 (10%)

Query: 38  QAHAAQVQAQQSAKDLSGSPDKAGKADAL---KKTLQVSNLSPLLTVEQLRQLFSFCGT- 93
                 V+ + S K  + +P        L   +  + V + S   T +QL Q+    G  
Sbjct: 23  MEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVY 82

Query: 94  -VVECT-ITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKP 144
            VVE     +     SK +A +  +        L  L    + G  ++V  A       
Sbjct: 83  DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 61  GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEAT-AA 119
           G        L + NL+  +    LR L    G +V      ++  A  +Y+  EEA  A 
Sbjct: 1   GAMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQ 60

Query: 120 LALNNMDVGGRPLNVEMAK 138
           +ALNN  +    +  E   
Sbjct: 61  MALNNCVLANTTIFAESPS 79

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 16/90 (17%), Positives = 28/90 (31%), Gaps = 6/90 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH-----FAYI 108
           SGS  K    +     + V  +        +R  F     V    +             +
Sbjct: 3   SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLV 61

Query: 109 EYSKPEEATAALALNNMDVGGRPLNVEMAK 138
           ++  P++   AL  N M +  R + V  A 
Sbjct: 62  KFLSPQDTFEALKRNRMLMIQRYVEVSPAT 91

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 48.3 bits (115), Expect = 3e-07
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 13/84 (15%)

Query: 67  KKTLQVSNLSPLLTVEQL---RQLFSFCGTVVECTIT---------DSKHFAYIEYSKPE 114
           K  + V  LS  L   ++    + F   G + +  I               AY+ Y + E
Sbjct: 15  KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74

Query: 115 EATAAL-ALNNMDVGGRPLNVEMA 137
           +A  A+  +NN+ V GR L   + 
Sbjct: 75  DALRAIQCVNNVVVDGRTLKASLG 98

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 48.0 bits (114), Expect = 4e-07
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 68  KTLQVSN--LSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNN 124
           ++L V+N  L   ++  QL  +   CG V    +  +K +++  Y   EE+  A   LN 
Sbjct: 26  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 85

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 14/69 (20%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAALALNNMDVGGR 130
           V   +  +T ++LR+ FS  G V++  I    + FA++ ++  + A +     ++ + G 
Sbjct: 10  VGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG-EDLIIKGI 68

Query: 131 PLNVEMAKS 139
            +++  A+ 
Sbjct: 69  SVHISNAEP 77

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TDSKHFAYIEYSKPEEATAALALNNMDVGGR 130
           V   +  +T E+L+Q F   G VV+  I    + FA++ ++  + A +     ++ + G 
Sbjct: 16  VGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG-EDLIIKGI 74

Query: 131 PLNVEMAKSFPQKPS 145
            +++  A+    K +
Sbjct: 75  SVHISNAEPKHNKLN 89

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 46.3 bits (111), Expect = 7e-07
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           +  LS   T E LR+ F   G V EC +  D     S+ F ++ +         LA +  
Sbjct: 5   IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRH 64

Query: 126 DVGGRPLNVEMA 137
           ++  + ++ ++A
Sbjct: 65  ELDSKTIDPKVA 76

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 60  AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH-----FAYIEYSKPE 114
           +G +     T+++      +T + + +  +     V   I  + H     + ++++S  E
Sbjct: 3   SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEE 61

Query: 115 EATAALALNNMDVGGRPLNVEMAKSFPQK 143
           E   AL  N   +GGR + V   KS P  
Sbjct: 62  EVKQALKCNREYMGGRYIEVFREKSGPSS 90

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 5/56 (8%)

Query: 80  TVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
               + ++FS  G +      +    +K + ++EY+ P  A  A+   +   +  +
Sbjct: 20  LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>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 = 46.5 bits (111), Expect = 9e-07
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 8/78 (10%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT--ITD-----SKHFAYIEYSKPEEATAA 119
             +L + +L P +    + + F+  G  V     I +        + ++E++    A   
Sbjct: 9   AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68

Query: 120 L-ALNNMDVGGRPLNVEM 136
           L  +N   + G       
Sbjct: 69  LHKINGKPLPGATPAKRF 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 9/55 (16%), Positives = 23/55 (41%), Gaps = 5/55 (9%)

Query: 81  VEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
              + ++FS  G +      +    +K + ++EY+ P  A  A+   +   +  +
Sbjct: 35  KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 27/98 (27%), Positives = 38/98 (38%), Gaps = 6/98 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAY 107
           SGS             L V  L    T E LR  FS  G VV+C I  D     S+ F +
Sbjct: 3   SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           +++  P      LA     + GR ++ +       +PS
Sbjct: 63  VKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPS 100

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 45.5 bits (109), Expect = 1e-06
 Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           V  LS   TVE ++  F   G V +  +  D      + F ++ +   +       ++  
Sbjct: 4   VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFH 63

Query: 126 DVGGRPLNVEMA 137
           ++  + +  + A
Sbjct: 64  EINNKMVECKKA 75

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.1 bits (109), Expect = 2e-06
 Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQ----LFSFCGTVVECTI---TDSKHFAYIEYSKPEEATAALA 121
            +QVSN+   L+ ++L+Q     F+  G V    +   TD +  A ++    ++A  A+ 
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70

Query: 122 -LNNMDVGGRPLNVEMAKSFPQKPS 145
            L+   +G + + V +A       S
Sbjct: 71  SLHRYKIGSKKILVSLATGASGPSS 95

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 13/90 (14%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAY 107
           S + + AGK       + V  LS   + + L+  F+  G VV+CTI  D     S+ F +
Sbjct: 5   SKNEEDAGK-------MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGF 57

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMA 137
           I +         L      + GR ++ + A
Sbjct: 58  ILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 44.8 bits (107), Expect = 2e-06
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           V  LSP    E++R+ F   G V    +  D      + F +I + + E     +     
Sbjct: 4   VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 63

Query: 126 DVGGRPLNVEMA 137
           +VG     +++A
Sbjct: 64  NVGLSKCEIKVA 75

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 20/106 (18%), Positives = 40/106 (37%), Gaps = 6/106 (5%)

Query: 45  QAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-- 101
            +       SG   +     +    + +  LS   T E LR+ F   G V EC +  D  
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

Query: 102 ---SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKP 144
              S+ F ++ +         LA +  ++  + ++ ++A     +P
Sbjct: 63  TKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQP 108

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 72  VSNLSPLLTVEQLRQLFS-FCGTVVECTI-TD----SKHFAYIEYSKPEEATAALALNN- 124
           V +L+P +    L + F     +     +  D    SK + +++++   E   AL     
Sbjct: 14  VGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQG 73

Query: 125 -MDVGGRPLNVEMAKSFPQKPSHLNSS 150
            + +G +P+ + +A     +   + S 
Sbjct: 74  AVGLGSKPVRLSVAIPKASRVKPVESG 100

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 7/91 (7%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITDSKH-----FAY 107
           SGS   +         +++  L    + E++ Q FS    V    T+           A+
Sbjct: 3   SGSSGNSPDTAN-DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAK 138
           ++++  E A  AL  +   +G R + +  + 
Sbjct: 62  VQFASQEIAEKALKKHKERIGHRYIEIFKSS 92

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.8 bits (108), Expect = 4e-06
 Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 9/108 (8%)

Query: 36  ALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVV 95
           ++Q+    + A  +A D   +             + V NL   +T++ L Q+FS  GTV+
Sbjct: 1   SVQSGNLALAASAAAVDAGMAMAGQSPV----LRIIVENLFYPVTLDVLHQIFSKFGTVL 56

Query: 96  ECTITDSKH--FAYIEYSKPEEATAALAL---NNMDVGGRPLNVEMAK 138
           +       +   A ++Y+ P  A  A       N+      L ++ +K
Sbjct: 57  KIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.5 bits (106), Expect = 5e-06
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAY 107
           SGS             L V  L    T + L++ FS  G V+   +  D     SK F +
Sbjct: 3   SGSSGVKRAVQKTSD-LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           + +++ E     ++  +M + GR  + ++  S   + S
Sbjct: 62  VRFTEYETQVKVMSQRHM-IDGRWCDCKLPNSKQSQDS 98

>3eml_A Human adenosine A2A receptor/T4 lysozyme chimera; caffeine, GPCR, membrane protein, LCP, mesophase, structural genomics, PSI-2; HET: ZMA STE; 2.60A {Homo sapiens} PDB: 3qak_A* Length = 488

 Score = 48.6 bits (115), Expect = 6e-06
 Identities = 22/187 (11%), Positives = 53/187 (28%), Gaps = 8/187 (4%)

Query: 247 YQRTYR-ARSRSKSRSPVSFHRRRRSRSFSPP---YRHRRGHR-SRSPLRSRHYSKYDNE 301
           Y R +  AR +      +      R + +      Y    GH  ++SP  +   S+ D  
Sbjct: 212 YLRIFLAARRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKA 271

Query: 302 RLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARK 361
                +     D + +  +    + V    ++  + P           +  +        
Sbjct: 272 IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGET 331

Query: 362 SSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRS---RSKSMERHDEEKDEARDGKSQHRER 418
                + S +  +  R      +      +     R+K +              +  +E 
Sbjct: 332 GVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYRSTLQKEV 391

Query: 419 KRSRSLS 425
             ++SL+
Sbjct: 392 HAAKSLA 398

>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 = 44.9 bits (106), Expect = 8e-06
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEEATAALAL 122
            +++  L    T E++ Q FS    V                 A+++++  E A  AL  
Sbjct: 44  FVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK 103

Query: 123 NNMDVGGRPLNVEMAK 138
           +   +G R + V  + 
Sbjct: 104 HKERIGHRYIEVFKSS 119

>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 = 47.5 bits (112), Expect = 1e-05
 Identities = 29/220 (13%), Positives = 52/220 (23%)

Query: 218 DEDKETKQKSRSPSTSRARSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPP 277
           +     +  +         S    R     +   R     +        R R        
Sbjct: 207 NIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRS 266

Query: 278 YRHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVS 337
               +  R RS  RS+   +    R S    R   +R R+E        +    ++    
Sbjct: 267 RSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAP 326

Query: 338 PHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKS 397
           P            P   +E    +               R+  R+ D   +++   R   
Sbjct: 327 PDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSE 386

Query: 398 MERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSP 437
             R +                  SR +  E E      +P
Sbjct: 387 RGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAP 426

>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 = 46.8 bits (110), Expect = 2e-05
 Identities = 34/233 (14%), Positives = 64/233 (27%)

Query: 236 RSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHY 295
           R  +        +            SP+    R R R      R R   + R   RSR  
Sbjct: 201 RGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSR 260

Query: 296 SKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQ 355
            +    R   ++ R  +    ++ D        R R+        ++  R   G      
Sbjct: 261 DRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPS 320

Query: 356 ESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQH 415
           E+                  +    +  D   + R   RS+   R D ++D  RD + + 
Sbjct: 321 EAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKR 380

Query: 416 RERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIAD 468
            ER   R         G   +    +  +   +   S         ++  + +
Sbjct: 381 GERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENGYLME 433

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 30/237 (12%), Positives = 58/237 (24%)

Query: 256 RSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRS 315
           R +         RR     +  +  R                + +        R    R 
Sbjct: 188 RPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRE 247

Query: 316 RRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRG 375
           R +      S    RR+         +    +    K R        SR  ++  +  + 
Sbjct: 248 RDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKE 307

Query: 376 NRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGR 435
                  D A+P     +        +   D     + + R+R R R  S   E   R  
Sbjct: 308 ELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRD 367

Query: 436 SPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKM 492
                  + + K   R       +        D+  +    +       S+  +G +
Sbjct: 368 RDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYL 424

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 32/256 (12%), Positives = 56/256 (21%)

Query: 219 EDKETKQKSRSPSTSRARSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPY 278
                 ++ R+    R R                    S       +  R          
Sbjct: 173 RVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRD 232

Query: 279 RHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSP 338
           R R   R R         + +  R  +RD R  +    +E           + + R    
Sbjct: 233 RDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRS 292

Query: 339 HSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSM 398
              +         K          +                    D       + R +  
Sbjct: 293 SRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDR 352

Query: 399 ERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSAL 458
           ER    + E    + + R+R R R   R +    RGR  A      +        + S  
Sbjct: 353 ERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRD 412

Query: 459 DKYKSSEIADDSRDDR 474
              +S         + 
Sbjct: 413 MYMESEGGDGYLAPEN 428

>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 = 43.7 bits (102), Expect = 2e-04
 Identities = 42/338 (12%), Positives = 83/338 (24%), Gaps = 9/338 (2%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALA 121
           KTL V+ ++   T  +LR+ F   G +    +         + +A+IEY    +  +A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLPMMMQQAVAMQQMQFQQALLMQQTL 181
             +   G +     +     +  +            +   +                   
Sbjct: 163 HAD---GKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRY 219

Query: 182 TAQQAANRAASMKSATELAAARAAEISKKLKADGLVDEDKETKQKSRSPSTSRARSRSKS 241
             +   +         +    R     ++ K           +++         R RS+ 
Sbjct: 220 DERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRE 279

Query: 242 RSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNE 301
           RS    +   R  SRS+ R+     R+   R                P          + 
Sbjct: 280 RSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDG 339

Query: 302 RLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARK 361
                +     DR RR S  S       R + R      ++  R         +     +
Sbjct: 340 PDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQ 399

Query: 362 SSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSME 399
            +               S   D             + E
Sbjct: 400 DNGLEGLGNDSRDMYMESEGGDGYLAPENGYLMEAAPE 437

>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 = 43.3 bits (101), Expect = 2e-04
 Identities = 48/249 (19%), Positives = 78/249 (31%)

Query: 278 YRHRRGHRSRSPLRSRHYSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVS 337
            R R     R                       G D + R  +    SP+P R + R   
Sbjct: 179 ERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRE 238

Query: 338 PHSRKSYRSDSGSPKHRQESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKS 397
              R+  R      + R+  S  +  R+ S+  +  R +R   ++ D   K R     + 
Sbjct: 239 RERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRER 298

Query: 398 MERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSA 457
             R  E K+E R G     E   +     +D   G       +  E K + R R R  S 
Sbjct: 299 ARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSH 358

Query: 458 LDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADGK 517
             + +     D  RD    ++   R   +  +   GGG             SR +  + +
Sbjct: 359 RSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESE 418

Query: 518 HHRGSRSPR 526
              G  +P 
Sbjct: 419 GGDGYLAPE 427

>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 = 43.3 bits (101), Expect = 2e-04
 Identities = 31/276 (11%), Positives = 65/276 (23%), Gaps = 1/276 (0%)

Query: 295 YSKYDNERLSTRDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHR 354
           Y   D +++  R      +R R                +R         +     + ++ 
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

Query: 355 QESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQ 414
           +               +       S   D  + + R RSR +       +K+E R  + +
Sbjct: 221 ERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRER 280

Query: 415 HRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDR 474
            +++ R R            R      +           S +           +   D  
Sbjct: 281 SKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGP 340

Query: 475 LRNRHKRRSRSKSVEGKMGGGSRDKKPKHHDRRRSRSISADGKHHRGSRSPRGLDESRTK 534
                K R R +            ++ +  DR R R     G+                +
Sbjct: 341 DGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDRE-HKRGERGSERGRDEARGGGGGQ 399

Query: 535 LGRRSRSKSIERKLYRNRGRSRSADGRRRKSMLSPA 570
                   +  R +Y                ++  A
Sbjct: 400 DNGLEGLGNDSRDMYMESEGGDGYLAPENGYLMEAA 435

>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 = 41.4 bits (96), Expect = 9e-04
 Identities = 28/229 (12%), Positives = 53/229 (23%)

Query: 378 NSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLSREDEHHGRGRSP 437
                   +P+        +     +            R  +R            R R  
Sbjct: 180 RGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRER 239

Query: 438 AGNVDENKSKLRGRSRSVSALDKYKSSEIADDSRDDRLRNRHKRRSRSKSVEGKMGGGSR 497
                  +       R   + D+ + S   D     R R R K + R +           
Sbjct: 240 ERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERA 299

Query: 498 DKKPKHHDRRRSRSISADGKHHRGSRSPRGLDESRTKLGRRSRSKSIERKLYRNRGRSRS 557
            ++ +  +  R            G   P                +   R   R R RS  
Sbjct: 300 RRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHR 359

Query: 558 ADGRRRKSMLSPANLDRSESNRRRHSASQSKDHANSESAETRDYKSMHH 606
           ++  RR+      + DR      R S     +       +    + + +
Sbjct: 360 SERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGN 408

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 45.1 bits (106), Expect = 1e-05
 Identities = 31/153 (20%), Positives = 60/153 (39%), Gaps = 12/153 (7%)

Query: 26  AAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLR 85
           +A  A+ A  ++Q+    + A  +A D   +             + V NL   +T++ L 
Sbjct: 9   SAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPV----LRIIVENLFYPVTLDVLH 64

Query: 86  QLFSFCGTVVECTITDSKH--FAYIEYSKPEEATAAL-ALNNMDV--GGRPLNVEMAKSF 140
           Q+FS  GTV++       +   A ++Y+ P  A  A  +L+  ++      L ++ +K  
Sbjct: 65  QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 124

Query: 141 P---QKPSHLNSSLAGSSLPMMMQQAVAMQQMQ 170
               +  +  +       LP    Q    Q M 
Sbjct: 125 SLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMA 157

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 6/80 (7%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-TD-----SKHFAYIEYSKPEEATAALALNNM 125
           +  LS   T E LR  +   G + +C +  D     S+ F ++ +S   E  AA+A    
Sbjct: 32  IGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPH 91

Query: 126 DVGGRPLNVEMAKSFPQKPS 145
            + GR +  + A +  +  S
Sbjct: 92  SIDGRVVEPKRAVAREESGS 111

>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 = 43.3 bits (102), Expect = 2e-05
 Identities = 11/99 (11%), Positives = 26/99 (26%), Gaps = 6/99 (6%)

Query: 45  QAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITDSK 103
                         ++         + +  L      + +   F     V +   I    
Sbjct: 3   SGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP 62

Query: 104 H-----FAYIEYSKPEEATAALALNNMDVGGRPLNVEMA 137
           +       ++E+    +  AAL  +   +G R + V   
Sbjct: 63  NGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI 101

>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 = 41.3 bits (97), Expect = 8e-05
 Identities = 15/92 (16%), Positives = 29/92 (31%), Gaps = 2/92 (2%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKP 113
           S        +   +  + VS L P  + + L+      G V    +        +E+ + 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-YRDGTGVVEFVRK 60

Query: 114 EEATAALA-LNNMDVGGRPLNVEMAKSFPQKP 144
           E+ T A+  L+N             +     P
Sbjct: 61  EDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP 92

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 41.4 bits (97), Expect = 9e-05
 Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 8/93 (8%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFC---GTVVECTITDSKH-----F 105
             S    G        +++  L    ++E ++   S C     V       ++       
Sbjct: 4   GSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGE 63

Query: 106 AYIEYSKPEEATAALALNNMDVGGRPLNVEMAK 138
           A++E    ++   AL  +   +G R + V  + 
Sbjct: 64  AFVELESEDDVKLALKKDRESMGHRYIEVFKSH 96

>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 = 41.8 bits (98), Expect = 1e-04
 Identities = 13/99 (13%), Positives = 29/99 (29%), Gaps = 4/99 (4%)

Query: 45  QAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD--- 101
                         +          + +  L    T   +   FS    V          
Sbjct: 24  MTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDG 83

Query: 102 -SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS 139
                A +E++  EEA AA++ +  ++  R + + +  +
Sbjct: 84  RVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNST 122

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 5/90 (5%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQ-LRQLFSFCGTVVECTITDSKHFAYIEYSK 112
           SGS  + G+ +  ++ + + +      +   L QL    G +    I +  + A+IE + 
Sbjct: 3   SGSSGQKGRVET-RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMAT 61

Query: 113 PEEATAALALNNMD---VGGRPLNVEMAKS 139
            E+A AA+         V G+P+ V +++ 
Sbjct: 62  TEDAQAAVDYYTTTPALVFGKPVRVHLSQK 91

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH-----FAYIEYSKPEEATAALAL 122
             + +  L    T   +   FS     +   I           A +E++  E+A AA+A 
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 74

Query: 123 NNMDVGGRPLNVEMA 137
           +  ++  R + + + 
Sbjct: 75  DKANMQHRYVELFLN 89

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFC---GTVVECTITDSKH-----FAYIEYSKPEEATAAL 120
            ++   L    T+E +   FS C             ++       A IE    ++   AL
Sbjct: 13  LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72

Query: 121 ALNNMDVGGRPLNVEMAK 138
             + M +G R + V    
Sbjct: 73  EKHRMYMGQRYVEVYEIN 90

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 4/76 (5%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVV---ECTITDSKHFAYIEYSKPEEATAALA-LNNM 125
           + + NL    + + L+ L                D      +E+   E    AL  LNN+
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 126 DVGGRPLNVEMAKSFP 141
           +  G  + VE   + P
Sbjct: 91  EFRGSVITVERDDNPP 106

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 5/107 (4%)

Query: 48  QSAKDLSGSPDKAGKADALK-KTLQVSNL-SPLLTVEQLRQLFSFCGTVVECTITDSKHF 105
            S K   G PD+         + + +SNL     +   + +L    G +    +   K  
Sbjct: 5   SSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ 64

Query: 106 AYIEYSKPEEATAAL---ALNNMDVGGRPLNVEMAKSFPQKPSHLNS 149
           A+IE    E+A A +       +   GR + V++++ + +  S  +S
Sbjct: 65  AFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGPSS 111

>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 = 42.9 bits (100), Expect = 3e-04
 Identities = 68/551 (12%), Positives = 137/551 (24%), Gaps = 164/551 (29%)

Query: 43  QVQAQQSAKDLSGSPDKAGKADALKKTL--QVSNLSPLLTVEQLRQLFSFCGTVV--ECT 98
            + +++    +  S D       L  TL  +   +      E LR  + F  + +  E  
Sbjct: 44  SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR 103

Query: 99  ITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPSHLN---------- 148
                   YIE            L N +      NV   + + +    L           
Sbjct: 104 QPSMMTRMYIEQRDR--------LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155

Query: 149 --------SSLAGSSLPMMMQQAVAMQQMQFQ-------------QALLMQQTLTAQ--- 184
                   + +A               +M F+               L M Q L  Q   
Sbjct: 156 DGVLGSGKTWVALDVC----LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 185 ---QAANRAASMKSATELAAARAAEI--SKKLKADGLV-DE--DKETKQ----KSRSPST 232
                ++ ++++K       A    +  SK  +   LV     + +         +   T
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLT 271

Query: 233 SRARSRSKSRSPVHYQRTYRARSRSKSRSPVSFHRRRRSRSFS-----PPYRHRRGHRSR 287
           +R +  +   S             S     ++                 P    R   + 
Sbjct: 272 TRFKQVTDFLSAATTTH------ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325

Query: 288 SPL--------------RSRHYSKYDNERLSTR-----DTRDGADRSRRESDIS---HHS 325
           +P                  ++   + ++L+T      +  + A+  +    +S     +
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385

Query: 326 PVP------------------------------RRRKSRSVSPHSRKSYRSDSGSPKHRQ 355
            +P                              ++ K  ++S  S   Y       ++  
Sbjct: 386 HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI--YLELKVKLENEY 443

Query: 356 ESSARKSSRAHSKSPKRHRGNRNSPRNDDAKPK-----YRHRSRSKSMERHDEEKDEAR- 409
                     H      +   +    +D   P      Y H         H E     R 
Sbjct: 444 A--------LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495

Query: 410 ---DGKSQHRERKRSRSLSREDEHHGRGRSPAGNVDENKSKLRGRSRSVSALDKYKSSEI 466
              D           R L ++  H     + +G++            ++  L  YK    
Sbjct: 496 VFLD----------FRFLEQKIRHDSTAWNASGSILN----------TLQQLKFYKPYIC 535

Query: 467 ADDSRDDRLRN 477
            +D + +RL N
Sbjct: 536 DNDPKYERLVN 546

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.9 bits (93), Expect = 4e-04
 Identities = 11/94 (11%), Positives = 30/94 (31%), Gaps = 9/94 (9%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC----TITDSKH----- 104
           + +      +   +  +++  L    T E++   F     +                   
Sbjct: 10  TSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG 69

Query: 105 FAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK 138
            A++ ++  E A  AL  +   +G R + +  + 
Sbjct: 70  DAFVLFACEEYAQNALRKHKDLLGKRYIELFRST 103

>2rh1_A Beta-2-adrenergic receptor/T4-lysozyme chimera; GPCR, 7TM, fusion, lipidic cubic phase, lipidic, mesophase, cholesterol, membrane protein; HET: MAL CAU CLR PLM 12P; 2.40A {Homo sapiens} PDB: 3p0g_A* 3d4s_A* 3ny8_A* 3ny9_A* 3nya_A* 3pds_A* Length = 500

 Score = 42.4 bits (99), Expect = 4e-04
 Identities = 16/181 (8%), Positives = 45/181 (24%), Gaps = 2/181 (1%)

Query: 247 YQRTYR-ARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLST 305
           Y R ++ A+ +      +      R + +     +          +S   +   +E    
Sbjct: 226 YSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKA 285

Query: 306 RDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRA 365
                    ++ E++   +  V    +    +   +  Y S     +    +   +    
Sbjct: 286 IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGET 345

Query: 366 HSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLS 425
                          R D+A      +SR  +   +  ++             K      
Sbjct: 346 GVAGFTNSLRMLQQKRWDEAAVN-LAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEH 404

Query: 426 R 426
           +
Sbjct: 405 K 405

>3pbl_A D(3) dopamine receptor, lysozyme chimera; structural genomics, PSI-2, protein structure initiative, AC technologies center for gene to 3D structure; HET: ETQ MAL; 2.89A {Homo sapiens} Length = 481

 Score = 42.1 bits (98), Expect = 5e-04
 Identities = 16/185 (8%), Positives = 39/185 (21%), Gaps = 5/185 (2%)

Query: 247 YQRTYR-ARSRSKSRSPVSFHRRRRSRSFSPPYRHRRGHRSRSPLRSRHYSKYDNERLST 305
           Y R Y   + R +             R       ++      +       +K  +   + 
Sbjct: 217 YARIYVVLKQRRRKNIFEMLRIDEGLRL----KIYKDTEGYYTIGIGHLLTKSPSLNAAK 272

Query: 306 RDTRDGADRSRRESDISHHSPVPRRRKSRSVSPHSRKSYRSDSGSPKHRQESSARKSSRA 365
            +      R+         +     +   +      ++ +             A   +  
Sbjct: 273 SELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMV 332

Query: 366 HSKSPKRHRGNRNSPRNDDAKPKYRHRSRSKSMERHDEEKDEARDGKSQHRERKRSRSLS 425
                    G  NS R    K              +++  + A+   +  R         
Sbjct: 333 FQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGV 392

Query: 426 REDEH 430
              E 
Sbjct: 393 PLREK 397

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	682
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.73
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.7
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.69
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.68
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.68
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.68
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.67
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.67
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.67
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.67
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.67
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.67
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.67
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.66
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.66
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.66
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.66
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.66
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.66
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.65
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.65
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.65
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.65
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.65
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.65
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.65
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.65
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.65
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.65
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.65
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.65
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.64
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.64
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.64
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.64
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.64
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.64
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.64
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.64
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.64
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.64
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.63
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.63
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.63
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.63
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.63
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.63
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.63
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.63
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.62
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.62
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.62
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.62
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.62
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.62
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.62
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.62
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.62
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.62
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.62
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.62
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.61
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.61
2div_A	99	TRNA selenocysteine associated protein; structural	99.6
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.6
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.6
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.6
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.6
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.6
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.6
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.6
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.6
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.6
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.6
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.6
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.6
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.59
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.59
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.59
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.59
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.59
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.58
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.58
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.58
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.58
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.58
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.57
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.57
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.57
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.56
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.56
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.56
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.55
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.55
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.55
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.55
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.54
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.54
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.54
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.53
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.53
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.53
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.26
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.51
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.5
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.5
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.5
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.49
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.48
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.48
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.48
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.45
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.45
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.45
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.44
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.43
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.43
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.43
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.42
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.42
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.42
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.41
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.41
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.41
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.4
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.4
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.4
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.4
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.39
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.39
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.39
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.38
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.38
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.37
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.36
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.35
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.31
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.3
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.3
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.29
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.26
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.23
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.19
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.15
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.15
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.09
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.98
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.69
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.5
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.46
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.2
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	97.73
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.72
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.55
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.09
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.07
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.34
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.19
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.89
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.55
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	93.37
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	92.19
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	82.65
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.74

>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=99.84  E-value=2.1e-19  Score=199.14  Aligned_cols=80  Identities=21%  Similarity=0.342  Sum_probs=73.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ...+.++|||+|||+.||+++|.+||.+||.|+.|.|+      ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|.
T Consensus        98 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~  177 (437)
T 3pgw_S           98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  177 (437)
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999997      25899999999999999999 899999999999999


Q ss_pred             ecccCCC
Q 005698          136 MAKSFPQ  142 (682)
Q Consensus       136 ~a~~~~~  142 (682)
                      |+.+...
T Consensus       178 ~a~~~~~  184 (437)
T 3pgw_S          178 VERGRTV  184 (437)
T ss_pred             EeCCCCC
Confidence            9986544

>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=99.73  E-value=1e-17  Score=148.14  Aligned_cols=75  Identities=25%  Similarity=0.440  Sum_probs=69.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||+.+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.||
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            346899999999999999999999999999999987      25689999999999999999 89999999999999999


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      ++
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.8e-17  Score=147.11  Aligned_cols=81  Identities=17%  Similarity=0.225  Sum_probs=73.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC--CceecCceEEEEecccC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN--NMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln--g~~l~Gr~L~V~~a~~~  140 (682)
                      +...++|||+|||+.+|+++|+++|.+||.|+.|.|+..+|||||+|.+.++|+.|| .|+  +..|.|+.|.|.|+...
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            345889999999999999999999999999999999988999999999999999999 676  47999999999999876


Q ss_pred             CCCC
Q 005698          141 PQKP  144 (682)
Q Consensus       141 ~~~~  144 (682)
                      ....
T Consensus        93 ~~~~   96 (105)
T 1sjq_A           93 ELKT   96 (105)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            5544

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.69  E-value=5.8e-17  Score=146.77  Aligned_cols=76  Identities=24%  Similarity=0.408  Sum_probs=70.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+    .++|||||+|.+.++|+.|| .|||+.|+|+.|.|.++....
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            6789999999999999999999999999999997    35789999999999999999 899999999999999988654


Q ss_pred             C
Q 005698          142 Q  142 (682)
Q Consensus       142 ~  142 (682)
                      .
T Consensus        85 ~   85 (115)
T 4f25_A           85 E   85 (115)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.1e-16  Score=140.42  Aligned_cols=82  Identities=17%  Similarity=0.210  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc--CCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL--NNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L--ng~~l~Gr~L~V~~a~~  139 (682)
                      ...+.++|||+|||+.+|+++|+++|.+||.|..|.|+..+|||||+|.+.++|+.|| .|  ++..|.|+.|.|.|+..
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   90 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   90 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCc
Confidence            4456789999999999999999999999999999999988999999999999999999 65  57889999999999987


Q ss_pred             CCCCC
Q 005698          140 FPQKP  144 (682)
Q Consensus       140 ~~~~~  144 (682)
                      .....
T Consensus        91 ~~~~~   95 (101)
T 2cq1_A           91 KELKT   95 (101)
T ss_dssp             SSCCC
T ss_pred             ccCcC
Confidence            65443

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.69  E-value=8.7e-17  Score=142.56  Aligned_cols=77  Identities=16%  Similarity=0.190  Sum_probs=71.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCce--ecCceEEEEecccC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMD--VGGRPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~--l~Gr~L~V~~a~~~  140 (682)
                      ..+.++|||+|||+.+|+++|.++|.+||.|..|.|+..+|||||+|.+.++|..|| .|||..  |.|+.|.|+|++..
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            346889999999999999999999999999999999988999999999999999999 798865  78999999999864

>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=99.68  E-value=3.6e-16  Score=138.11  Aligned_cols=83  Identities=27%  Similarity=0.404  Sum_probs=75.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+    ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|
T Consensus        10 ~~~~~~~~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           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345668999999999999999999999999999999998    34899999999999999999 7999999999999999


Q ss_pred             cccCCCCC
Q 005698          137 AKSFPQKP  144 (682)
Q Consensus       137 a~~~~~~~  144 (682)
                      +.......
T Consensus        90 a~~~~~~~   97 (103)
T 2cq3_A           90 ATARVMTN   97 (103)
T ss_dssp             CCSSCCCC
T ss_pred             cccCCCCC
Confidence            98765544

>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=99.68  E-value=3.1e-16  Score=138.51  Aligned_cols=82  Identities=29%  Similarity=0.450  Sum_probs=74.5

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ..+...++|||+|||+.+|+++|+++|..||.|..|.|+.    .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
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 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            3456689999999999999999999999999999999973    5799999999999999999 7999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9875543

>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=99.68  E-value=3.6e-16  Score=139.65  Aligned_cols=82  Identities=23%  Similarity=0.406  Sum_probs=74.4

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ......++|||+|||+.+|+++|+++|.+||.|..|.|.   ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            345567899999999999999999999999999999997   35789999999999999999 89999999999999999


Q ss_pred             ccCCCC
Q 005698          138 KSFPQK  143 (682)
Q Consensus       138 ~~~~~~  143 (682)
                      ......
T Consensus        97 ~~~~~~  102 (109)
T 1x4a_A           97 RSGRGT  102 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            876543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=144.10  Aligned_cols=75  Identities=16%  Similarity=0.191  Sum_probs=70.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .+.++|||+||++.+|+++|+++|.+||.|..|.|+      .++|||||+|.+.++|+.|| .|||+.|.|+.|.|.++
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            457899999999999999999999999999999986      35789999999999999999 89999999999999998


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            64

>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=99.68  E-value=1.3e-16  Score=145.99  Aligned_cols=83  Identities=18%  Similarity=0.231  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC--CceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN--NMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln--g~~l~Gr~L~V~~a~~  139 (682)
                      ...+.++|||+|||+.+|+++|+++|.+||.|+.|.|+..+|||||+|.+.++|+.|| .|+  +..|.|+.|.|.|+..
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  106 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH  106 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccC
Confidence            3445789999999999999999999999999999999988999999999999999999 787  4789999999999987


Q ss_pred             CCCCCC
Q 005698          140 FPQKPS  145 (682)
Q Consensus       140 ~~~~~~  145 (682)
                      ......
T Consensus       107 k~~~~~  112 (119)
T 2ad9_A          107 KELKTD  112 (119)
T ss_dssp             SSCCCC
T ss_pred             CCCCcc
Confidence            665543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.68  E-value=2.7e-16  Score=141.65  Aligned_cols=84  Identities=23%  Similarity=0.418  Sum_probs=75.4

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      .......++|||+|||+.+|+++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||+.|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34556789999999999999999999999999999999972      3689999999999999999 7999999999999


Q ss_pred             EEecccCCCCC
Q 005698          134 VEMAKSFPQKP  144 (682)
Q Consensus       134 V~~a~~~~~~~  144 (682)
                      |.|+.......
T Consensus        89 V~~a~~~~~~~   99 (115)
T 2dgo_A           89 TNWATRKPPAP   99 (115)
T ss_dssp             EEESSCCCCCS
T ss_pred             EEEccCCCCCC
Confidence            99998765543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.68  E-value=8.1e-17  Score=138.87  Aligned_cols=73  Identities=26%  Similarity=0.236  Sum_probs=70.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...-|||+||++.+|+++|+++|.+||+|..|.|..++|||||+|.+.++|+.|| .|||..|.|+.|.|.+|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4678999999999999999999999999999999989999999999999999999 899999999999999984

>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=99.67  E-value=9.4e-17  Score=143.03  Aligned_cols=77  Identities=22%  Similarity=0.303  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCC--ceecCceEEEEeccc
Q 005698           64 DALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNN--MDVGGRPLNVEMAKS  139 (682)
Q Consensus        64 ~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng--~~l~Gr~L~V~~a~~  139 (682)
                      ..+.++|||+|||+ .+|+++|.++|.+||.|..|.|+..+|||||+|.+.++|+.|| .||+  ..|.|+.|.|.|+..
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            34678999999999 9999999999999999999999988899999999999999999 7875  569999999999985


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus        92 ~   92 (102)
T 1x4d_A           92 Y   92 (102)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.67  E-value=1.4e-16  Score=135.59  Aligned_cols=76  Identities=29%  Similarity=0.414  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc-CCceecCceEEEEecc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL-NNMDVGGRPLNVEMAK  138 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L-ng~~l~Gr~L~V~~a~  138 (682)
                      .+...++|||+|||+.+++++|+++|.+||.|..|.|+..+|||||+|.+.++|+.|| .| ||..|.|+.|.|.|++
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            3456789999999999999999999999999999999988999999999999999999 68 9999999999999974

>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=99.67  E-value=2.2e-16  Score=138.07  Aligned_cols=79  Identities=29%  Similarity=0.428  Sum_probs=73.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceec--CceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVG--GRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~--Gr~L~V~~a~~  139 (682)
                      ...+.++|||+|||+.+|+++|+++|..||.|..|.|...+|||||+|.+.++|+.|| .|||..|.  |+.|.|.|+.+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~   92 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCC
Confidence            3445789999999999999999999999999999999977999999999999999999 79999999  99999999987


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ..
T Consensus        93 ~~   94 (97)
T 1why_A           93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.5e-16  Score=134.84  Aligned_cols=79  Identities=27%  Similarity=0.444  Sum_probs=73.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ....++|||+|||+.+|+++|+++|.+||.|..|.|+  +|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.....
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            3467899999999999999999999999999999998  899999999999999999 8999999999999999987654


Q ss_pred             CC
Q 005698          143 KP  144 (682)
Q Consensus       143 ~~  144 (682)
                      ..
T Consensus        83 ~~   84 (90)
T 2dnq_A           83 AS   84 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.67  E-value=2.3e-16  Score=140.86  Aligned_cols=81  Identities=14%  Similarity=0.165  Sum_probs=72.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCC--ceecCceEEEEecccC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNN--MDVGGRPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng--~~l~Gr~L~V~~a~~~  140 (682)
                      ..+.++|||+|||+.+++++|+++|.+||.|..|.|+..+|||||+|.+.++|+.|| .|++  ..|.|+.|.|.|+...
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            346789999999999999999999999999999999988999999999999999999 6765  5699999999999876


Q ss_pred             CCCC
Q 005698          141 PQKP  144 (682)
Q Consensus       141 ~~~~  144 (682)
                      ....
T Consensus        92 ~~~~   95 (104)
T 1wex_A           92 RITR   95 (104)
T ss_dssp             SCCC
T ss_pred             cccC
Confidence            5443

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=4.4e-16  Score=136.50  Aligned_cols=81  Identities=19%  Similarity=0.333  Sum_probs=74.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ....++|||+|||..+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.||.|||..|.|+.|.|.|+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4467899999999999999999999999999999997      2579999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 005698          138 KSFPQKP  144 (682)
Q Consensus       138 ~~~~~~~  144 (682)
                      .......
T Consensus        87 ~~~~~~~   93 (99)
T 2dgs_A           87 EPRDSKS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccC
Confidence            8765543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.3e-16  Score=135.58  Aligned_cols=80  Identities=30%  Similarity=0.568  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+  ++||||+|.+.++|+.|| .|||..|.|+.|.|.|+....
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            34567899999999999999999999999999999998  779999999999999999 899999999999999998765


Q ss_pred             CCC
Q 005698          142 QKP  144 (682)
Q Consensus       142 ~~~  144 (682)
                      ...
T Consensus        84 ~~~   86 (92)
T 2dgt_A           84 RTA   86 (92)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=138.76  Aligned_cols=81  Identities=26%  Similarity=0.388  Sum_probs=73.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567999999999999999999999999999999997      25799999999999999999 799999999999999


Q ss_pred             ecccCCCC
Q 005698          136 MAKSFPQK  143 (682)
Q Consensus       136 ~a~~~~~~  143 (682)
                      |+......
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99875443

>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=99.67  E-value=3.8e-16  Score=136.75  Aligned_cols=80  Identities=29%  Similarity=0.328  Sum_probs=73.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|
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            3457899999999999999999999999999999997      25699999999999999999 8999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9876544

>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=99.67  E-value=3e-16  Score=140.25  Aligned_cols=79  Identities=23%  Similarity=0.365  Sum_probs=73.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCCC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      ...++|||+|||..+|+++|+++|..||.|..|.|+..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+......
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            35789999999999999999999999999999999977999999999999999999 89999999999999999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=138.77  Aligned_cols=83  Identities=33%  Similarity=0.440  Sum_probs=75.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+    ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
T Consensus        10 ~~~~~~~~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           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345578999999999999999999999999999999998    35799999999999999999 7999999999999999


Q ss_pred             cccCCCCC
Q 005698          137 AKSFPQKP  144 (682)
Q Consensus       137 a~~~~~~~  144 (682)
                      +.......
T Consensus        90 a~~~~~~~   97 (103)
T 2d9p_A           90 AQRKEERQ   97 (103)
T ss_dssp             CSSCCCCC
T ss_pred             ecccccCC
Confidence            98765543

>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=99.66  E-value=2.5e-16  Score=142.01  Aligned_cols=83  Identities=27%  Similarity=0.414  Sum_probs=74.2

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||+.|.|+.|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3445678999999999999999999999999999999872      3589999999999999999 89999999999999


Q ss_pred             EecccCCCCC
Q 005698          135 EMAKSFPQKP  144 (682)
Q Consensus       135 ~~a~~~~~~~  144 (682)
                      .|+.......
T Consensus       100 ~~a~~~~~~~  109 (115)
T 2cpz_A          100 QLKRSKNDSK  109 (115)
T ss_dssp             ECCCCSCCCC
T ss_pred             EEcCCCCcCC
Confidence            9998765443

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.66  E-value=1.7e-16  Score=142.37  Aligned_cols=79  Identities=22%  Similarity=0.364  Sum_probs=72.2

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..+...++|||+|||+.+|+++|+++|.+||.|..|.|.  +|||||+|.+.++|+.|| .|||..|+|+.|.|.|+...
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            345668999999999999999999999999999999998  999999999999999999 79999999999999999875


Q ss_pred             CC
Q 005698          141 PQ  142 (682)
Q Consensus       141 ~~  142 (682)
                      ..
T Consensus       104 ~~  105 (108)
T 2jvo_A          104 AK  105 (108)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>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=99.66  E-value=3.6e-16  Score=137.22  Aligned_cols=80  Identities=31%  Similarity=0.405  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|...+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+....
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            4456789999999999999999999999999999999988999999999999999999 899999999999999998754


Q ss_pred             C
Q 005698          142 Q  142 (682)
Q Consensus       142 ~  142 (682)
                      .
T Consensus        91 ~   91 (99)
T 2cpj_A           91 S   91 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=5.2e-16  Score=137.69  Aligned_cols=82  Identities=22%  Similarity=0.355  Sum_probs=74.4

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-------CCCeEEEEeCCHHHHHHHH-Hc-CCceecCceE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-------SKHFAYIEYSKPEEATAAL-AL-NNMDVGGRPL  132 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-------~kg~aFVeF~s~e~A~~Al-~L-ng~~l~Gr~L  132 (682)
                      ..+...++|||+|||+.+|+++|+++|..||.|..|.|+.       .+|||||+|.+.++|+.|| .| ||..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            3456789999999999999999999999999999999973       3799999999999999999 79 9999999999


Q ss_pred             EEEecccCCCC
Q 005698          133 NVEMAKSFPQK  143 (682)
Q Consensus       133 ~V~~a~~~~~~  143 (682)
                      .|.|+......
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.9e-16  Score=135.24  Aligned_cols=77  Identities=35%  Similarity=0.406  Sum_probs=70.9

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+.+++++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345568899999999999999999999999999999997      25789999999999999999 89999999999999


Q ss_pred             Eecc
Q 005698          135 EMAK  138 (682)
Q Consensus       135 ~~a~  138 (682)
                      .|++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9975

>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=99.66  E-value=3.9e-16  Score=138.22  Aligned_cols=82  Identities=28%  Similarity=0.365  Sum_probs=74.0

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecC---ceE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGG---RPL  132 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~G---r~L  132 (682)
                      ......++|||+|||+.+|+++|.++|..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||..|.|   +.|
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            3445689999999999999999999999999999999983     3789999999999999999 799999998   999


Q ss_pred             EEEecccCCCC
Q 005698          133 NVEMAKSFPQK  143 (682)
Q Consensus       133 ~V~~a~~~~~~  143 (682)
                      .|.|+......
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999876554

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.6e-16  Score=137.75  Aligned_cols=82  Identities=21%  Similarity=0.392  Sum_probs=74.1

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345568999999999999999999999999999999997      25689999999999999999 79999999999999


Q ss_pred             EecccCCCC
Q 005698          135 EMAKSFPQK  143 (682)
Q Consensus       135 ~~a~~~~~~  143 (682)
                      .|+......
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=5.6e-16  Score=134.54  Aligned_cols=78  Identities=28%  Similarity=0.401  Sum_probs=72.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            57899999999999999999999999999999997      24789999999999999999 799999999999999998


Q ss_pred             cCCCC
Q 005698          139 SFPQK  143 (682)
Q Consensus       139 ~~~~~  143 (682)
                      .....
T Consensus        84 ~~~~~   88 (95)
T 2dnz_A           84 ERLDG   88 (95)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            76543

>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=99.66  E-value=4.6e-16  Score=137.67  Aligned_cols=78  Identities=31%  Similarity=0.417  Sum_probs=72.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCCC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      ...++|||+|||+.+|+++|+++|..||.|..|.|+  ++||||+|.+.++|+.|| .|||+.|.|+.|.|.|+......
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            457899999999999999999999999999999998  789999999999999999 79999999999999999876544


Q ss_pred             C
Q 005698          144 P  144 (682)
Q Consensus       144 ~  144 (682)
                      .
T Consensus        87 ~   87 (103)
T 2dgu_A           87 R   87 (103)
T ss_dssp             C
T ss_pred             c
Confidence            3

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=6.3e-16  Score=138.18  Aligned_cols=79  Identities=18%  Similarity=0.220  Sum_probs=72.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecC-----ceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGG-----RPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G-----r~L~V~~a~  138 (682)
                      ...++|||+|||+.+|+++|++||.+||.|+.|.|+.. |||||+|.+.++|+.|| .|||+.|.|     +.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~   91 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   91 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCC
Confidence            35789999999999999999999999999999999854 99999999999999999 799999999     999999998


Q ss_pred             cCCCCC
Q 005698          139 SFPQKP  144 (682)
Q Consensus       139 ~~~~~~  144 (682)
                      ......
T Consensus        92 ~~~~~~   97 (108)
T 1x4c_A           92 PRSPSY   97 (108)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            765443

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.5e-16  Score=134.87  Aligned_cols=78  Identities=33%  Similarity=0.543  Sum_probs=72.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+  ++||||+|.+.++|+.|| .|||..|.|+.|.|.|+.....
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            4567899999999999999999999999999999998  779999999999999999 7999999999999999987644


Q ss_pred             C
Q 005698          143 K  143 (682)
Q Consensus       143 ~  143 (682)
                      .
T Consensus        84 ~   84 (90)
T 2dnp_A           84 K   84 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.66  E-value=2.7e-16  Score=133.54  Aligned_cols=75  Identities=28%  Similarity=0.474  Sum_probs=69.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+++++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
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            3468899999999999999999999999999999986      25899999999999999999 8999999999999999


Q ss_pred             cc
Q 005698          137 AK  138 (682)
Q Consensus       137 a~  138 (682)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=3.2e-16  Score=137.05  Aligned_cols=79  Identities=34%  Similarity=0.510  Sum_probs=71.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ...++|||+|||+.+|+++|+++|..||.|..|.|+         ..+|||||+|.+.++|+.|| .|||..|.|+.|.|
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            357899999999999999999999999999999987         23579999999999999999 79999999999999


Q ss_pred             EecccCCCC
Q 005698          135 EMAKSFPQK  143 (682)
Q Consensus       135 ~~a~~~~~~  143 (682)
                      .|+......
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.7e-16  Score=138.91  Aligned_cols=82  Identities=28%  Similarity=0.396  Sum_probs=73.9

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|
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 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345568999999999999999999999999999999997      24679999999999999999 79999999999999


Q ss_pred             EecccCCCC
Q 005698          135 EMAKSFPQK  143 (682)
Q Consensus       135 ~~a~~~~~~  143 (682)
                      .|+......
T Consensus        90 ~~a~~~~~~   98 (103)
T 2cq0_A           90 EWAKPSTNS   98 (103)
T ss_dssp             EESSCCCCS
T ss_pred             EECCCCCCC
Confidence            999876543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.6e-16  Score=139.92  Aligned_cols=74  Identities=26%  Similarity=0.363  Sum_probs=71.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..++|||+|||..+++++|+++|..||.|..|.|...+|||||+|.+.++|+.|| .|||..|+|+.|.|.|++.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            4689999999999999999999999999999999988999999999999999999 8999999999999999875

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3e-16  Score=138.21  Aligned_cols=82  Identities=27%  Similarity=0.439  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34468999999999999999999999999999999996      35899999999999999999 899999999999999


Q ss_pred             ecccCCCCC
Q 005698          136 MAKSFPQKP  144 (682)
Q Consensus       136 ~a~~~~~~~  144 (682)
                      |+.+.....
T Consensus        88 ~a~~~~~~~   96 (102)
T 2cqb_A           88 LAKPMRIKE   96 (102)
T ss_dssp             ECCCCCCCC
T ss_pred             eCCCCCCCC
Confidence            998765544

>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=99.66  E-value=2.1e-16  Score=143.18  Aligned_cols=69  Identities=19%  Similarity=0.245  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ...+|||+|||+.+|+++|++||.+||+|+.|.|+.. |||||+|.+.++|+.|| .|||+.|+|+.|.|.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            3689999999999999999999999999999999854 99999999999999999 799999999984443

>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=99.65  E-value=3.3e-16  Score=141.07  Aligned_cols=76  Identities=22%  Similarity=0.233  Sum_probs=72.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..++|||+|||+.+|+++|+++|.+||.|..|.|+..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+....
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            4679999999999999999999999999999999988999999999999999999 899999999999999998643

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.1e-15  Score=134.22  Aligned_cols=79  Identities=28%  Similarity=0.413  Sum_probs=72.5

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFC--GTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~--G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ......++|||+|||+.+|+++|+++|..|  |.|..|.+.  +|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   87 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            344567899999999999999999999999  999999987  899999999999999999 799999999999999998


Q ss_pred             cCCC
Q 005698          139 SFPQ  142 (682)
Q Consensus       139 ~~~~  142 (682)
                      +...
T Consensus        88 ~~~~   91 (99)
T 2cpd_A           88 PVDK   91 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.65  E-value=2.4e-16  Score=134.44  Aligned_cols=75  Identities=20%  Similarity=0.359  Sum_probs=68.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||..+++++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            478999999999999999999999999999999972      4689999999999999999 799999999999999997


Q ss_pred             cC
Q 005698          139 SF  140 (682)
Q Consensus       139 ~~  140 (682)
                      ..
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.65  E-value=3.5e-16  Score=141.57  Aligned_cols=79  Identities=20%  Similarity=0.292  Sum_probs=72.0

Q ss_pred             CCCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC--CceecCceEEEEecc
Q 005698           63 ADALKKTLQVSNLSPL-LTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN--NMDVGGRPLNVEMAK  138 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~-vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln--g~~l~Gr~L~V~~a~  138 (682)
                      ...+.++|||+|||+. +|+++|+++|.+||.|..|.|+..+|||||+|.+.++|+.|| .||  +..|.|+.|.|.|+.
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  100 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSE  100 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEEC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECc
Confidence            3556889999999998 999999999999999999999988999999999999999999 675  567999999999997


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      ...
T Consensus       101 ~~~  103 (112)
T 1x4f_A          101 KYK  103 (112)
T ss_dssp             SCS
T ss_pred             ccc
Confidence            644

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=7.4e-16  Score=135.30  Aligned_cols=80  Identities=26%  Similarity=0.393  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445678999999999999999999999999999999973     3589999999999999999 8999999999999999


Q ss_pred             cccCCC
Q 005698          137 AKSFPQ  142 (682)
Q Consensus       137 a~~~~~  142 (682)
                      +.+...
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            987543

>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=99.65  E-value=5.2e-16  Score=136.30  Aligned_cols=76  Identities=24%  Similarity=0.388  Sum_probs=70.6

Q ss_pred             CCCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           63 ADALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .....++|||+|||+ .+++++|.++|..||.|..|.|.  +|||||+|.+.++|+.|| .|||..|+|+.|.|.|+...
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            344689999999998 99999999999999999999996  899999999999999999 79999999999999998754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.65  E-value=2.1e-16  Score=142.90  Aligned_cols=75  Identities=20%  Similarity=0.231  Sum_probs=70.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC-CeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCG-TVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G-~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ...+|||+|||+.+|+++|+++|..|| +|..|.|.  ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.++...
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            468999999999999999999999999 99999996  57899999999999999999 89999999999999998754

>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=99.65  E-value=4.5e-16  Score=136.15  Aligned_cols=77  Identities=21%  Similarity=0.308  Sum_probs=71.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHH----HHHhcCCCeEEEEEec---CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           66 LKKTLQVSNLSPLLTVEQLR----QLFSFCGTVVECTITD---SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~----~~F~~~G~V~~v~i~~---~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ..++|||+|||+.+++++|+    ++|.+||.|..|.|+.   .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            46899999999999999999    9999999999999982   2899999999999999999 79999999999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .+...
T Consensus        88 ~~~~~   92 (96)
T 2dgx_A           88 TGASG   92 (96)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            86544

>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=99.65  E-value=5.1e-16  Score=132.57  Aligned_cols=75  Identities=21%  Similarity=0.434  Sum_probs=69.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------c-CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------D-SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~-~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|+      . .+|||||+|.+.++|+.|| .|||..|+|+.|.|.++
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            46899999999999999999999999999999986      1 6899999999999999999 79999999999999998


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.1e-16  Score=135.64  Aligned_cols=79  Identities=27%  Similarity=0.394  Sum_probs=72.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEE-EEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v-~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..| .|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            57899999999999999999999999999999 8862      5799999999999999999 69999999999999999


Q ss_pred             ccCCCCC
Q 005698          138 KSFPQKP  144 (682)
Q Consensus       138 ~~~~~~~  144 (682)
                      .......
T Consensus        84 ~~~~~~~   90 (96)
T 1x5t_A           84 FKKDSKG   90 (96)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            8765443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=5.3e-16  Score=136.61  Aligned_cols=80  Identities=26%  Similarity=0.409  Sum_probs=73.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
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            44678999999999999999999999999999999972      5789999999999999999 8999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.65  E-value=4.5e-16  Score=131.56  Aligned_cols=73  Identities=22%  Similarity=0.416  Sum_probs=68.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .+|||+|||+.+++++|.++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.+.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            5899999999999999999999999999999872      3789999999999999999 79999999999999999864

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.8e-16  Score=139.94  Aligned_cols=77  Identities=10%  Similarity=0.170  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .+...++|||+|||+.+|+++|.++|.+||.|..|.|+     .++|||||+|.+.++|+.||.+||..|+|+.|.|.|+
T Consensus         7 ~~~~~~~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            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   86 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEH
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34457899999999999999999999999999999997     3689999999999999999999999999999999987


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            64

>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=99.65  E-value=1e-15  Score=136.69  Aligned_cols=81  Identities=25%  Similarity=0.301  Sum_probs=73.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcC------CceecC
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALN------NMDVGG  129 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Ln------g~~l~G  129 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .||      |+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            44568899999999999999999999999999999997      36899999999999999999 799      999999


Q ss_pred             ceEEEEecccCCCC
Q 005698          130 RPLNVEMAKSFPQK  143 (682)
Q Consensus       130 r~L~V~~a~~~~~~  143 (682)
                      +.|.|.|+......
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.65  E-value=1.3e-16  Score=138.65  Aligned_cols=76  Identities=20%  Similarity=0.369  Sum_probs=68.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCC-CeEEEEEe------cCCCeEEEEeCCHHHHHHHH-Hc-CCceecCceEEEEec
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCG-TVVECTIT------DSKHFAYIEYSKPEEATAAL-AL-NNMDVGGRPLNVEMA  137 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G-~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~L-ng~~l~Gr~L~V~~a  137 (682)
                      .++|||+|||+.+|+++|+++|..|| +|..|.|+      .++|||||+|.+.++|+.|| .| ++..|+|+.|.|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 89999986      46799999999999999999 56 567899999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .+.+.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87554

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.1e-15  Score=137.39  Aligned_cols=80  Identities=28%  Similarity=0.402  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .....++|||+|||+.+|+++|++||..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            445678999999999999999999999999999999973     3689999999999999999 7999999999999999


Q ss_pred             cccCCC
Q 005698          137 AKSFPQ  142 (682)
Q Consensus       137 a~~~~~  142 (682)
                      +.....
T Consensus        91 a~~~~~   96 (114)
T 2do0_A           91 DERALP   96 (114)
T ss_dssp             CSCCCC
T ss_pred             cccCCC
Confidence            975443

>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=99.64  E-value=6e-16  Score=134.99  Aligned_cols=75  Identities=25%  Similarity=0.376  Sum_probs=70.2

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||..+++++|.++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|+|+.|.|.|+..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            6799999999999999999999999999999997      24799999999999999999 8999999999999999986


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ..
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.9e-16  Score=139.99  Aligned_cols=79  Identities=28%  Similarity=0.433  Sum_probs=72.7

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ......++|||+|||..+|+++|+++|..||.|..|.|+    ..+|||||+|.+.++|+.|| .|||..|+|+.|.|.+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345568999999999999999999999999999999997    34899999999999999999 7999999999999999


Q ss_pred             cccC
Q 005698          137 AKSF  140 (682)
Q Consensus       137 a~~~  140 (682)
                      +...
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=5.3e-16  Score=134.55  Aligned_cols=77  Identities=29%  Similarity=0.418  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+++++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999997      24689999999999999999 799999999999999


Q ss_pred             eccc
Q 005698          136 MAKS  139 (682)
Q Consensus       136 ~a~~  139 (682)
                      |++.
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9874

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.5e-16  Score=138.04  Aligned_cols=78  Identities=24%  Similarity=0.317  Sum_probs=71.5

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            3457899999999999999999999999999999997      23689999999999999999 7999999999999999


Q ss_pred             cccCC
Q 005698          137 AKSFP  141 (682)
Q Consensus       137 a~~~~  141 (682)
                      +....
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.64  E-value=4.9e-16  Score=140.60  Aligned_cols=77  Identities=26%  Similarity=0.418  Sum_probs=70.4

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+.+++++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|+|+.|.|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345567899999999999999999999999999999997      34799999999999999999 79999999999999


Q ss_pred             Eecc
Q 005698          135 EMAK  138 (682)
Q Consensus       135 ~~a~  138 (682)
                      .|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9974

>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=99.64  E-value=9e-16  Score=139.29  Aligned_cols=79  Identities=24%  Similarity=0.388  Sum_probs=72.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999999999983     4699999999999999999 79999999999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .....
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            86543

>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=99.64  E-value=6.6e-16  Score=138.02  Aligned_cols=79  Identities=22%  Similarity=0.274  Sum_probs=72.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
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            4457899999999999999999999999999999997      24799999999999999999 7999999999999999


Q ss_pred             cccCCC
Q 005698          137 AKSFPQ  142 (682)
Q Consensus       137 a~~~~~  142 (682)
                      +.....
T Consensus       103 a~~~~~  108 (110)
T 1oo0_B          103 CFVKGP  108 (110)
T ss_dssp             SEESSC
T ss_pred             cccCCC
Confidence            987543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=5.4e-16  Score=135.68  Aligned_cols=78  Identities=23%  Similarity=0.365  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .....++|||+|||+.+|+++|+++|..||.|. |.|+  ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            345578999999999999999999999999996 5554  67899999999999999999 8999999999999999986


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ..
T Consensus        94 ~~   95 (97)
T 2e5j_A           94 QR   95 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.64  E-value=7.8e-16  Score=136.49  Aligned_cols=82  Identities=27%  Similarity=0.324  Sum_probs=73.8

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCcee---cCce
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDV---GGRP  131 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l---~Gr~  131 (682)
                      ..+...++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            345568999999999999999999999999999999997      25799999999999999999 7999988   8999


Q ss_pred             EEEEecccCCCC
Q 005698          132 LNVEMAKSFPQK  143 (682)
Q Consensus       132 L~V~~a~~~~~~  143 (682)
                      |.|.|+......
T Consensus        88 l~v~~a~~~~~~   99 (106)
T 2dgp_A           88 IQVKPADSESRG   99 (106)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEECCccccc
Confidence            999999876543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.64  E-value=5.7e-16  Score=132.42  Aligned_cols=75  Identities=24%  Similarity=0.389  Sum_probs=69.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .+...++|||+|||+.+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.||.++|..|+|+.|.|.+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45568999999999999999999999999999999997      236899999999999999998899999999999988


Q ss_pred             c
Q 005698          137 A  137 (682)
Q Consensus       137 a  137 (682)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.64  E-value=5.2e-16  Score=133.95  Aligned_cols=78  Identities=27%  Similarity=0.389  Sum_probs=72.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...++|||+|||+.+++++|+++|..||.|..|.|+.    .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   85 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN   85 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            4578999999999999999999999999999999973    5799999999999999999 7999999999999999987


Q ss_pred             CCC
Q 005698          140 FPQ  142 (682)
Q Consensus       140 ~~~  142 (682)
                      ...
T Consensus        86 ~~~   88 (92)
T 2dgv_A           86 ASG   88 (92)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=2.3e-15  Score=131.67  Aligned_cols=79  Identities=29%  Similarity=0.382  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .....++|||+||  .+|+++|+++|.+||.|..|.|...+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+....
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            4456789999997  8999999999999999999999988999999999999999999 899999999999999998765


Q ss_pred             CC
Q 005698          142 QK  143 (682)
Q Consensus       142 ~~  143 (682)
                      ..
T Consensus        89 ~~   90 (97)
T 1x5p_A           89 ML   90 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.63  E-value=7.1e-16  Score=138.22  Aligned_cols=81  Identities=30%  Similarity=0.413  Sum_probs=73.4

Q ss_pred             cCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceE
Q 005698           60 AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL  132 (682)
Q Consensus        60 ~~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L  132 (682)
                      ........++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|
T Consensus        19 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           19 LQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             SCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             cccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34456678999999999999999999999999999999997      24689999999999999999 799999999999


Q ss_pred             EEEecccC
Q 005698          133 NVEMAKSF  140 (682)
Q Consensus       133 ~V~~a~~~  140 (682)
                      .|.++...
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99998764

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.1e-15  Score=136.08  Aligned_cols=80  Identities=23%  Similarity=0.271  Sum_probs=72.3

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      ...+...++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .||+ .|.|+.|.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            3456678999999999999999999999999999999997      25789999999999999999 7888 89999999


Q ss_pred             EEecccCC
Q 005698          134 VEMAKSFP  141 (682)
Q Consensus       134 V~~a~~~~  141 (682)
                      |.|+....
T Consensus        90 V~~a~~~~   97 (116)
T 2cqd_A           90 VNLAYLGA   97 (116)
T ss_dssp             EEESTTTC
T ss_pred             EEEcccCC
Confidence            99997643

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=8.8e-16  Score=137.85  Aligned_cols=82  Identities=28%  Similarity=0.428  Sum_probs=73.7

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeE--------EEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCce
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVV--------ECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMD  126 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~--------~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~  126 (682)
                      ..+...++|||+|||+.+|+++|+++|..||.|.        .|.|+      ..+|||||+|.+.++|+.|| .|||+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3556789999999999999999999999999998        58886      34789999999999999999 799999


Q ss_pred             ecCceEEEEecccCCCC
Q 005698          127 VGGRPLNVEMAKSFPQK  143 (682)
Q Consensus       127 l~Gr~L~V~~a~~~~~~  143 (682)
                      |.|+.|.|.|+......
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999876543

>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=99.63  E-value=4.6e-16  Score=135.09  Aligned_cols=77  Identities=31%  Similarity=0.509  Sum_probs=70.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .+...++|||+|||+.+++++|+++|..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            344578999999999999999999999999999999972     3689999999999999999 7999999999999999


Q ss_pred             ccc
Q 005698          137 AKS  139 (682)
Q Consensus       137 a~~  139 (682)
                      +..
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.63  E-value=4e-16  Score=135.20  Aligned_cols=79  Identities=24%  Similarity=0.391  Sum_probs=70.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCC-eEEEEEecCCCeEEEEeCCHHHHHHHH-HcCC-ceecCceEEEEecccCC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGT-VVECTITDSKHFAYIEYSKPEEATAAL-ALNN-MDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~-V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng-~~l~Gr~L~V~~a~~~~  141 (682)
                      ...++|||+|||+.+|+++|+++|.+||. |..+.| ..+|||||+|.+.++|+.|| .||| +.|+|+.|.|.|+....
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            45789999999999999999999999999 555555 46899999999999999999 7999 99999999999998765


Q ss_pred             CCC
Q 005698          142 QKP  144 (682)
Q Consensus       142 ~~~  144 (682)
                      ...
T Consensus        85 ~~~   87 (93)
T 2cqh_A           85 LRS   87 (93)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.63  E-value=5.8e-16  Score=135.34  Aligned_cols=77  Identities=23%  Similarity=0.358  Sum_probs=70.9

Q ss_pred             CCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           64 DALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        64 ~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..+.++|||+|||+ .+|+++|.++|..||.|..|.|.  +|||||+|.+.++|+.|| .|||..|.|+.|.|.|+....
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            34588999999998 99999999999999999999997  899999999999999999 799999999999999998654


Q ss_pred             C
Q 005698          142 Q  142 (682)
Q Consensus       142 ~  142 (682)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.63  E-value=9e-16  Score=140.49  Aligned_cols=80  Identities=24%  Similarity=0.306  Sum_probs=72.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
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            3457899999999999999999999999999999997      24899999999999999999 7999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus        99 a~~~~~~  105 (126)
T 3ex7_B           99 CFVRGPP  105 (126)
T ss_dssp             SEESSSC
T ss_pred             ecCCCCC
Confidence            9876544

>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=99.63  E-value=1.1e-15  Score=136.09  Aligned_cols=79  Identities=16%  Similarity=0.255  Sum_probs=72.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCC-eEEEEEe-------cCCCeEEEEeCCHHHHHHHH-HcC--CceecCceEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGT-VVECTIT-------DSKHFAYIEYSKPEEATAAL-ALN--NMDVGGRPLN  133 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~-V~~v~i~-------~~kg~aFVeF~s~e~A~~Al-~Ln--g~~l~Gr~L~  133 (682)
                      ...++|||+|||+.+|+++|.++|..||. |..|.|+       ..+|||||+|.+.++|+.|| .||  ++.|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35789999999999999999999999998 9999997       57899999999999999999 796  5999999999


Q ss_pred             EEecccCCCC
Q 005698          134 VEMAKSFPQK  143 (682)
Q Consensus       134 V~~a~~~~~~  143 (682)
                      |.|+.+....
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999876544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.63  E-value=2.8e-16  Score=138.77  Aligned_cols=75  Identities=19%  Similarity=0.258  Sum_probs=70.0

Q ss_pred             CCCCEEEEeCCCC------CCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecC-c
Q 005698           65 ALKKTLQVSNLSP------LLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGG-R  130 (682)
Q Consensus        65 ~~~~tL~V~NLp~------~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G-r  130 (682)
                      ...++|||+|||+      .+++++|.++|.+||.|..|.|+      .++|||||+|.+.++|+.|| .|||+.|.| +
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            3478999999999      99999999999999999999987      36799999999999999999 899999999 9


Q ss_pred             eEEEEeccc
Q 005698          131 PLNVEMAKS  139 (682)
Q Consensus       131 ~L~V~~a~~  139 (682)
                      .|.|.++.+
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999999875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=1.6e-15  Score=134.05  Aligned_cols=80  Identities=21%  Similarity=0.297  Sum_probs=72.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .....++|||+|||+.+|+++|+++|..|| |..|.|+      ..+|||||+|.+.++|+.||.|||..|.|+.|.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDI   89 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEE
Confidence            344578999999999999999999999997 9999997      246899999999999999999999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.63  E-value=3.2e-16  Score=137.69  Aligned_cols=76  Identities=22%  Similarity=0.425  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCC--eEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCc----eecCc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGT--VVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNM----DVGGR  130 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~--V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~----~l~Gr  130 (682)
                      ...-.||||+|||+.+|+++|.++|.+||.  |..|.|+      .++|||||+|.+.++|+.|| .|||.    .|+|+
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            445789999999999999999999999995  5688876      36899999999999999999 89996    59999


Q ss_pred             eEEEEeccc
Q 005698          131 PLNVEMAKS  139 (682)
Q Consensus       131 ~L~V~~a~~  139 (682)
                      .|.|.||+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999874

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.62  E-value=1.9e-15  Score=140.73  Aligned_cols=85  Identities=25%  Similarity=0.425  Sum_probs=76.0

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      ...+...++|||+|||..+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3455668999999999999999999999999999999997      24789999999999999999 7999999999999


Q ss_pred             EEecccCCCCCC
Q 005698          134 VEMAKSFPQKPS  145 (682)
Q Consensus       134 V~~a~~~~~~~~  145 (682)
                      |.|+........
T Consensus       116 v~~a~~~~~~~~  127 (139)
T 1u6f_A          116 VALAASGHQRPG  127 (139)
T ss_dssp             EEESSCCCCCCC
T ss_pred             EEECCCCCCCCC
Confidence            999987765543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=1.1e-15  Score=141.34  Aligned_cols=76  Identities=24%  Similarity=0.413  Sum_probs=70.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHH----HHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           65 ALKKTLQVSNLSPLLTVEQLR----QLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~----~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .+.++|||+|||+.+++++|+    ++|++||.|+.|.|.   ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            457899999999999999876    799999999999886   57899999999999999999 8999999999999999


Q ss_pred             cccC
Q 005698          137 AKSF  140 (682)
Q Consensus       137 a~~~  140 (682)
                      +...
T Consensus       107 a~~~  110 (127)
T 2a3j_A          107 SETP  110 (127)
T ss_dssp             CCCC
T ss_pred             ccCc
Confidence            9864

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.62  E-value=1.1e-15  Score=133.29  Aligned_cols=78  Identities=19%  Similarity=0.401  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHH----HHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           64 DALKKTLQVSNLSPLLTVEQLR----QLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~----~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ..+.++|||+|||+.+++++|+    ++|.+||.|..|.|.   ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3467899999999999999999    999999999999997   56899999999999999999 799999999999999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      |+....
T Consensus        85 ~a~~~~   90 (97)
T 1nu4_A           85 YAKTDS   90 (97)
T ss_dssp             ECSSCC
T ss_pred             EccCCC
Confidence            998643

>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=99.62  E-value=4.9e-16  Score=139.86  Aligned_cols=77  Identities=23%  Similarity=0.366  Sum_probs=71.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      +...++|||+|||+.+|+++|++||..||.|..|.|+      ..+|||||+|.+.++|+.||.|||+.|.|+.|.|.|+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEec
Confidence            3446899999999999999999999999999999997      3579999999999999999999999999999999998


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      ...
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            754

>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=99.62  E-value=1e-15  Score=135.91  Aligned_cols=74  Identities=24%  Similarity=0.403  Sum_probs=69.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...++|||+|||+.+|+++|+++|..||.|..|.|+     ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            457899999999999999999999999999999997     35789999999999999999 799999999999999985

>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=99.62  E-value=1.3e-15  Score=130.52  Aligned_cols=74  Identities=34%  Similarity=0.475  Sum_probs=69.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.||.|||..|.|+.|.|.++...
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            5799999999999999999999999999999987      2478999999999999999999999999999999998763

>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=99.62  E-value=5.5e-16  Score=139.32  Aligned_cols=79  Identities=25%  Similarity=0.360  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHH---HHHhcCCCeEEEEEec---------CCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLR---QLFSFCGTVVECTITD---------SKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~---~~F~~~G~V~~v~i~~---------~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      .....++|||+|||+.+++++|.   ++|.+||.|..|.|+.         .+|||||+|.+.++|+.|| .|||..|+|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34457899999999999999999   9999999999999972         2379999999999999999 799999999


Q ss_pred             ceEEEEecccCC
Q 005698          130 RPLNVEMAKSFP  141 (682)
Q Consensus       130 r~L~V~~a~~~~  141 (682)
                      +.|.|.|+.+..
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998765

>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=99.62  E-value=1.4e-15  Score=144.57  Aligned_cols=80  Identities=26%  Similarity=0.349  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567999999999999999999999999999999996      24689999999999999999 799999999999999


Q ss_pred             ecccCCC
Q 005698          136 MAKSFPQ  142 (682)
Q Consensus       136 ~a~~~~~  142 (682)
                      |+.+...
T Consensus       115 ~a~~~~~  121 (156)
T 1h2v_Z          115 WDAGFKE  121 (156)
T ss_dssp             EESCCCT
T ss_pred             ECCCCCC
Confidence            9986543

>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=99.62  E-value=1.7e-15  Score=134.06  Aligned_cols=79  Identities=23%  Similarity=0.350  Sum_probs=72.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|+++|..|| |..|.|+       ..+|||||+|.+.++|+.||.|||..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEE
Confidence            34578999999999999999999999999 9999997       237899999999999999999999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9876544

>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=99.62  E-value=1.9e-16  Score=136.74  Aligned_cols=75  Identities=20%  Similarity=0.242  Sum_probs=63.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCC--CeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCG--TVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G--~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      .+|||+|||+.+|+++|+++|..||  .|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999987      34689999999999999999 899999999999999988


Q ss_pred             cCCC
Q 005698          139 SFPQ  142 (682)
Q Consensus       139 ~~~~  142 (682)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>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=99.62  E-value=1e-15  Score=141.70  Aligned_cols=79  Identities=27%  Similarity=0.413  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ...+.++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999997      35799999999999999999 799999999999999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      |+....
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            987643

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.62  E-value=1.7e-15  Score=135.80  Aligned_cols=81  Identities=20%  Similarity=0.316  Sum_probs=69.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .....++|||+|||+.+|+++|.++|..||.|..|.|+      ..+|||||+|.+.++|+.||.++|..|+|+.|.|.+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~  100 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV  100 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEE
Confidence            44567899999999999999999999999999999997      247999999999999999996557999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9876543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=133.32  Aligned_cols=75  Identities=23%  Similarity=0.371  Sum_probs=69.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE--------EEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE--------CTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVG  128 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~--------v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~  128 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..        |.|+      ..+|||||+|.+.++|+.|| .|||..|.
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            446899999999999999999999999999999        8886      23689999999999999999 79999999


Q ss_pred             CceEEEEecc
Q 005698          129 GRPLNVEMAK  138 (682)
Q Consensus       129 Gr~L~V~~a~  138 (682)
                      |+.|.|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999974

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.61  E-value=1.7e-15  Score=136.48  Aligned_cols=77  Identities=22%  Similarity=0.347  Sum_probs=71.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ...++|||+|||+.+|+++|.++|..||.|..|.|+   ..+|||||+|.+.++|+.|| .|||..|+|+.|.|.|+.+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   85 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNAN   85 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            357899999999999999999999999999999996   46799999999999999999 79999999999999999864


Q ss_pred             C
Q 005698          141 P  141 (682)
Q Consensus       141 ~  141 (682)
                      .
T Consensus        86 ~   86 (115)
T 3lqv_A           86 R   86 (115)
T ss_dssp             H
T ss_pred             h
Confidence            3

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.61  E-value=1.6e-15  Score=134.92  Aligned_cols=78  Identities=19%  Similarity=0.406  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEeCCCCCC------CHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCc-
Q 005698           63 ADALKKTLQVSNLSPLL------TVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGR-  130 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~v------teedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr-  130 (682)
                      .+...++|||+|||+.+      |+++|.++|.+||.|..|.|+    .++|||||+|.+.++|+.|| .|||..|.|+ 
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            34457899999999999      889999999999999999997    46899999999999999999 7999999998 


Q ss_pred             eEEEEecccC
Q 005698          131 PLNVEMAKSF  140 (682)
Q Consensus       131 ~L~V~~a~~~  140 (682)
                      .|.|.|+...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998754

>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=99.61  E-value=1.8e-15  Score=135.43  Aligned_cols=74  Identities=26%  Similarity=0.499  Sum_probs=69.6

Q ss_pred             CCCCEEEEeCCCCC-CCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           65 ALKKTLQVSNLSPL-LTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp~~-vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ...++|||+|||+. +|+++|+++|.+||.|..|.|.  +|||||+|.+.++|+.|| .|||..|+|+.|.|.|+...
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEEE--TTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            34689999999999 9999999999999999999994  899999999999999999 89999999999999999754

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.5e-15  Score=134.23  Aligned_cols=80  Identities=18%  Similarity=0.288  Sum_probs=72.7

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhc-CCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCce-ecCceEEEE
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSF-CGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMD-VGGRPLNVE  135 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~-~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~-l~Gr~L~V~  135 (682)
                      ....++|||+|||+.+|+++|+++|.. ||.|..|.|+.     .+|||||+|.+.++|+.|| .|||.. |.|+.|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            446789999999999999999999999 99999999972     5789999999999999999 799999 999999999


Q ss_pred             ecccCCCC
Q 005698          136 MAKSFPQK  143 (682)
Q Consensus       136 ~a~~~~~~  143 (682)
                      |+......
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99765543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.6e-15  Score=132.78  Aligned_cols=78  Identities=17%  Similarity=0.348  Sum_probs=70.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeE-EEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCce----
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVV-ECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRP----  131 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~-~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~----  131 (682)
                      ....++|||+|||+.+++++|+++|..||.|. .|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.    
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            34579999999999999999999999999999 999872      4589999999999999999 69999999999    


Q ss_pred             EEEEecccCC
Q 005698          132 LNVEMAKSFP  141 (682)
Q Consensus       132 L~V~~a~~~~  141 (682)
                      |.|.|+....
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999998643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.60  E-value=1e-15  Score=134.69  Aligned_cols=75  Identities=25%  Similarity=0.468  Sum_probs=70.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ++|||+|||+.+|+++|+++|..||.|..|.|+. .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            5899999999999999999999999999999985 4999999999999999999 7999999999999999987653

>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=99.60  E-value=9.2e-16  Score=134.07  Aligned_cols=78  Identities=17%  Similarity=0.259  Sum_probs=69.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+++++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34557899999999999999999999999999866554      24799999999999999999 899999999999999


Q ss_pred             ecccC
Q 005698          136 MAKSF  140 (682)
Q Consensus       136 ~a~~~  140 (682)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.60  E-value=7.8e-16  Score=127.84  Aligned_cols=69  Identities=16%  Similarity=0.327  Sum_probs=64.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      +|||+|||+.+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.||.|||..|+|+.|.|.+|
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999986      2468999999999999999999999999999999875

>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=99.60  E-value=4.9e-15  Score=130.73  Aligned_cols=82  Identities=21%  Similarity=0.303  Sum_probs=72.2

Q ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        61 ~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      .......++|||+|||+.+++++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.||. +++.|+|+.|.|
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v   87 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDC   87 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEE
Confidence            34556688999999999999999999999999999999972      36899999999999999996 478999999999


Q ss_pred             EecccCCCC
Q 005698          135 EMAKSFPQK  143 (682)
Q Consensus       135 ~~a~~~~~~  143 (682)
                      .|+......
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqg_A           88 KLPNSKQSQ   96 (103)
T ss_dssp             ECCCTTCCC
T ss_pred             EecCCCCcC
Confidence            999876543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.60  E-value=3.7e-15  Score=136.24  Aligned_cols=81  Identities=21%  Similarity=0.309  Sum_probs=73.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ....++|||+|||+.+++++|+++|..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            34578999999999999999999999999999999972     6799999999999999999 79999999999999999


Q ss_pred             ccCCCCC
Q 005698          138 KSFPQKP  144 (682)
Q Consensus       138 ~~~~~~~  144 (682)
                      ......+
T Consensus       112 ~~~~~~~  118 (124)
T 2kt5_A          112 ASQIDLE  118 (124)
T ss_dssp             CCTTCCC
T ss_pred             CCCCCCC
Confidence            8765443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.4e-15  Score=134.73  Aligned_cols=83  Identities=27%  Similarity=0.399  Sum_probs=73.6

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHcCCceecCceEEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVE  135 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~  135 (682)
                      ..+...++|||+|||+.+|+++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.||.+||+.|.|+.|.|.
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~   90 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPK   90 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            3456789999999999999999999999999999999972      3589999999999999999449999999999999


Q ss_pred             ecccCCCCC
Q 005698          136 MAKSFPQKP  144 (682)
Q Consensus       136 ~a~~~~~~~  144 (682)
                      ++.+....+
T Consensus        91 ~a~~~~~~~   99 (105)
T 2dh8_A           91 PCTPRGMQP   99 (105)
T ss_dssp             CSCCSSCCT
T ss_pred             EccCCCCCC
Confidence            998765443

>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=99.60  E-value=2.8e-15  Score=141.53  Aligned_cols=79  Identities=22%  Similarity=0.389  Sum_probs=73.2

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ......++|||+|||+.+|+++|.++|..||.|..|.|+ ..+|||||+|.+.++|..|| .|||..|.|+.|.|.|+.+
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  147 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG  147 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCC
Confidence            445567999999999999999999999999999999998 45999999999999999999 7999999999999999976


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus       148 ~  148 (150)
T 2i2y_A          148 E  148 (150)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.60  E-value=2.2e-15  Score=135.55  Aligned_cols=81  Identities=27%  Similarity=0.349  Sum_probs=72.2

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCe----EEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTV----VECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V----~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ..+.++|||+|||+.+|+++|.++|..||.|    +.+.+.  ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3457899999999999999999999999998    566665  56799999999999999999 7999999999999999


Q ss_pred             cccCCCCC
Q 005698          137 AKSFPQKP  144 (682)
Q Consensus       137 a~~~~~~~  144 (682)
                      +.......
T Consensus       102 a~~~~~~~  109 (115)
T 2cpx_A          102 GKNKKQRS  109 (115)
T ss_dssp             CCCCSCCC
T ss_pred             ccCCCCCC
Confidence            98765543

>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=99.60  E-value=2.3e-15  Score=136.53  Aligned_cols=79  Identities=22%  Similarity=0.321  Sum_probs=72.1

Q ss_pred             CCCCEEEE--eCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCcee-----cCceEEEEe
Q 005698           65 ALKKTLQV--SNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV-----GGRPLNVEM  136 (682)
Q Consensus        65 ~~~~tL~V--~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l-----~Gr~L~V~~  136 (682)
                      .+.++|||  |||++.+|+++|+++|.+||+|..|.|+..+|||||+|.+.++|+.|| .|||.+|     .|..|.|.|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            45789999  779999999999999999999999999888999999999999999999 8999998     689999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +...+..
T Consensus       103 a~~~p~~  109 (114)
T 2cq2_A          103 VEKVQWS  109 (114)
T ss_dssp             ESCCCCS
T ss_pred             cccCccc
Confidence            9866543

>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=99.60  E-value=1.8e-15  Score=136.55  Aligned_cols=78  Identities=13%  Similarity=0.139  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCe-EEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTV-VECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V-~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .+...++|||+|||+.+|+++|++||..||.| ..|.|+     ..+|||||+|.+.++|+.||.+||..|.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            44567899999999999999999999999999 788886     368999999999999999996699999999999999


Q ss_pred             cccC
Q 005698          137 AKSF  140 (682)
Q Consensus       137 a~~~  140 (682)
                      +...
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8753

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=3.3e-15  Score=134.86  Aligned_cols=79  Identities=24%  Similarity=0.381  Sum_probs=71.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...++|||+|||+.+|+++|++||..||.|..|.|+      ..+|||||+|.+.++|+.||.+||..|.|+.|.|.|+.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECC
Confidence            345899999999999999999999999999999997      24789999999999999999559999999999999998


Q ss_pred             cCCCC
Q 005698          139 SFPQK  143 (682)
Q Consensus       139 ~~~~~  143 (682)
                      .....
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            76543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=2.9e-15  Score=131.76  Aligned_cols=80  Identities=30%  Similarity=0.358  Sum_probs=69.5

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .+...++|||+|||+.+|+++|+++|.+||.|.-+...  ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+..
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            45568999999999999999999999999988322211  46899999999999999999 7999999999999999987


Q ss_pred             CCC
Q 005698          140 FPQ  142 (682)
Q Consensus       140 ~~~  142 (682)
                      ...
T Consensus        91 ~~~   93 (101)
T 2fc9_A           91 RGS   93 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.60  E-value=6.9e-16  Score=136.21  Aligned_cols=77  Identities=32%  Similarity=0.439  Sum_probs=70.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||+.+++++|+++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+
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            3468999999999999999999999999999999872      3799999999999999999 79999999999999998


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      ....
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            8643

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.60  E-value=1.5e-15  Score=141.65  Aligned_cols=81  Identities=27%  Similarity=0.413  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999996      35789999999999999999 799999999999999


Q ss_pred             ecccCCCC
Q 005698          136 MAKSFPQK  143 (682)
Q Consensus       136 ~a~~~~~~  143 (682)
                      |+......
T Consensus       123 ~a~~~~~~  130 (135)
T 2lea_A          123 MARYGRPP  130 (135)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99875543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.59  E-value=1.9e-15  Score=144.67  Aligned_cols=74  Identities=24%  Similarity=0.249  Sum_probs=68.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC--CeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCG--TVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G--~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ..++|||+|||+.+|+++|+++|..||  .|..|.|+      ..+|||||+|.+.++|+.|| .|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  99999996      35789999999999999999 8999999999999999


Q ss_pred             ccc
Q 005698          137 AKS  139 (682)
Q Consensus       137 a~~  139 (682)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            874

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.59  E-value=1e-15  Score=141.58  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=72.9

Q ss_pred             cCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE--EEEe------cCCCeEEEEeCCHHHHHHHH-HcCCc----e
Q 005698           60 AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE--CTIT------DSKHFAYIEYSKPEEATAAL-ALNNM----D  126 (682)
Q Consensus        60 ~~~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~--v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~----~  126 (682)
                      ....+...++|||+|||+.+|+++|+++|..||.|..  |.|+      ..+|||||+|.+. +|..|| .|||.    .
T Consensus        16 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           16 EPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3445567899999999999999999999999999966  8886      3679999999999 999999 89999    9


Q ss_pred             ecCceEEEEecccCCC
Q 005698          127 VGGRPLNVEMAKSFPQ  142 (682)
Q Consensus       127 l~Gr~L~V~~a~~~~~  142 (682)
                      |+|+.|.|.|+.+...
T Consensus        95 ~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           95 IDGKTINVEFAKGSKR  110 (131)
T ss_dssp             GGGCCCCCEECCCSCC
T ss_pred             CCCEEEEEEECCCCCC
Confidence            9999999999987543

>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=99.59  E-value=1.1e-15  Score=134.57  Aligned_cols=76  Identities=24%  Similarity=0.355  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-------CCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-------SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-------~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+++++|+++|..|| |..|.|+.       .+|||||+|.+.++|+.||.|||..|+|+.|.|.+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEe
Confidence            34579999999999999999999999999 99999972       47899999999999999999999999999999999


Q ss_pred             cccC
Q 005698          137 AKSF  140 (682)
Q Consensus       137 a~~~  140 (682)
                      +...
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8764

>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=99.59  E-value=2.5e-15  Score=144.52  Aligned_cols=80  Identities=23%  Similarity=0.286  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ....++|||+|||+.+|+++|++||.+||.|..|.|+.      .+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|
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            34568999999999999999999999999999999972      4699999999999999999 7999999999999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      +......
T Consensus       149 a~~~~~~  155 (165)
T 1rk8_A          149 CFVKGPK  155 (165)
T ss_dssp             SEECC--
T ss_pred             ecCCCCC
Confidence            9876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.59  E-value=2.6e-15  Score=137.04  Aligned_cols=75  Identities=29%  Similarity=0.454  Sum_probs=69.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.||.|||+.|.|+.|.|.|+...
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCCC
Confidence            5799999999999999999999999999999986      2478999999999999999999999999999999999864


Q ss_pred             C
Q 005698          141 P  141 (682)
Q Consensus       141 ~  141 (682)
                      .
T Consensus       116 ~  116 (124)
T 2jwn_A          116 M  116 (124)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.58  E-value=9e-15  Score=129.83  Aligned_cols=78  Identities=21%  Similarity=0.200  Sum_probs=69.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-EEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~-v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .....+|||+|||+.+|+++|++||..||.|.. |.|+     ..+|||||+|.+.++|+.||.+|+..|+|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            345789999999999999999999999999987 7775     4689999999999999999955999999999999988


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      ....
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.58  E-value=2.5e-15  Score=129.19  Aligned_cols=74  Identities=18%  Similarity=0.266  Sum_probs=70.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..++|||+|||+.+++++|+++|.+| .|..|.|...+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+...
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            46899999999999999999999999 9999999888999999999999999999 79999999999999998754

>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=99.58  E-value=6e-15  Score=140.12  Aligned_cols=81  Identities=27%  Similarity=0.413  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ......+|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34557899999999999999999999999999999997      36799999999999999999 799999999999999


Q ss_pred             ecccCCCC
Q 005698          136 MAKSFPQK  143 (682)
Q Consensus       136 ~a~~~~~~  143 (682)
                      |+......
T Consensus       146 ~a~~~~~~  153 (158)
T 2kn4_A          146 MARYGRPP  153 (158)
T ss_dssp             EECCSSCC
T ss_pred             ECCCCCCC
Confidence            99876443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.58  E-value=2e-15  Score=127.60  Aligned_cols=68  Identities=18%  Similarity=0.370  Sum_probs=63.3

Q ss_pred             CCEEEEeCCCCCC------CHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCc-eEEE
Q 005698           67 KKTLQVSNLSPLL------TVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGR-PLNV  134 (682)
Q Consensus        67 ~~tL~V~NLp~~v------teedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr-~L~V  134 (682)
                      .++|||+|||..+      |+++|.++|.+||.|..|.|+    .++|||||+|.+.++|+.|| .|||..|.|+ .|.|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3689999999999      789999999999999999987    46899999999999999999 7999999999 8876

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.8e-15  Score=127.82  Aligned_cols=77  Identities=22%  Similarity=0.297  Sum_probs=70.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      .....+|||+|||+.+|+++|+++|..| .|..|.|+     ..+|||||+|.+.++|+.||.|||..|.|+.|.|.++.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            3457899999999999999999999999 99999987     24789999999999999999999999999999999998


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      ..+
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            653

>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=99.58  E-value=9.8e-16  Score=132.98  Aligned_cols=74  Identities=19%  Similarity=0.275  Sum_probs=66.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.++.
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            46899999999999999999999999999877665      35699999999999999999 799999999999999876


Q ss_pred             c
Q 005698          139 S  139 (682)
Q Consensus       139 ~  139 (682)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=8.9e-16  Score=130.63  Aligned_cols=74  Identities=20%  Similarity=0.296  Sum_probs=67.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .+.++|||+|||+.+++++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.++
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            357899999999999999999999999999999987      24799999999999999999 79999999999988765


Q ss_pred             c
Q 005698          138 K  138 (682)
Q Consensus       138 ~  138 (682)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.58  E-value=6.5e-15  Score=136.62  Aligned_cols=76  Identities=26%  Similarity=0.454  Sum_probs=69.6

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ......++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345568999999999999999999999999999999996      35899999999999999999 89999999999999


Q ss_pred             Eec
Q 005698          135 EMA  137 (682)
Q Consensus       135 ~~a  137 (682)
                      .||
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            985

>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=99.58  E-value=7.3e-15  Score=132.03  Aligned_cols=79  Identities=18%  Similarity=0.275  Sum_probs=70.9

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCcee--------
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDV--------  127 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l--------  127 (682)
                      ..+...++|||+|||+.+|+++|+++|..||.|..|.|+.     .+|||||+|.+.++|+.|| .|||..|        
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            4456679999999999999999999999999999999972     4689999999999999999 7999999        


Q ss_pred             cCceEEEEecccC
Q 005698          128 GGRPLNVEMAKSF  140 (682)
Q Consensus       128 ~Gr~L~V~~a~~~  140 (682)
                      .|+.|.|.|+.+.
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999998753

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.57  E-value=3.2e-15  Score=136.08  Aligned_cols=77  Identities=16%  Similarity=0.230  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC---eEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGT---VVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~---V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      .....++|||+|||+.+|+++|++||..||.   |..|.|+     ..+|||||+|.+.++|+.||.|||..|+|+.|.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            3456789999999999999999999999999   8888887     3578999999999999999999999999999999


Q ss_pred             Eeccc
Q 005698          135 EMAKS  139 (682)
Q Consensus       135 ~~a~~  139 (682)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98864

>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=99.57  E-value=4.9e-15  Score=142.43  Aligned_cols=75  Identities=25%  Similarity=0.348  Sum_probs=68.7

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEEecccCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMAKSFP  141 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~a~~~~  141 (682)
                      ..+|||+||++.+|+++|+++|++||.|..|.|.  ..+|||||+|.+.++|+.|| .|||..|.|  +.|.|+|++...
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            4579999999999999999999999999999997  34679999999999999999 899999966  999999998753

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1e-14  Score=126.71  Aligned_cols=77  Identities=22%  Similarity=0.263  Sum_probs=67.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCC-CeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccCCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK-HFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~k-g~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ..++|||+|||+.+|+++|+++|..||.|..|.+.... .||||+|.+.++|+.||.|||..|+|+.|.|.++.....
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCcCCC
Confidence            46799999999999999999999999999998333211 299999999999999999999999999999998875543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=3e-15  Score=130.24  Aligned_cols=80  Identities=23%  Similarity=0.284  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .+...++|||+|||+.+|+++|+++|..||.|..|... ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.+.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            44567899999999999999999999999999887222 46799999999999999999 79999999999999999765


Q ss_pred             CC
Q 005698          141 PQ  142 (682)
Q Consensus       141 ~~  142 (682)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.56  E-value=2e-15  Score=138.24  Aligned_cols=76  Identities=14%  Similarity=0.175  Sum_probs=67.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEE-Ee-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-IT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~-i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .....+|||+|||+.+|+++|.+||..||.|..|. |.     ..+|||||+|.+.++|+.||.|||..|+|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            44568999999999999999999999999997733 33     3579999999999999999999999999999999998


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>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=99.56  E-value=2.7e-15  Score=133.21  Aligned_cols=77  Identities=17%  Similarity=0.198  Sum_probs=68.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      .....+|||+|||+.+|+++|++||..||.| .|.|+     .++|||||+|.+.++|+.||.||+..|.|+.|.|.++.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            3457899999999999999999999999954 88886     35789999999999999999889999999999999887


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      ...
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=9.7e-15  Score=127.05  Aligned_cols=76  Identities=26%  Similarity=0.392  Sum_probs=68.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEE-Ee--cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECT-IT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~-i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ...++|||+|||+.+|+++|+++|..||.|..|. |+  ...++|||+|.+.++|+.|| .|||..|.|+.|.|.|+.+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            3478999999999999999999999999999994 66  24456999999999999999 79999999999999999865

>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=99.56  E-value=6.9e-15  Score=125.38  Aligned_cols=71  Identities=27%  Similarity=0.468  Sum_probs=67.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC----C-------CeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFC----G-------TVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~----G-------~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      ..++|||+|||+.+|+++|+++|..|    |       .|..|.|...+|||||+|.+.++|+.||.|||..|.|+.|.|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~~l~g~~~~g~~l~V   84 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   84 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHGGGTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHHhcCCCEECCeEEEE
Confidence            47899999999999999999999999    8       999999998899999999999999999999999999999999


Q ss_pred             Ee
Q 005698          135 EM  136 (682)
Q Consensus       135 ~~  136 (682)
                      ..
T Consensus        85 ~r   86 (87)
T 2hzc_A           85 RR   86 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            73

>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=99.56  E-value=1.1e-15  Score=131.46  Aligned_cols=75  Identities=29%  Similarity=0.442  Sum_probs=65.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ++|||+|||..+++++|+++|..||.|..|.|+      ..+|||||+|.+.+ |+.|| .|||..|+|+.|.|.+|...
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            589999999999999999999999999999997      34789999999999 99999 79999999999999999875


Q ss_pred             CCC
Q 005698          141 PQK  143 (682)
Q Consensus       141 ~~~  143 (682)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.56  E-value=1.6e-15  Score=133.42  Aligned_cols=80  Identities=21%  Similarity=0.330  Sum_probs=69.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      .....+|||+|||+.+|+++|+++|..||.|..+.|.     ..+|||||+|.+.++|+.||.|||..|.|+.|.|.|+.
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcC
Confidence            3457899999999999999999999999987662222     57899999999999999999999999999999999998


Q ss_pred             cCCCC
Q 005698          139 SFPQK  143 (682)
Q Consensus       139 ~~~~~  143 (682)
                      .....
T Consensus        94 ~~~~~   98 (101)
T 1fj7_A           94 GRDGT   98 (101)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            75443

>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=99.55  E-value=2.1e-15  Score=125.07  Aligned_cols=69  Identities=22%  Similarity=0.370  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      +|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.||.++|..|.|+.|.|.+|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            69999999999999999999999999999986      3579999999999999999977999999999999875

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=1.2e-14  Score=133.91  Aligned_cols=73  Identities=26%  Similarity=0.256  Sum_probs=66.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCe-EEEEeCCHHHHHHHH-HcCCceecC--ceEEEEecccCC
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHF-AYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMAKSFP  141 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~-aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~a~~~~  141 (682)
                      .|||+||++.+|+++|.++|++||.|..|.|....|| |||+|.+.++|..|| .|||..|.|  +.|.|.||+...
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            4679999999999999999999999999999754596 999999999999999 899999988  689999998654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=9.6e-15  Score=128.51  Aligned_cols=82  Identities=27%  Similarity=0.312  Sum_probs=69.3

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ......++|||+|||+.+|+++|+++|..|+.|.-+...   ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            345568999999999999999999999998655443322   34689999999999999999 79999999999999999


Q ss_pred             ccCCCC
Q 005698          138 KSFPQK  143 (682)
Q Consensus       138 ~~~~~~  143 (682)
                      .+....
T Consensus        90 ~~~~~~   95 (102)
T 2fc8_A           90 KPKGEG   95 (102)
T ss_dssp             CCCCSS
T ss_pred             cCCCCC
Confidence            876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=2.8e-15  Score=124.84  Aligned_cols=69  Identities=22%  Similarity=0.392  Sum_probs=64.3

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ++|||+|||+.+++++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|+ ..|+|+.|.|.+|
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            479999999999999999999999999999987      24789999999999999999 677 9999999999987

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.55  E-value=1.2e-14  Score=125.69  Aligned_cols=75  Identities=21%  Similarity=0.335  Sum_probs=62.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHHHcCC--ceecCceEEEEecccC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAALALNN--MDVGGRPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al~Lng--~~l~Gr~L~V~~a~~~  140 (682)
                      .....+|||+|||+.+|+++|+++|++||.|..|.|+ .++|||||+|.+.++|+.   |+|  +.+.|+.|.|.++.+.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS---LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEEECC--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEEEcCCC
Confidence            4468899999999999999999999999999999998 579999999999999884   344  4456999999998765


Q ss_pred             C
Q 005698          141 P  141 (682)
Q Consensus       141 ~  141 (682)
                      .
T Consensus        85 ~   85 (89)
T 3d2w_A           85 H   85 (89)
T ss_dssp             -
T ss_pred             C
Confidence            3

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=1.4e-14  Score=134.31  Aligned_cols=74  Identities=27%  Similarity=0.389  Sum_probs=68.5

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCe-EEEEeCCHHHHHHHH-HcCCceecC--ceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHF-AYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~-aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~a~~~  140 (682)
                      .-.|||+||++.+|+++|.++|++||.|..|.|. ..+|| |||+|.+.++|+.|| .|||..|.|  +.|+|+|++..
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            4578899999999999999999999999999887 55788 999999999999999 899999998  89999999865

>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=99.54  E-value=7.5e-15  Score=137.52  Aligned_cols=79  Identities=23%  Similarity=0.271  Sum_probs=69.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE--------EEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE--------CTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL  132 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~--------v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L  132 (682)
                      .+.++|||+|||+.+|+++|.++|..||.|..        |.+.   ..+|||||+|.+.++|..|| .|||+.|.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            45789999999999999999999999998876        3333   57899999999999999999 799999999999


Q ss_pred             EEEecccCCCC
Q 005698          133 NVEMAKSFPQK  143 (682)
Q Consensus       133 ~V~~a~~~~~~  143 (682)
                      .|.|+......
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999865443

>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=99.54  E-value=4.9e-15  Score=132.23  Aligned_cols=77  Identities=19%  Similarity=0.155  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC---eEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGT---VVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~---V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      ......+|||+|||+.+|+++|++||..||.   |..|.|+     ..+|||||+|.+.++|+.||.|||..|+|+.|.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEV   86 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEE
Confidence            3446789999999999999999999999998   8899887     3678999999999999999999999999999999


Q ss_pred             Eeccc
Q 005698          135 EMAKS  139 (682)
Q Consensus       135 ~~a~~  139 (682)
                      .++..
T Consensus        87 ~~a~~   91 (107)
T 2lmi_A           87 YEINN   91 (107)
T ss_dssp             EECCH
T ss_pred             EECCH
Confidence            98764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=130.04  Aligned_cols=72  Identities=17%  Similarity=0.170  Sum_probs=67.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..+|||+|||+.+|+++|++||..| .|..|.|+     ..+|||||+|.+.++|+.||.|||..|+|+.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            4799999999999999999999999 89999997     368999999999999999999999999999999988753

>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=99.54  E-value=7.3e-15  Score=149.14  Aligned_cols=74  Identities=20%  Similarity=0.231  Sum_probs=68.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCC--CeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCG--TVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G--~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      ..++|||+||++.||+++|++||..||  .|+.|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567999999999999999999999999  99999997      35789999999999999999 7999999999999999


Q ss_pred             ccc
Q 005698          137 AKS  139 (682)
Q Consensus       137 a~~  139 (682)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.53  E-value=1.3e-14  Score=141.53  Aligned_cols=77  Identities=22%  Similarity=0.355  Sum_probs=71.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...++|||+|||+.+++++|++||..||.|+.|.|+     ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            446899999999999999999999999999999997     35799999999999999999 799999999999999997


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            643

>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=99.53  E-value=1.6e-14  Score=123.88  Aligned_cols=77  Identities=18%  Similarity=0.290  Sum_probs=66.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccCCCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      ..++|||+|||+.+|+++|+++|..||.|..|.|+ ..+|||||+|.+.++|+.|+.. ++.+.|+.|.|.++.+....
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCCCCCC
Confidence            47899999999999999999999999999999997 5689999999999999865432 45678999999998876543

>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=99.53  E-value=8.9e-15  Score=136.90  Aligned_cols=77  Identities=16%  Similarity=0.215  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCC---eEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGT---VVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~---V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      .....++|||+|||+.+|+++|++||..||.   |..|.|+     .++|||||+|.+.++|+.||.|||..|+|+.|.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            3445789999999999999999999999999   8888887     3578999999999999999999999999999999


Q ss_pred             Eeccc
Q 005698          135 EMAKS  139 (682)
Q Consensus       135 ~~a~~  139 (682)
                      .++..
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            98753

>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=99.52  E-value=2.9e-14  Score=142.16  Aligned_cols=75  Identities=21%  Similarity=0.246  Sum_probs=70.2

Q ss_pred             CCCEEEEeCCC-CCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLS-PLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp-~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..++|||+||| +.+|+++|.++|..||.|..|.|+ ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|++..
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP   80 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCC
Confidence            47899999999 899999999999999999999998 46799999999999999999 89999999999999998753

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.5e-14  Score=123.71  Aligned_cols=73  Identities=27%  Similarity=0.290  Sum_probs=65.1

Q ss_pred             CCE-EEEeCCCCCCCHHH----HHHHHhcC-CCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKT-LQVSNLSPLLTVEQ----LRQLFSFC-GTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~t-L~V~NLp~~vteed----L~~~F~~~-G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..| |||+|||+.+++++    |.++|.+| |+|+.|.    .|||||+|.+.++|+.|| .|||..|.|+.|.|.||+.
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            444 99999999999988    55899999 5999983    499999999999999999 8999999999999999987


Q ss_pred             CCCC
Q 005698          140 FPQK  143 (682)
Q Consensus       140 ~~~~  143 (682)
                      ....
T Consensus        84 ~sd~   87 (96)
T 2diu_A           84 NREL   87 (96)
T ss_dssp             SCCC
T ss_pred             Ccce
Confidence            6543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.26  E-value=1.4e-15  Score=137.51  Aligned_cols=80  Identities=21%  Similarity=0.333  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE--------EEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE--------CTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVG  128 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~--------v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~  128 (682)
                      ....++|||+|||+.+++++|+++|..||.|..        |.|+      ..+|||||+|.+.++|+.|| .|||..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            446789999999999999999999999999998        7775      35789999999999999999 79999999


Q ss_pred             CceEEEEecccCCCC
Q 005698          129 GRPLNVEMAKSFPQK  143 (682)
Q Consensus       129 Gr~L~V~~a~~~~~~  143 (682)
                      |+.|.|.|+......
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.51  E-value=2.9e-14  Score=134.51  Aligned_cols=94  Identities=24%  Similarity=0.370  Sum_probs=79.1

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ++|||+|||+.+|+++|.++|..||.|..|.|+     ..+|||||+|.+.++|..|| .|||..|.|+.|.|.|+....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            589999999999999999999999999999997     35689999999999999999 899999999999999998765


Q ss_pred             CCCCCCCCCccCCchhhhhH
Q 005698          142 QKPSHLNSSLAGSSLPMMMQ  161 (682)
Q Consensus       142 ~~~~~~~~~~~~~~~P~~~~  161 (682)
                      .........+...++|....
T Consensus        81 ~~~~~~~~~l~v~nl~~~~t  100 (166)
T 3md3_A           81 QSSSDDTFNLFVGDLNVNVD  100 (166)
T ss_dssp             CCCCTTCEEEEEESCCTTCC
T ss_pred             CCCCCCCceEEECCCCCCCC
Confidence            54433334455556665443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.50  E-value=1.5e-14  Score=144.35  Aligned_cols=95  Identities=22%  Similarity=0.334  Sum_probs=76.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      +.++|||+|||+.+|+++|++||.+||+|+.|.|+      ..+|||||+|.+.++|+.|| .||+..|.|+.|.|.++.
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            56899999999999999999999999999999997      25689999999999999999 899999999999999987


Q ss_pred             cCCCCCCCCCCCccCCchhhhh
Q 005698          139 SFPQKPSHLNSSLAGSSLPMMM  160 (682)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~P~~~  160 (682)
                      ............+.+.+||...
T Consensus        94 ~~~~~~~~~~~~l~v~nl~~~~  115 (213)
T 4f02_A           94 RDPSLRKSGVGNIFIKNLDKSI  115 (213)
T ss_dssp             CCTHHHHHCTTEEEEESCCTTC
T ss_pred             ccccccccccccceECCccccc
Confidence            5432221112234455555543

>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=99.50  E-value=8.8e-15  Score=137.44  Aligned_cols=78  Identities=18%  Similarity=0.195  Sum_probs=69.4

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      .....+|||+|||+.+|+++|++||..|| |+.|.|+     .++|||||+|.+.++|+.||.||+..|.|+.|.|.++.
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            34578999999999999999999999999 7789887     46899999999999999999999999999999999887


Q ss_pred             cCCC
Q 005698          139 SFPQ  142 (682)
Q Consensus       139 ~~~~  142 (682)
                      ....
T Consensus       122 ~~~~  125 (139)
T 2hgn_A          122 TTGA  125 (139)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            6543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.50  E-value=3.1e-14  Score=145.20  Aligned_cols=79  Identities=25%  Similarity=0.337  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeCCCCCC---------CHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCcee------
Q 005698           64 DALKKTLQVSNLSPLL---------TVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV------  127 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~v---------teedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l------  127 (682)
                      +...++||||||+..+         ++++|.++|.+||+|+.|.|+..+|||||+|.+.++|+.|| +|+|..|      
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~  210 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDK  210 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTST
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccc
Confidence            4567899999999998         79999999999999999999989999999999999999999 8999999      


Q ss_pred             ------cCceEEEEecccCCC
Q 005698          128 ------GGRPLNVEMAKSFPQ  142 (682)
Q Consensus       128 ------~Gr~L~V~~a~~~~~  142 (682)
                            .|+.|.|.||...+.
T Consensus       211 e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          211 EWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TGGGGGGSCCCEEEECC----
T ss_pred             cccccCCCCEEEEEEccCCCC
Confidence                  899999999986543

>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=99.49  E-value=3.6e-14  Score=131.09  Aligned_cols=74  Identities=23%  Similarity=0.240  Sum_probs=66.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeE--EEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVV--ECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~--~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ....+|||+|||+.+|+++|++||..| .|+  .|.|+     .++|||||+|.+.++|+.||.+++..|+|+.|.|.++
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            457899999999999999999999999 676  88887     3689999999999999999977889999999999887


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      ..
T Consensus       119 ~~  120 (126)
T 2hgm_A          119 SQ  120 (126)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.49  E-value=1.4e-14  Score=127.54  Aligned_cols=76  Identities=17%  Similarity=0.341  Sum_probs=69.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...++|||+|||+.+++++|.++|..||.|..|.|+.     .+|||||+|.+.++|+.||. +|..|+|+.|.|.++..
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECCc
Confidence            3468999999999999999999999999999999973     56999999999999999999 99999999999999886


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ..
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
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=99.48  E-value=2.2e-14  Score=131.96  Aligned_cols=73  Identities=15%  Similarity=0.122  Sum_probs=65.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCe----EEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTV----VECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V----~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      ...+|||+|||+.+|+++|++||..||.|    ..|.|+     .++|||||+|.+.++|+.||.+|+..|.|+.|.|..
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~~  101 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFR  101 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            46899999999999999999999999976    577776     357999999999999999996699999999999987


Q ss_pred             cc
Q 005698          137 AK  138 (682)
Q Consensus       137 a~  138 (682)
                      +.
T Consensus       102 a~  103 (123)
T 2dha_A          102 ST  103 (123)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>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=99.48  E-value=9.9e-14  Score=131.44  Aligned_cols=92  Identities=24%  Similarity=0.387  Sum_probs=76.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+.
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            468999999999999999999999999999999872      4689999999999999999 799999999999999998


Q ss_pred             cCCCCCCCCCCCccCCchhhh
Q 005698          139 SFPQKPSHLNSSLAGSSLPMM  159 (682)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~P~~  159 (682)
                      +......  ...+...++|..
T Consensus        82 ~~~~~~~--~~~l~v~nl~~~  100 (168)
T 1b7f_A           82 PGGESIK--DTNLYVTNLPRT  100 (168)
T ss_dssp             CCSSTTT--TCEEEEESCCTT
T ss_pred             CCcccCC--CCCEEEeCCCCC
Confidence            6543221  233444555544

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.48  E-value=6.5e-14  Score=139.73  Aligned_cols=74  Identities=24%  Similarity=0.401  Sum_probs=69.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...+|||+|||+.+|+++|.++|..||.|+.|.|+    ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|.|+..
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            35799999999999999999999999999999997    35799999999999999999 8999999999999999875

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.46  E-value=1.5e-13  Score=129.53  Aligned_cols=76  Identities=21%  Similarity=0.404  Sum_probs=70.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ......+|||+|||+.+|+++|.++|..||.|..|.|+      ..+|||||+|.+.++|..|| .|||..|+|+.|.|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            44567899999999999999999999999999999997      24689999999999999999 799999999999999


Q ss_pred             ecc
Q 005698          136 MAK  138 (682)
Q Consensus       136 ~a~  138 (682)
                      ||+
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            986

>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=99.45  E-value=2.2e-13  Score=128.52  Aligned_cols=92  Identities=27%  Similarity=0.480  Sum_probs=75.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+.      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57999999999999999999999999999999973      3489999999999999999 7999999999999999876


Q ss_pred             CCCCCCCCCCCccCCchhhhh
Q 005698          140 FPQKPSHLNSSLAGSSLPMMM  160 (682)
Q Consensus       140 ~~~~~~~~~~~~~~~~~P~~~  160 (682)
                      .....  ....+...++|...
T Consensus        82 ~~~~~--~~~~l~v~nl~~~~  100 (167)
T 1fxl_A           82 SSASI--RDANLYVSGLPKTM  100 (167)
T ss_dssp             CCGGG--TTCEEEEESCCTTC
T ss_pred             CcccC--CCCcEEECCCCCcC
Confidence            43221  12234445555443

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.45  E-value=2e-13  Score=134.86  Aligned_cols=78  Identities=24%  Similarity=0.449  Sum_probs=71.5

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||..+|+++|+++|..||.|..|.|+.      .+|||||+|.+.++|..|| .|||..|+|+.|.|.|+
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            3468999999999999999999999999999999972      3789999999999999999 79999999999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      ...+.
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            87643

>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=99.45  E-value=1.4e-13  Score=133.97  Aligned_cols=78  Identities=29%  Similarity=0.404  Sum_probs=70.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ....++|||+|||+.+|+++|.++|..||.|..|.|+.      .+|||||+|.+.++|+.||.++|..|.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecc
Confidence            34578999999999999999999999999999999872      468999999999999999977999999999999998


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      ....
T Consensus        90 ~~~~   93 (196)
T 1l3k_A           90 VSRE   93 (196)
T ss_dssp             CC--
T ss_pred             cCcc
Confidence            7643

>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=99.44  E-value=1.1e-13  Score=131.11  Aligned_cols=75  Identities=16%  Similarity=0.378  Sum_probs=69.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...+|||+|||+.+|+++|.++|..||.|..|.|+      .++|||||+|.+.++|..||.|+|..|+|+.|.|.|+.+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCC
Confidence            36799999999999999999999999999999987      246899999999999999999999999999999999976


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.43  E-value=2.8e-13  Score=136.65  Aligned_cols=78  Identities=31%  Similarity=0.440  Sum_probs=71.9

Q ss_pred             CCCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .....++|||+|||+ .+++++|+++|..||.|..|.|+ ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+..
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            345689999999999 99999999999999999999998 44799999999999999999 7999999999999999975


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus       110 ~  110 (229)
T 2adc_A          110 Q  110 (229)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.43  E-value=2.7e-13  Score=131.91  Aligned_cols=79  Identities=18%  Similarity=0.242  Sum_probs=68.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|..||.++|..|+|+.|.|.|+.
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecC
Confidence            346899999999999999999999999999999997      24789999999999999999778999999999999998


Q ss_pred             cCCCC
Q 005698          139 SFPQK  143 (682)
Q Consensus       139 ~~~~~  143 (682)
                      +....
T Consensus       182 ~k~~~  186 (196)
T 1l3k_A          182 SKQEM  186 (196)
T ss_dssp             -----
T ss_pred             ChhHh
Confidence            76543

>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=99.43  E-value=3.4e-13  Score=139.49  Aligned_cols=76  Identities=21%  Similarity=0.306  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecC-CCeEEEEeCCHHHHHHHH-HcCCceec-CceEEEEecc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS-KHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEMAK  138 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~-kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~V~~a~  138 (682)
                      .....++|||+|||..+|+++|+++|..||.|..|.|+.. +|||||+|.+.++|..|| .|||..|. |+.|.|.|++
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            3445789999999999999999999999999999999854 499999999999999999 79999999 9999999986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.42  E-value=3.5e-13  Score=131.27  Aligned_cols=78  Identities=24%  Similarity=0.382  Sum_probs=71.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||+.+++++|.++|..||.|..|.|..      .+|||||+|.+.++|+.|| .|||..|+|+.|.|.|+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            5678999999999999999999999999999999972      3789999999999999999 79999999999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .+...
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.42  E-value=4.1e-13  Score=138.16  Aligned_cols=77  Identities=26%  Similarity=0.353  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .....++|||+|||+.+|+++|.++|..||.|..|.|...+|||||+|.+.++|..|| .|||..|.|+.|.|.|+..
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            3455689999999999999999999999999999999988999999999999999999 7999999999999999874

>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=99.42  E-value=3e-13  Score=128.75  Aligned_cols=73  Identities=26%  Similarity=0.419  Sum_probs=68.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ....+|||+|||+.+|+++|.++|..||.|..|.|..      .+|||||+|.+.++|..|| .|||..|+|+.|.|.||
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            4478999999999999999999999999999999972      3689999999999999999 79999999999999987

>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=99.41  E-value=5.5e-13  Score=137.90  Aligned_cols=79  Identities=19%  Similarity=0.398  Sum_probs=72.0

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHH----HHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLR----QLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~----~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ...+.++|||+|||+.+|+++|+    ++|..||.|..|.|+   ..+|||||+|.+.++|+.|| .|||..|.|+.|.|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            34568999999999999999966    999999999999987   46799999999999999999 89999999999999


Q ss_pred             EecccCC
Q 005698          135 EMAKSFP  141 (682)
Q Consensus       135 ~~a~~~~  141 (682)
                      .|+....
T Consensus        85 ~~a~~~~   91 (282)
T 3pgw_A           85 QYAKTDS   91 (282)
T ss_pred             EEeccCc
Confidence            9997544

>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=99.41  E-value=5.2e-13  Score=127.14  Aligned_cols=93  Identities=25%  Similarity=0.418  Sum_probs=78.2

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC----C-------CeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFC----G-------TVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~----G-------~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      ..++|||+|||+.+|+++|.++|..|    |       .|..+.+...+|||||+|.+.++|+.||.|||..|.|+.|.|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v   82 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   82 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEECEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceeee
Confidence            36899999999999999999999999    7       888999888899999999999999999999999999999999


Q ss_pred             EecccCCCCCCCCCCCccCCchhhhh
Q 005698          135 EMAKSFPQKPSHLNSSLAGSSLPMMM  160 (682)
Q Consensus       135 ~~a~~~~~~~~~~~~~~~~~~~P~~~  160 (682)
                      .++.......  ....+...++|...
T Consensus        83 ~~~~~~~~~~--~~~~l~v~nlp~~~  106 (172)
T 2g4b_A           83 RRPHDYQPLP--GAHKLFIGGLPNYL  106 (172)
T ss_dssp             ECCSSCCCCT--TTTCEEEECCCTTC
T ss_pred             cCCcccCCCC--CCCEEEEEcCCCcC
Confidence            9877543322  23344555666544

>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=99.41  E-value=4.3e-13  Score=132.56  Aligned_cols=74  Identities=9%  Similarity=0.189  Sum_probs=67.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+.+|+++|.++|..||.|..|.|+     ..+|||||+|.+.++|+.||.+.+..|+|+.|.|.|+...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            5899999999999999999999999999999997     3579999999999999999976677999999999998754

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.40  E-value=5.7e-13  Score=129.76  Aligned_cols=75  Identities=25%  Similarity=0.494  Sum_probs=69.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC----C-------CeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFC----G-------TVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~----G-------~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      ..++|||+|||+.+|+++|.++|..|    |       .|..+.+...+|||||+|.+.++|+.||.|||..|.|+.|.|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v   82 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   82 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEE
Confidence            46899999999999999999999999    6       788888888899999999999999999999999999999999


Q ss_pred             EecccC
Q 005698          135 EMAKSF  140 (682)
Q Consensus       135 ~~a~~~  140 (682)
                      .++...
T Consensus        83 ~~~~~~   88 (198)
T 2yh0_A           83 RRPHDY   88 (198)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.40  E-value=5.4e-13  Score=131.71  Aligned_cols=74  Identities=28%  Similarity=0.477  Sum_probs=67.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            6799999999999999999999999999999996      26899999999999999999 6999999999999988764


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus       108 ~  108 (216)
T 2qfj_A          108 I  108 (216)
T ss_dssp             C
T ss_pred             c
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=99.40  E-value=4.2e-13  Score=128.48  Aligned_cols=98  Identities=20%  Similarity=0.302  Sum_probs=79.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-----EEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-----CTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~-----v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..     +.....+|||||+|.+.++|+.||.|||..|.|+.|.|.++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecC
Confidence            4556899999999999999999999999986544     22236789999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCCccCCchhhhh
Q 005698          138 KSFPQKPSHLNSSLAGSSLPMMM  160 (682)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~P~~~  160 (682)
                      .............+...++|..+
T Consensus        89 ~~~~~~~~~~~~~l~v~nlp~~~  111 (175)
T 1fje_B           89 KGRDSKKVRAARTLLAKNLSFNI  111 (175)
T ss_dssp             CCSSCSTTGGGGEEEEESCCSSC
T ss_pred             CCccccccccCCEEEEeCCCCCC
Confidence            87655444334445556666543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=3.2e-13  Score=121.77  Aligned_cols=71  Identities=15%  Similarity=0.256  Sum_probs=59.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      ...++|||+|||+.+|+++|+++|.+||.|. +.|+         ..+|||||+|.+.++|+.|| .|+  .|+|+.|.|
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            3578999999999999999999999999999 7665         23799999999999999999 773  366776666


Q ss_pred             Eecc
Q 005698          135 EMAK  138 (682)
Q Consensus       135 ~~a~  138 (682)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            5544

>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=99.40  E-value=4.5e-13  Score=128.26  Aligned_cols=77  Identities=23%  Similarity=0.300  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .....++|||+|||+.+|+++|+++|..||.|..| ..  ..+|||||+|.+.++|..|| .|||..|.|+.|.|.|+.+
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSS
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCC
Confidence            34457899999999999999999999999999888 32  57899999999999999999 7999999999999999976


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus       174 k  174 (175)
T 1fje_B          174 K  174 (175)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.5e-12  Score=117.03  Aligned_cols=79  Identities=19%  Similarity=0.256  Sum_probs=68.9

Q ss_pred             CCCCCCEEEEeCCCCCCC-----------HHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceec
Q 005698           63 ADALKKTLQVSNLSPLLT-----------VEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVG  128 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vt-----------eedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~  128 (682)
                      ...+.++|+|.||.....           +++|+++|.+||.|..|.|.  ..+|||||+|.+.++|+.|| .|||..|+
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            345688999999954332           58999999999999999776  46899999999999999999 89999999


Q ss_pred             CceEEEEecccCC
Q 005698          129 GRPLNVEMAKSFP  141 (682)
Q Consensus       129 Gr~L~V~~a~~~~  141 (682)
                      |+.|.|.|+.+..
T Consensus        91 gr~l~v~~a~~~~  103 (112)
T 2dit_A           91 GRQITAQAWDGTT  103 (112)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CcEEEEEEeCCCC
Confidence            9999999987654

>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=99.39  E-value=1.1e-12  Score=124.11  Aligned_cols=75  Identities=36%  Similarity=0.550  Sum_probs=68.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLN  133 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~  133 (682)
                      ......+|||+|||..+++++|.++|..||.|..|.|..      .+|||||+|.+.++|..|| .|||..|.|  +.|.
T Consensus        85 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~  164 (168)
T 1b7f_A           85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS  164 (168)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEE
Confidence            345678999999999999999999999999999999872      3589999999999999999 799999988  9999


Q ss_pred             EEec
Q 005698          134 VEMA  137 (682)
Q Consensus       134 V~~a  137 (682)
                      |.||
T Consensus       165 V~~A  168 (168)
T 1b7f_A          165 VRLA  168 (168)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9986

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.39  E-value=4.4e-13  Score=131.23  Aligned_cols=74  Identities=30%  Similarity=0.461  Sum_probs=69.5

Q ss_pred             CCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+ .+++++|.++|..||.|..|.|+ ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+...
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            58999999999 99999999999999999999998 44799999999999999999 79999999999999998754

>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=99.38  E-value=6.9e-13  Score=126.26  Aligned_cols=74  Identities=24%  Similarity=0.418  Sum_probs=67.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceec---CceEEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVG---GRPLNVE  135 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~---Gr~L~V~  135 (682)
                      ....+|||+|||+.+|+++|+++|..||.|..|.|+.     ++|||||+|.+.++|..|| .|||..|.   |+.|.|.
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            3578999999999999999999999999999999972     4789999999999999999 89998776   4999999


Q ss_pred             ecc
Q 005698          136 MAK  138 (682)
Q Consensus       136 ~a~  138 (682)
                      ||.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            973

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.38  E-value=1.2e-12  Score=132.00  Aligned_cols=76  Identities=36%  Similarity=0.482  Sum_probs=70.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCC-CeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceec-CceEEEEecccC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCG-TVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G-~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~V~~a~~~  140 (682)
                      .+.++|||+|||+.+++++|+++|..|| .|..|.|+ ..+|||||+|.+.++|..|| .|||..|. |+.|.|.|+++.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            3468999999999999999999999999 99999995 57899999999999999999 79999999 999999998753

>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=99.38  E-value=7.5e-13  Score=125.99  Aligned_cols=95  Identities=22%  Similarity=0.256  Sum_probs=75.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--------cCCCeEEEEeCCHHHHHHHH-HcCCceec---CceEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--------DSKHFAYIEYSKPEEATAAL-ALNNMDVG---GRPLN  133 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~---Gr~L~  133 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|+        ..+|||||+|.+.++|+.|| .|||..|.   ++.|.
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            36799999999999999999999999999999987        24689999999999999999 79998876   57888


Q ss_pred             EEecccCCCCCCCCCCCccCCchhhhhH
Q 005698          134 VEMAKSFPQKPSHLNSSLAGSSLPMMMQ  161 (682)
Q Consensus       134 V~~a~~~~~~~~~~~~~~~~~~~P~~~~  161 (682)
                      |.++........ ....+...++|....
T Consensus        82 ~~~~~~~~~~~~-~~~~l~v~nl~~~~t  108 (175)
T 3nmr_A           82 MKPADSEKNNAV-EDRKLFIGMISKKCT  108 (175)
T ss_dssp             EEECGGGCCSCG-GGSEEEEESCCTTCC
T ss_pred             EccccccccccC-CCCeEEEcCCCCcCC
Confidence            888776543321 223345556655433

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.38  E-value=1.1e-12  Score=128.49  Aligned_cols=76  Identities=36%  Similarity=0.482  Sum_probs=70.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCC-CeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceec-CceEEEEecccC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCG-TVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G-~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~V~~a~~~  140 (682)
                      .+.++|||+|||..+++++|.++|..|| .|..|.|+ ..+|||||+|.+.++|..|| .|||..|+ |+.|.|.|+++.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            4578999999999999999999999999 99999995 57899999999999999999 79999999 999999998753

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.37  E-value=1.8e-12  Score=115.72  Aligned_cols=75  Identities=20%  Similarity=0.247  Sum_probs=66.4

Q ss_pred             CCCCEEEEeCCCC-----CCCHHHHHHHHhcCCCeEEEEEec-------CCCeEEEEeCCHHHHHHHH-HcCCceecCce
Q 005698           65 ALKKTLQVSNLSP-----LLTVEQLRQLFSFCGTVVECTITD-------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRP  131 (682)
Q Consensus        65 ~~~~tL~V~NLp~-----~vteedL~~~F~~~G~V~~v~i~~-------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~  131 (682)
                      .+.++|+|.||..     .-++++|+++|++||.|..|.|+.       ++|||||+|.+.++|..|+ .|||..|+|+.
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            4578999999962     237899999999999999999972       4799999999999999999 89999999999


Q ss_pred             EEEEeccc
Q 005698          132 LNVEMAKS  139 (682)
Q Consensus       132 L~V~~a~~  139 (682)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>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=99.36  E-value=1.3e-12  Score=123.27  Aligned_cols=74  Identities=31%  Similarity=0.450  Sum_probs=66.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec------CCCeEEEEeCCHHHHHHHH-HcCCceecCce--EEE
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRP--LNV  134 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~--L~V  134 (682)
                      .....+|||+|||+.+++++|.++|..||.|..|.|..      .+|||||+|.+.++|..|| .|||..|.|+.  |.|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            34578999999999999999999999999999999872      3689999999999999999 79999999965  888


Q ss_pred             Eec
Q 005698          135 EMA  137 (682)
Q Consensus       135 ~~a  137 (682)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.35  E-value=8.8e-13  Score=121.23  Aligned_cols=73  Identities=15%  Similarity=0.149  Sum_probs=63.0

Q ss_pred             CCEEEEeCC----CCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCC----HHH----HHHHHH---cCCc
Q 005698           67 KKTLQVSNL----SPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSK----PEE----ATAALA---LNNM  125 (682)
Q Consensus        67 ~~tL~V~NL----p~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s----~e~----A~~Al~---Lng~  125 (682)
                      .+.|||+||    |+.+++++|++||..||+|..|.|+      .++|||||+|.+    .++    |..||.   |||.
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            478999999    9999999999999999999999997      468999999996    333    677763   7999


Q ss_pred             eecCceEEEEeccc
Q 005698          126 DVGGRPLNVEMAKS  139 (682)
Q Consensus       126 ~l~Gr~L~V~~a~~  139 (682)
                      .|+|+.|.|.+...
T Consensus        82 ~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           82 FIMGFKFEVILNKH   95 (136)
T ss_dssp             EETTEEEEEEECCT
T ss_pred             eecCcEEEEEECcc
Confidence            99999999997653

>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=99.33  E-value=1.6e-12  Score=123.06  Aligned_cols=73  Identities=21%  Similarity=0.341  Sum_probs=66.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|+      .++|||||+|.+.++|+.||. ++..|+|+.|.|.++..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            36799999999999999999999999999999987      356999999999999999996 36799999999998764

>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=99.31  E-value=4.5e-12  Score=131.14  Aligned_cols=72  Identities=21%  Similarity=0.319  Sum_probs=68.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|.++|..|| |..|.|...+|||||+|.+.++|..|| .|||..|.|+.|.|.|+.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            378999999999999999999999999 999999888999999999999999999 899999999999999865

>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=99.31  E-value=2.6e-12  Score=133.54  Aligned_cols=76  Identities=24%  Similarity=0.381  Sum_probs=67.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec----CCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~----~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      .+...++|||+|||+.+|+++|.+||..||.|..|.|+.    .+|||||+|.+.++|+.||.|||..|.|+.|.|.++.
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~  116 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLT  116 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEECC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEECC
Confidence            445689999999999999999999999999999999973    5799999999999999999999999999999999874

>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=99.30  E-value=2.3e-12  Score=128.46  Aligned_cols=73  Identities=15%  Similarity=0.218  Sum_probs=65.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCe--EEEEEec----CCCeEEEEeCCHHHHHHHH-HcCCceecCc----eEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTV--VECTITD----SKHFAYIEYSKPEEATAAL-ALNNMDVGGR----PLN  133 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V--~~v~i~~----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr----~L~  133 (682)
                      .+..+|||+|||+.+|+++|+++|.+||.|  ..|.|..    .+|||||+|.+.++|..|| .|||+.|.|.    +|.
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            456799999999999999999999999999  8888873    3589999999999999999 8999999985    677


Q ss_pred             EEec
Q 005698          134 VEMA  137 (682)
Q Consensus       134 V~~a  137 (682)
                      |.||
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            7765

>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=99.30  E-value=3.8e-12  Score=132.27  Aligned_cols=78  Identities=24%  Similarity=0.364  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCeEEEEEec-------CCCeEEEEeCCHHHHHHHHHcCCceecCceEEE
Q 005698           63 ADALKKTLQVSNLSPL-LTVEQLRQLFSFCGTVVECTITD-------SKHFAYIEYSKPEEATAALALNNMDVGGRPLNV  134 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~-vteedL~~~F~~~G~V~~v~i~~-------~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V  134 (682)
                      .....++|||+|||+. +|+++|.++|..||.|..|.|+.       .+|||||+|.+.++|..||.|||..|+|+.|.|
T Consensus       206 ~~~~~~~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          206 ATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISV  285 (292)
T ss_dssp             -CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             cCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEE
Confidence            3445789999999999 99999999999999999999962       368999999999999999999999999999999


Q ss_pred             EecccC
Q 005698          135 EMAKSF  140 (682)
Q Consensus       135 ~~a~~~  140 (682)
                      .|+.+.
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999864

>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=99.29  E-value=5.3e-12  Score=130.64  Aligned_cols=80  Identities=28%  Similarity=0.363  Sum_probs=72.1

Q ss_pred             CCCCCCEEEEeCCCCCC-CHHHHHHHHhcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLL-TVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~v-teedL~~~F~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+.+ |+++|.++|..||.|..|.|+.     .+|||||+|.+.++|..|| .|||..|+|+.|.|.
T Consensus       180 ~~~~~~~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          180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            34567899999999995 9999999999999999999873     4789999999999999999 799999999999999


Q ss_pred             ecccCCC
Q 005698          136 MAKSFPQ  142 (682)
Q Consensus       136 ~a~~~~~  142 (682)
                      |+.+...
T Consensus       260 ~a~~~~~  266 (284)
T 3smz_A          260 FCAPGPP  266 (284)
T ss_dssp             ECCSSSC
T ss_pred             EecCCCc
Confidence            9986543

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.27  E-value=7.3e-12  Score=134.08  Aligned_cols=76  Identities=25%  Similarity=0.406  Sum_probs=67.5

Q ss_pred             CCCCCCEEEEeC--CCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceec---Cc--eEEE
Q 005698           63 ADALKKTLQVSN--LSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVG---GR--PLNV  134 (682)
Q Consensus        63 ~~~~~~tL~V~N--Lp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~---Gr--~L~V  134 (682)
                      ...+..+|||||  |++.+|+++|+++|++||+|..|.|...+|||||+|.+.++|+.|| .|||.+|.   |+  .|.|
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~   93 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            356788999999  5789999999999999999999999888999999999999999999 89999884   44  5777


Q ss_pred             Eecc
Q 005698          135 EMAK  138 (682)
Q Consensus       135 ~~a~  138 (682)
                      .|+.
T Consensus        94 ~~~~   97 (345)
T 3tht_A           94 NFVE   97 (345)
T ss_dssp             EECS
T ss_pred             EEee
Confidence            7774

>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=99.26  E-value=6.4e-11  Score=121.72  Aligned_cols=76  Identities=29%  Similarity=0.374  Sum_probs=67.3

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcC-Cceec---CceEEEE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALN-NMDVG---GRPLNVE  135 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Ln-g~~l~---Gr~L~V~  135 (682)
                      ...+|||+|||+.+|+++|.++|..||.|..|.|+     ..+|||||+|.+.++|..|| .|| |..+.   |+.|.|.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            46899999999999999999999999999999987     24799999999999999999 784 55554   8999999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      ++....
T Consensus       175 ~~~~~~  180 (261)
T 3sde_A          175 PMEQFD  180 (261)
T ss_dssp             ECCCEE
T ss_pred             eccccC
Confidence            987643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=3.2e-11  Score=106.76  Aligned_cols=75  Identities=17%  Similarity=0.225  Sum_probs=63.4

Q ss_pred             CCEEEEeCCC-------CCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           67 KKTLQVSNLS-------PLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        67 ~~tL~V~NLp-------~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...|.|.-..       ..+|+++|+++|.+||+|..|.|+ ..+|||||+|.+.++|+.|| .+++  +.|+.|.|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            5566666443       468999999999999999999998 67899999999999999999 5544  67999999999


Q ss_pred             ccCCCC
Q 005698          138 KSFPQK  143 (682)
Q Consensus       138 ~~~~~~  143 (682)
                      ......
T Consensus        88 ~~~~~~   93 (100)
T 2d9o_A           88 EGQPQD   93 (100)
T ss_dssp             SCCCCC
T ss_pred             cCCCCC
Confidence            876543

>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=99.23  E-value=2.2e-11  Score=108.65  Aligned_cols=75  Identities=19%  Similarity=0.222  Sum_probs=65.0

Q ss_pred             CCCCEEEEeCC--CCCCC--------HHHHHHHHhcCCCeEEEEEec--------CCCeEEEEeCCHHHHHHHH-HcCCc
Q 005698           65 ALKKTLQVSNL--SPLLT--------VEQLRQLFSFCGTVVECTITD--------SKHFAYIEYSKPEEATAAL-ALNNM  125 (682)
Q Consensus        65 ~~~~tL~V~NL--p~~vt--------eedL~~~F~~~G~V~~v~i~~--------~kg~aFVeF~s~e~A~~Al-~Lng~  125 (682)
                      .+.++|+|.||  +..+.        +++|+++|++||.|..|.|+.        .+|||||+|.+.++|..|| .|||.
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            35789999998  33332        379999999999999999972        4799999999999999999 89999


Q ss_pred             eecCceEEEEeccc
Q 005698          126 DVGGRPLNVEMAKS  139 (682)
Q Consensus       126 ~l~Gr~L~V~~a~~  139 (682)
                      .|+|+.|.|.++..
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            99999999998754

>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=99.19  E-value=6.7e-12  Score=111.80  Aligned_cols=67  Identities=22%  Similarity=0.420  Sum_probs=58.7

Q ss_pred             EEeCCCCCCCHHHHHHHH------------hcCCCeEEEEEec-----CCCeEEEEeCCHHHHHHHH-HcCCceecCceE
Q 005698           71 QVSNLSPLLTVEQLRQLF------------SFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL  132 (682)
Q Consensus        71 ~V~NLp~~vteedL~~~F------------~~~G~V~~v~i~~-----~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L  132 (682)
                      ++.||+..+++++|+++|            ++||.|..|.|+.     ++|||||+|.+.++|+.|+ .|||..|+|+.|
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            367788888888877766            9999999999982     4799999999999999999 899999999999


Q ss_pred             EEEec
Q 005698          133 NVEMA  137 (682)
Q Consensus       133 ~V~~a  137 (682)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.15  E-value=7.4e-11  Score=107.57  Aligned_cols=74  Identities=19%  Similarity=0.167  Sum_probs=64.1

Q ss_pred             CCCEEEEeCCCC--C---CCHHHHHHHHhcCCCeEEEEEec----------CCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           66 LKKTLQVSNLSP--L---LTVEQLRQLFSFCGTVVECTITD----------SKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        66 ~~~tL~V~NLp~--~---vteedL~~~F~~~G~V~~v~i~~----------~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      +.++|+|.||-.  .   --++||+++|++||.|..|.|+.          .+|||||+|.+.++|..|| .|||..|+|
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            378999999942  2   23689999999999999999972          2389999999999999999 899999999


Q ss_pred             ceEEEEeccc
Q 005698          130 RPLNVEMAKS  139 (682)
Q Consensus       130 r~L~V~~a~~  139 (682)
                      +.|.|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.15  E-value=1.1e-10  Score=105.68  Aligned_cols=74  Identities=18%  Similarity=0.201  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCCCCCC----------HHHHHHHHhcCCCeEEEEEec--CCCeEEEEeCCHHHHHHHH-HcCCceecCceE
Q 005698           66 LKKTLQVSNLSPLLT----------VEQLRQLFSFCGTVVECTITD--SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL  132 (682)
Q Consensus        66 ~~~tL~V~NLp~~vt----------eedL~~~F~~~G~V~~v~i~~--~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L  132 (682)
                      +.++|+|.||-....          ++||+++|++||.|..|.|..  .+|||||+|.+.++|+.|| .|||..|+|+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            577899999843221          258899999999999999973  4799999999999999999 899999999999


Q ss_pred             EEEeccc
Q 005698          133 NVEMAKS  139 (682)
Q Consensus       133 ~V~~a~~  139 (682)
                      .|.|+..
T Consensus        86 ~v~~~~~   92 (114)
T 3s6e_A           86 TAAYVPL   92 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEEEcH
Confidence            9999863

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.09  E-value=3e-10  Score=103.79  Aligned_cols=76  Identities=18%  Similarity=0.179  Sum_probs=68.0

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCC-HHHHHHHH-HcC--CceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPL-LTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSK-PEEATAAL-ALN--NMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~-vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s-~e~A~~Al-~Ln--g~~l~Gr~L~V~~a~  138 (682)
                      -..+..|||+||+.. +++++|+++|..||+|.+|.|.....+|||.|.+ ..+|..|| .||  |..|+|..+.|++..
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            346889999999999 9999999999999999999999777799999999 89999999 784  789999988887655


Q ss_pred             c
Q 005698          139 S  139 (682)
Q Consensus       139 ~  139 (682)
                      .
T Consensus        95 G   95 (121)
T 1owx_A           95 G   95 (121)
T ss_dssp             H
T ss_pred             C
Confidence            3

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=1.2e-09  Score=94.25  Aligned_cols=74  Identities=19%  Similarity=0.218  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCCC----CCCH----HHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           66 LKKTLQVSNLSP----LLTV----EQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        66 ~~~tL~V~NLp~----~vte----edL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      +.-||+|..++.    .+..    .+|.+.|.+||+|+.|+|.  .+.+||+|.+.++|.+||.|||+.|+|+.|+|.++
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~--~d~~fVtF~d~~sAlaAi~mnG~~v~Gr~LkV~lk   83 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFV--EDKMWVTFLEGSSALNVLSLNGKELLNRTITIALK   83 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEEC--SSSEEEEESSHHHHHHGGGGTTCEETTEEEEEEEC
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEe--cCCEEEEECChHHHHHHHhcCCeEeCCeEEEEEeC
Confidence            456888887662    2323    6799999999999999998  45699999999999999999999999999999998


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      .+..
T Consensus        84 t~dW   87 (91)
T 2dnr_A           84 SPSG   87 (91)
T ss_dssp             CCSS
T ss_pred             CCCc
Confidence            8643

>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=98.69  E-value=1.4e-08  Score=88.11  Aligned_cols=72  Identities=24%  Similarity=0.353  Sum_probs=60.5

Q ss_pred             CCCCEEEEeCCCCC------CCH---HHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEE
Q 005698           65 ALKKTLQVSNLSPL------LTV---EQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVE  135 (682)
Q Consensus        65 ~~~~tL~V~NLp~~------vte---edL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~  135 (682)
                      ++.-||+|..++..      ..+   .+|.+.|.+||+|+.|+|..  .-+||+|.+.++|.+||.|||+.|+|+.|+|.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~--d~~fVtF~d~~sAl~AI~ldG~~v~Gr~L~V~   90 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ--GQMLVTFADSHSALSVLDVDGMKVKGRAVKIS   90 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET--TEEEEECSCSHHHHHHHHGGGSEETTEEEEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEec--CcEEEEEcChHHHHHHHhcCCeeeCCeEEEEe
Confidence            34679999888632      232   56999999999999999983  33999999999999999999999999999998


Q ss_pred             ecc
Q 005698          136 MAK  138 (682)
Q Consensus       136 ~a~  138 (682)
                      +-.
T Consensus        91 ~k~   93 (95)
T 1ufw_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            643

>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=98.50  E-value=2.7e-07  Score=92.20  Aligned_cols=72  Identities=19%  Similarity=0.193  Sum_probs=60.2

Q ss_pred             CEEEEeCCC-----CCCCHHHHHHHHhcCCCeEEEEEe----------cCCCeEEEEeCCHHHHHHHH-HcCCceecCce
Q 005698           68 KTLQVSNLS-----PLLTVEQLRQLFSFCGTVVECTIT----------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRP  131 (682)
Q Consensus        68 ~tL~V~NLp-----~~vteedL~~~F~~~G~V~~v~i~----------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~  131 (682)
                      ..|.+.|+-     ..-.+++|.+.|.+||.|..|.|+          ..+||+||+|.+.++|..|| .|||..|+|+.
T Consensus       125 ~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~  204 (222)
T 3dxb_A          125 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK  204 (222)
T ss_dssp             SEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB
T ss_pred             ccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeE
Confidence            445555543     234568999999999999999996          35689999999999999999 89999999999


Q ss_pred             EEEEeccc
Q 005698          132 LNVEMAKS  139 (682)
Q Consensus       132 L~V~~a~~  139 (682)
                      |.|.++..
T Consensus       205 i~~~~~~~  212 (222)
T 3dxb_A          205 VVAEVYDQ  212 (222)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99998753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.46  E-value=4.3e-07  Score=80.47  Aligned_cols=71  Identities=15%  Similarity=0.137  Sum_probs=66.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-----CCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFC-----GTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~-----G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      +..++|-|-|||..|+...|..|+..|     |.|+.|.|...-+-|+|+|.+...|.+|. +|||.+|.|+.|+|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            347899999999999999999999999     99999999977888999999999999999 999999999999995

>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=98.20  E-value=5.1e-06  Score=73.26  Aligned_cols=78  Identities=15%  Similarity=0.140  Sum_probs=67.0

Q ss_pred             CCCEEEEeCCCCCC-C----HHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLL-T----VEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~v-t----eedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..++|+|+||+..| .    .+.|+++|..|+++....+..+-.=..|.|.+.++|..|- .|+++.|.|..|+|.++.+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            57899999998755 2    2578999999999998888876667899999999999999 8999999999999999986


Q ss_pred             CCCC
Q 005698          140 FPQK  143 (682)
Q Consensus       140 ~~~~  143 (682)
                      ....
T Consensus        84 ~~~~   87 (104)
T 1wey_A           84 LHIG   87 (104)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            5443

>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=97.73  E-value=8e-06  Score=90.26  Aligned_cols=37  Identities=16%  Similarity=0.248  Sum_probs=23.8

Q ss_pred             HHHHHhcCCCeEEEEEe--------cCCCeE-----EEEeCCHHHHHHHH
Q 005698           84 LRQLFSFCGTVVECTIT--------DSKHFA-----YIEYSKPEEATAAL  120 (682)
Q Consensus        84 L~~~F~~~G~V~~v~i~--------~~kg~a-----FVeF~s~e~A~~Al  120 (682)
                      |..||.+||.|..|..+        ...+|+     ||+|....++..++
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~   58 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPT   58 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccc
Confidence            67899999998887322        123344     77787765555444

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.72  E-value=0.00047  Score=60.57  Aligned_cols=74  Identities=20%  Similarity=0.257  Sum_probs=64.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-----CCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFC-----GTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~-----G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...++|.|.|||+.+.++.|.-||+.-     |+|..|....  +-|+|+|.+.+.|+..|.-..+.|+|..|.|....+
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEECCC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCCcceecCeEEEEEcCCC
Confidence            357899999999999999999999972     6899998874  889999999999999987778899999999976554


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus        84 ~   84 (104)
T 2dhx_A           84 R   84 (104)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.55  E-value=0.0003  Score=63.62  Aligned_cols=72  Identities=14%  Similarity=0.170  Sum_probs=62.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecC-ceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGG-RPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~G-r~L~V~~a~  138 (682)
                      ...-|.|-++|+.. ...|..+|.+||+|+........++-.|.|.+..+|++||..||..|+| -.|-|.++.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEECC
Confidence            46789999999875 5778899999999999988767899999999999999999999999985 667776653

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.09  E-value=0.0019  Score=55.83  Aligned_cols=62  Identities=18%  Similarity=0.146  Sum_probs=52.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec--------CCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD--------SKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~--------~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      ++|.|.+||+.+||+++.+.++.++.+.....+.        .-.-|||.|.+.+++..-. .++|+.|.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            5799999999999999999999999887766651        2246999999999998888 899998865

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.07  E-value=0.00043  Score=63.43  Aligned_cols=71  Identities=23%  Similarity=0.286  Sum_probs=57.0

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-EEEe-------------------cCCCeEEEEeCCHHHHHHHHHcCCce
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTIT-------------------DSKHFAYIEYSKPEEATAALALNNMD  126 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~-v~i~-------------------~~kg~aFVeF~s~e~A~~Al~Lng~~  126 (682)
                      ..-|.|-++|+..+ ..|.++|++||.|++ +.+.                   ...++..|+|.+..+|..||..||..
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            56788889987665 557789999999977 2111                   14678899999999999999999999


Q ss_pred             ecCceEEEEecc
Q 005698          127 VGGRPLNVEMAK  138 (682)
Q Consensus       127 l~Gr~L~V~~a~  138 (682)
                      |+|..|-|.++.
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988888764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.34  E-value=0.015  Score=50.60  Aligned_cols=53  Identities=26%  Similarity=0.397  Sum_probs=43.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL  122 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L  122 (682)
                      ...|+| ++|..+.-.||.++|..||.|. |.+++ -.-|||.|.+.+.|..|| .+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~Wid-DTsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWID-DTSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEE-TTEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEc-CCeEEEEecCHHHHHHHHHhc
Confidence            456666 9999999999999999999543 44442 467999999999999999 55

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.19  E-value=0.0076  Score=52.46  Aligned_cols=72  Identities=21%  Similarity=0.194  Sum_probs=53.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--------cCCCeEEEEeCCHHHHHHHH-HcCCceecCc-----eE
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGR-----PL  132 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr-----~L  132 (682)
                      .-.|.|..||+.+||+++.+.+..+-++.....+        ..-.-|||.|.+.+++..-. .++|..|.+.     ..
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            4579999999999999988888776555433332        12246899999999999888 8999988653     34


Q ss_pred             EEEecc
Q 005698          133 NVEMAK  138 (682)
Q Consensus       133 ~V~~a~  138 (682)
                      .|++|.
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            556554

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=95.89  E-value=0.0082  Score=52.32  Aligned_cols=52  Identities=27%  Similarity=0.424  Sum_probs=42.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN  123 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln  123 (682)
                      .|+| ++|+.+.-.||.++|..||. ..|.+++ -.-|||.|.+.+.|..|| .+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~Wid-DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWID-DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEE-TTEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEc-CCeEEEEecCHHHHHHHHHhcc
Confidence            4556 99999999999999999993 3444442 467999999999999999 554

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.55  E-value=0.0055  Score=67.78  Aligned_cols=61  Identities=11%  Similarity=0.173  Sum_probs=45.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCC-CeEEEEeCCHHHHHHHHHcCCceec
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK-HFAYIEYSKPEEATAALALNNMDVG  128 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~k-g~aFVeF~s~e~A~~Al~Lng~~l~  128 (682)
                      .+.|||. ++..+++.+|.++|.+||.|..+.+...+ .||+|||.+.+++..++...++.+.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~~~~p~~  114 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTHTPXX  114 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSSCCCCCC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhccCCCcc
Confidence            5799997 79999999999999999999999998544 5999999999999877744343333

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=93.37  E-value=0.033  Score=51.48  Aligned_cols=38  Identities=18%  Similarity=0.119  Sum_probs=35.0

Q ss_pred             cCCCeEEEEeCCHHHHHHHH-Hc-CCceecCceEEEEeccc
Q 005698          101 DSKHFAYIEYSKPEEATAAL-AL-NNMDVGGRPLNVEMAKS  139 (682)
Q Consensus       101 ~~kg~aFVeF~s~e~A~~Al-~L-ng~~l~Gr~L~V~~a~~  139 (682)
                      ..+|++||+|.+.++|+.|| .| ||..|+| .|.|.++..
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            56899999999999999999 89 9999999 999998865

>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=92.19  E-value=0.089  Score=48.75  Aligned_cols=25  Identities=16%  Similarity=-0.007  Sum_probs=21.8

Q ss_pred             cCCCeEEEEeCCHHHHHHHH-HcCCc
Q 005698          101 DSKHFAYIEYSKPEEATAAL-ALNNM  125 (682)
Q Consensus       101 ~~kg~aFVeF~s~e~A~~Al-~Lng~  125 (682)
                      ..+|||||+|.+.++|+.|| .+++.
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhccc
Confidence            46899999999999999999 67653

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=82.65  E-value=2.1  Score=34.70  Aligned_cols=67  Identities=18%  Similarity=0.220  Sum_probs=44.1

Q ss_pred             EEEEeC-CCCCCCHHHHHHHHhcCC-----CeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           69 TLQVSN-LSPLLTVEQLRQLFSFCG-----TVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        69 tL~V~N-Lp~~vteedL~~~F~~~G-----~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      +|||.. --..+..-+|..+|..-+     .|-.|.|.  ..|.||+.... .+..++ .|++..+.|+.|.|..+.
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~--d~~s~v~v~~~-~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIM--DNASYVEILNG-KGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEEC--SSCEEEEECTT-CHHHHHHHHTTCCC---CCCEEECC
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEe--CCcEEEEECHH-HHHHHHHHhccccCcCceEEEEECC
Confidence            567742 135778888888888655     45667776  67999998754 467777 899999999999998654

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=80.74  E-value=2.6  Score=47.00  Aligned_cols=54  Identities=24%  Similarity=0.394  Sum_probs=43.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN  123 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Ln  123 (682)
                      ...|+|+ +|..+...+|.++|..||.| .|.++ ....|||.|.+.+.|..+| +++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSSEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCCeEEEEECCHHHHHHHHHHHH
Confidence            3466666 99899999999999999954 45444 3567999999999999999 664

---

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	682
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	5e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-11
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	7e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-08
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-08
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	7e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	9e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	9e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	1e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	7e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	9e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.001
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002

>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 = 65.3 bits (159), Expect = 5e-14
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTI-----TDSKHFAYIEYSKPEEATAAL-ALN 123
           L VSNL   ++   +++LF+  GT+ +  +       S   A + + +  +A  A+   N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 124 NMDVGGRPLNVEMAKS 139
            + + GRP+N+++  S
Sbjct: 63  GVPLDGRPMNIQLVTS 78

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEEATAALALNNM 125
           +  LS   T E LR+ F   G V EC +           F ++ +         LA +  
Sbjct: 5   IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRH 64

Query: 126 DVGGRPLNVEMA 137
           ++  + ++ ++A
Sbjct: 65  ELDSKTIDPKVA 76

>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 = 63.0 bits (153), Expect = 4e-13
 Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 10/84 (11%)

Query: 64  DALKKT-LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEA 116
           +++K T L V+NL   +T +QL  +F   G++V+  I         +  A++ Y+K EEA
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 117 TAAL-ALNNMDV--GGRPLNVEMA 137
             A+ ALNN+    G +PL+V +A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 1e-12
 Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL- 120
           ++     T+    ++  LT + +RQ FS  G ++E  +   K ++++ +S  E A  A+ 
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV 72

Query: 121 ALNNMDVGGRPLNVEMAKSFP 141
           ++N   + G  +     K  P
Sbjct: 73  SVNGTTIEGHVVKCYWGKESP 93

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKHFAYIEYSKPEEATAAL-A 121
           +L V +L P +T   L + FS  G ++   +        S  +AY+ + +P +A  AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 122 LNNMDVGGRPLNVEMAK 138
           +N   + G+P+ +  ++
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 11/84 (13%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITD---------SKHFAYIEYSKPEEATAAL-A 121
           + NL+   T E L+ +FS  G +  CTI+          S  F ++EY KPE+A  AL  
Sbjct: 3   IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 62

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
           L    V G  L V +++    KP+
Sbjct: 63  LQGHTVDGHKLEVRISER-ATKPA 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.1 bits (148), Expect = 2e-12
 Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           +  L V NL P +T E++R+LF   G   E  I   K F +I       A  A   L+NM
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 67

Query: 126 DVGGRPLNVEMAKS 139
            + G+ L V  A  
Sbjct: 68  PLRGKQLRVRFACH 81

>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 = 60.0 bits (145), Expect = 5e-12
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-A 121
            L V+ L   +T  +L  LF   G +  C I        S  +A+++++   ++  A+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 122 LNNMDVGGRPLNVEMAK 138
           LN + V  + L V  A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>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 = 59.7 bits (144), Expect = 6e-12
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALA 121
           + L +  LS   T E LR  F   GT+ +C +        S+ F ++ Y+  EE  AA+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 122 LNNMDVGGRPLNVEMAKS 139
                V GR +  + A S
Sbjct: 67  ARPHKVDGRVVEPKRAVS 84

>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 = 59.2 bits (143), Expect = 1e-11
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK------HFAYIEYSKPEEATAAL- 120
            TL V NLS   T EQ+ +LFS  G + +  +   K       F ++EY    +A  A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 121 ALNNMDVGGRPLNVEMAKSF 140
            +N   +  R +  +    F
Sbjct: 68  YINGTRLDDRIIRTDWDAGF 87

>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 = 58.4 bits (141), Expect = 1e-11
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALALNNM 125
           V  LSP    E++R+ F   G V    +         + F +I + + E     +     
Sbjct: 4   VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 63

Query: 126 DVGGRPLNVEMA 137
           +VG     +++A
Sbjct: 64  NVGLSKCEIKVA 75

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (143), Expect = 1e-11
 Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 6/95 (6%)

Query: 55  GSPDKAGKAD--ALKKTLQVSNLSPLLTVEQ-LRQLFSFCGTVVECTITDSKHFAYIEYS 111
           GS   +GK D  ++   + + NL+ L+  +  +  +FS  G +V C++     FA+++Y 
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--GFAFVQYV 58

Query: 112 KPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
               A AA+   +   + G+ L++ +A       S
Sbjct: 59  NERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 58.2 bits (140), Expect = 2e-11
 Identities = 11/72 (15%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNM 125
           V  LS   TVE ++  F   G V +  +         + F ++ +   +       ++  
Sbjct: 4   VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFH 63

Query: 126 DVGGRPLNVEMA 137
           ++  + +  + A
Sbjct: 64  EINNKMVECKKA 75

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMD 126
           K L V NL    + E + + F+         +   + +A++ +S  E+A  A+ ALN   
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 127 VGGRPLNVEMAKSFPQ 142
           + G P+ V +AK   +
Sbjct: 69  LDGSPIEVTLAKPVDK 84

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 9/85 (10%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL 120
           K+ L V  L+  +  + L   F   G + +  I         + FA++E+   E+A AA+
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 121 -ALNNMDVGGRPLNVEMAKSFPQKP 144
             +N  ++ GR + V +AK  P + 
Sbjct: 65  DNMNESELFGRTIRVNLAK--PMRI 87

>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 = 58.5 bits (141), Expect = 4e-11
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD---SKHFAYIEYSKPEEATAAL-ALN 123
           + L + NL   +T E++  +F   G + +  + +   ++  AY+ Y    +A  A   L+
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 124 NMDVGGRPLNVEMAKS 139
             +V  R L V    +
Sbjct: 68  GFNVCNRYLVVLYYNA 83

>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 = 57.3 bits (138), Expect = 4e-11
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALALNNM 125
           +  LS   T + L+  FS  G VV+CT+        S+ F ++ + + E     +     
Sbjct: 4   IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEH 63

Query: 126 DVGGRPLNVEMA 137
            + G+ ++ + A
Sbjct: 64  KLNGKVIDPKRA 75

>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 = 57.3 bits (138), Expect = 6e-11
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-------DSKHFAYIEYSKPEEATAA 119
              + V N+       ++R+LFS  G +    +          + F ++++   ++A  A
Sbjct: 8   TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 120 LA--LNNMDVGGRPLNVEMAKS 139
                ++  + GR L +E A S
Sbjct: 68  FNALCHSTHLYGRRLVLEWADS 89

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 9e-11
 Identities = 9/84 (10%), Positives = 26/84 (30%), Gaps = 5/84 (5%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEA 116
           K D   +++ +       T++ +++     G V+   +        K   ++ +   E A
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 117 TAALALNNMDVGGRPLNVEMAKSF 140
              +           L +     +
Sbjct: 61  KKFVETPGQKYKETDLLILFKDDY 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 1e-10
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL 120
           K  L V+ L   +T E+ R LF   G +  C +        S  + ++ Y  P++A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 121 -ALNNMDVGGRPLNVEMAK 138
             LN + +  + + V  A+
Sbjct: 62  NTLNGLRLQTKTIKVSYAR 80

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL- 120
             L V  LS   T   LR++FS  G + + +I        S+ FA++ +   ++A  A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 121 ALNNMDVGGRPLNV 134
             N M++ GR + V
Sbjct: 70  RANGMELDGRRIRV 83

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMD 126
            TL V      +T   LR  FS  G +++ ++   ++ A++ Y K E A  A+  LN   
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 127 VGGRPLNVEMAKSFP 141
           V    L V +A+  P
Sbjct: 64  VESVQLKVNIARKQP 78

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.2 bits (132), Expect = 2e-10
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-A 121
           TL ++N  P  T   +R L      V             S+ FAYI+ +  E+A   +  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 122 LNNMDVGGRPLNVEMAK 138
           LN + + G  L  +++ 
Sbjct: 63  LNGLKIEGYTLVTKVSN 79

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS---KHFAYIEY 110
           SG     G A      + V NL P +  + +  +F   G + +  + +      FA++E+
Sbjct: 1   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 60

Query: 111 SKPEEATAAL-ALNNMDVGGRPLNVEMAKS 139
             P +A  A+   +  D  G  L VE  +S
Sbjct: 61  EDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 90

>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 = 54.5 bits (130), Expect = 3e-10
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS----KHFAYIEYSKPEEATAALALNN 124
           T+ V NL       ++ + F  CG ++   + DS      FA IE+++ + A AA+   +
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 61

Query: 125 MDVGGRPLNVEMA 137
             VG   + V   
Sbjct: 62  KVVGQNEIIVSHL 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 = 55.1 bits (132), Expect = 4e-10
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALA 121
           + L +  LS   T E LR  +   G + +C +        S+ F ++ +S   E  AA+A
Sbjct: 21  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 80

Query: 122 LNNMDVGGRPLNVEMAKS 139
                + GR +  + A +
Sbjct: 81  ARPHSIDGRVVEPKRAVA 98

>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 = 54.7 bits (131), Expect = 4e-10
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-A 121
            L V+++      +++++ F   G +    +        SK +A +EY   ++A AA  A
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 122 LNNMDVGGRPLNVEMAKS 139
           LN  ++ G+ + V+    
Sbjct: 69  LNGAEIMGQTIQVDWCFV 86

>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 = 54.7 bits (131), Expect = 4e-10
 Identities = 14/86 (16%), Positives = 30/86 (34%), Gaps = 11/86 (12%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI--------TDSKHFAYIEYSKPEEATAA- 119
            L +  +  +   E++ +  +     V   I          ++ FA++EY     A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 120 --LALNNMDVGGRPLNVEMAKSFPQK 143
             L    + + G  + V+ A+     
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDV 88

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.7 bits (131), Expect = 5e-10
 Identities = 30/92 (32%), Positives = 40/92 (43%), Gaps = 4/92 (4%)

Query: 54  SGSPDKAGKADAL-KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSK 112
           SGS  K G   A     L V  L P  ++  L + F   G++          FAYI+Y  
Sbjct: 3   SGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYES 62

Query: 113 PEEATAAL-ALNNMDVGG--RPLNVEMAKSFP 141
            + A AA   +    +GG  R L V+ AKS P
Sbjct: 63  LDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP 94

>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 = 54.6 bits (131), Expect = 5e-10
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-A 121
           T+ V  L   ++   L +LF   G VV   +         + + ++E+   E+A  A+  
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 122 LNNMDVGGRPLNVEMAKS 139
           ++ + + G+P+ V  A +
Sbjct: 71  MDMIKLYGKPIRVNKASA 88

>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 = 54.4 bits (130), Expect = 5e-10
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 11/88 (12%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----------SKHFAYIEYSKPEEA 116
           + L V N+   +T E +   F+    +   T               K+FA++E+   +E 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 117 TAALALNNMDVGGRPLNVEMAKSFPQKP 144
           T A+A + +   G+ L +     +   P
Sbjct: 62  TQAMAFDGIIFQGQSLKIRRPHDYQPLP 89

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 5e-10
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALA 121
            T  + NL   +T E +++ F            +       K F Y E+   +   +AL+
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPS 145
           LN   +G + + V++A     K S
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDS 99

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 6e-10
 Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 58  DKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYS 111
           D     +   +T+    L+  +    L   FS  G V +  I        SK  AY+E+ 
Sbjct: 9   DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 68

Query: 112 KPEEATAALALNNMDVGGRPLNVEMAKS 139
           + +    A+ L    + G P+ V+ +++
Sbjct: 69  EIQSVPLAIGLTGQRLLGVPIIVQASQA 96

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.0 bits (129), Expect = 7e-10
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 68  KTLQVSNLSPLLTVEQ-LRQLFSFCGTVVECTITD-------SKHFAYIEYSKPEEATAA 119
           + + + NLS  L  E  LR+ F   G++ +  I         +   A++ +   + A  A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 120 LALNNMDVGGRPLNVEMAKSFP 141
           L +N   +G R ++V +A   P
Sbjct: 65  LQMNRSLLGNREISVSLADKKP 86

>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 = 54.9 bits (131), Expect = 1e-09
 Identities = 32/149 (21%), Positives = 58/149 (38%), Gaps = 20/149 (13%)

Query: 13  LSQVPMAPSAAAMAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQV 72
           +SQ+P+         +Q     Q  Q    Q Q QQ       +P+       + + L V
Sbjct: 1   MSQIPLV--------SQYDPYGQTAQLQQLQQQQQQHIPPTQMNPE-----PDVLRNLMV 47

Query: 73  SNLSPLLTVEQLRQLFSF------CGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           + +   +   QLRQLF           V +     S+ + ++++     A  A+  LN  
Sbjct: 48  NYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107

Query: 126 DVGGRPLNVEMAKSFPQKPSHLNSSLAGS 154
           ++  + L V +A S  Q+P    +   G+
Sbjct: 108 NILNKRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 53.5 bits (128), Expect = 1e-09
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNM 125
           +TL   NLS  +T ++L+++F     +   +    SK  AYIE+    +A   L      
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 76

Query: 126 DVGGRPLNVEMAKS 139
           ++ GR +++     
Sbjct: 77  EIDGRSVSLYYTGE 90

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFS-FCGTVVECTITD-----SKHFAYIEYSKPEEATAALA 121
           K + V  +        LR  F  +    V   +TD      + FA++ +   +     + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 122 LNNMDVGGRPLNVEMA 137
                V G    V  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (132), Expect = 2e-09
 Identities = 21/127 (16%), Positives = 39/127 (30%), Gaps = 6/127 (4%)

Query: 25  MAAAQAIVAAQALQAHAAQVQAQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQL 84
            A  + + AA   + H    +  +  + +S    +   A    K + V  +        L
Sbjct: 55  YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 114

Query: 85  RQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK 138
           R  F   G +    I         + FA++ +   +     +      V G    V  A 
Sbjct: 115 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL 174

Query: 139 SFPQKPS 145
           S  +  S
Sbjct: 175 SKQEMAS 181

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.2 bits (90), Expect = 6e-04
 Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 6/85 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALA 121
           + L +  LS   T E LR  F   GT+ +C +        S+ F ++ Y+  EE  AA+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 122 LNNMDVGGRPLNVEMAKSFPQKPSH 146
                V GR +  + A S       
Sbjct: 67  ARPHKVDGRVVEPKRAVSREDSQRP 91

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI-------TDSKHFAYIEYSKPEEATAAL-ALN 123
           + NL P +  + L   FS  G +++           +SK +A+I ++  + + AA+ A+N
Sbjct: 3   IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 62

Query: 124 NMDVGGRPLNVEMAKSFPQK 143
              +  RP+ V  A     K
Sbjct: 63  GQYLCNRPITVSYAFKKDSK 82

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK----HFAYIEYSKPEEATAAL-AL 122
           +TL V NLS  +T   + QLFS  G    C +         + ++E+ +  +A AAL A+
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 123 NNMDVGGRPLNVEMAKSFPQK 143
           N   + G+ + V  A +   +
Sbjct: 69  NGRKILGKEVKVNWATTPSSQ 89

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 3e-09
 Identities = 18/95 (18%), Positives = 29/95 (30%), Gaps = 6/95 (6%)

Query: 69  TLQVSNLSPLL-----TVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL 122
            L     +  +     T  +   LF             S     I +S P  A  A   L
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRL 66

Query: 123 NNMDVGGRPLNVEMAKSFPQKPSHLNSSLAGSSLP 157
           +  +  G+ + +  A++     SHL       S P
Sbjct: 67  HKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGP 101

>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 = 52.0 bits (124), Expect = 3e-09
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAAL-ALN 123
            + + NL   +  + L   FS  G ++ C +      SK + ++ +   E A  A+  +N
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 69

Query: 124 NMDVGGRPLNVEMAKS 139
            M +  R + V   KS
Sbjct: 70  GMLLNDRKVFVGRFKS 85

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 14/79 (17%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVEC-TITDSKHFAYIEYSKPEEATAALALNNMD 126
             + V   +  +T ++LR+ FS  G V++       + FA++ ++  + A +     ++ 
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG-EDLI 64

Query: 127 VGGRPLNVEMAKSFPQKPS 145
           + G  +++  A+      S
Sbjct: 65  IKGISVHISNAEPKHNSNS 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 5e-09
 Identities = 15/81 (18%), Positives = 41/81 (50%), Gaps = 8/81 (9%)

Query: 67  KKTLQVSNLSPLLTVEQLRQ----LFSFCGTVVECTI---TDSKHFAYIEYSKPEEATAA 119
             T+ ++NL+  +  ++L++    +FS  G +++  +      +  A++ + +   AT A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 120 L-ALNNMDVGGRPLNVEMAKS 139
           L ++       +P+ ++ AK+
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKT 83

>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 = 51.3 bits (122), Expect = 8e-09
 Identities = 22/98 (22%), Positives = 35/98 (35%), Gaps = 7/98 (7%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEE 115
           + D     + V  L    T   LR+ F   G + E  +        S+ + ++  +    
Sbjct: 5   QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 64

Query: 116 ATAALALNNMDVGGRPLNVEMAKSFPQKPSHLNSSLAG 153
           A  A    N  + GR  NV +A     KP  L +  A 
Sbjct: 65  AERACKDPNPIIDGRKANVNLAYL-GAKPRSLQTGFAI 101

>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 = 50.8 bits (121), Expect = 1e-08
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL- 120
            T++V+NLS       L++LF   G++    +        SK FA+I + + E+A  A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 121 ALNNMDVGGRPLNVEMAK 138
            ++        LNVE AK
Sbjct: 69  GVSGFGYDHLILNVEWAK 86

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKHFAYIEYSKPEEAT 117
           ++ +  K L VSN+        LRQ+F   G +++  I      SK F ++ +    +A 
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADAD 65

Query: 118 AAL-ALNNMDVGGRPLNVEMAKSFPQ 142
            A   L+   V GR + V  A +   
Sbjct: 66  RAREKLHGTVVEGRKIEVNNATARVM 91

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-AL 122
           L +  L   L  +Q+++L +  G +    +        SK +A+ EY        A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 123 NNMDVGGRPLNVEMAKS 139
           N M +G + L V+ A  
Sbjct: 64  NGMQLGDKKLLVQRASV 80

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-A 121
            L VS L   +T ++L QLFS  G ++   I        S+   +I + K  EA  A+  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 122 LNNMDVGGR--PLNVEMA 137
           LN     G   P+ V+ A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>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 = 49.6 bits (118), Expect = 2e-08
 Identities = 9/61 (14%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRP 131
           V           +   F+  G +++  ++++ ++ +I Y    +A  AL+ +    G   
Sbjct: 9   VFGFPQASA-SYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESI 67

Query: 132 L 132
           +
Sbjct: 68  M 68

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 3e-08
 Identities = 28/76 (36%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVE--CTITDSKHFAYIEYSKPEEATAALA-LNN 124
            TL +SN+ P ++ E L+ LFS  G VV+        +  A I+    EEA  AL  L+N
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 70

Query: 125 MDVG-GRPLNVEMAKS 139
            D+G    L V  +KS
Sbjct: 71  HDLGENHHLRVSFSKS 86

>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 = 48.8 bits (116), Expect = 4e-08
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALA 121
             L V  L    T + L++ FS  G V+   +        SK F ++ +++ E     ++
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 122 LNNMDVGGRPLNVEMAKS 139
             +M + GR  + ++  S
Sbjct: 69  QRHM-IDGRWCDCKLPNS 85

>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 = 48.1 bits (114), Expect = 7e-08
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKHFAYIEYSKPEEATAAL-A 121
            ++V N+   ++++++   F     +                 A + +   +EATAA+  
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 122 LNNMDVGGRPLNVEMA 137
           LN+  +G R + + + 
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (114), Expect = 7e-08
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL---ALNN 124
           + L +  L   +T  ++  L    G V    +   K+ A++E +  E A   +   +   
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 68

Query: 125 MDVGGRPLNVEMAKS 139
             +  +P+ ++ +  
Sbjct: 69  PHLRNQPIYIQYSNH 83

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 48.0 bits (113), Expect = 9e-08
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 55  GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIE 109
           GS    G        L + NL+P  +V +L+   S      +  + D     ++ F Y++
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 60

Query: 110 YSKPEEATAALALNNMDVGGRPLNVEMAKS 139
           +   E+   AL L  + V G  + +E  K 
Sbjct: 61  FESAEDLEKALELTGLKVFGNEIKLEKPKG 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 = 48.6 bits (115), Expect = 9e-08
 Identities = 25/90 (27%), Positives = 36/90 (40%), Gaps = 7/90 (7%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL- 120
             L V NLS   + E L +LFS  G + E            K FA++ +  PE A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 121 ALNNMDVGGRPLNVEMAKSFPQKPSHLNSS 150
            ++     GR L+V  +    +      SS
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 48.2 bits (114), Expect = 9e-08
 Identities = 23/93 (24%), Positives = 33/93 (35%), Gaps = 15/93 (16%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD--------------SKHFAYIEYSKP 113
             + V  L+  +T++ L   F  CG V     T                K  A + Y  P
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 114 EEATAAL-ALNNMDVGGRPLNVEMAKSFPQKPS 145
             A AA+   +  D  G  L V +A+  P   S
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 70  LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEATAAL-ALN 123
           +++         E   ++    G V E  + D          Y+++ + E+A  A+  LN
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 124 NMDVGGRPLNVEM 136
           N    G+P++ E+
Sbjct: 90  NRWFNGQPIHAEL 102

>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 = 46.9 bits (111), Expect = 3e-07
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI--TDSKHFAYIEYSKPEEATAAL-ALNN 124
             + V NL   +T++ L Q+FS  GTV++      +++  A ++Y+ P  A  A  +L+ 
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDG 67

Query: 125 MDVGGRPLNVEMAKSFPQK 143
            ++      + +  S    
Sbjct: 68  QNIYNACCTLRIDFSKLTS 86

>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 = 46.7 bits (110), Expect = 4e-07
 Identities = 26/90 (28%), Positives = 39/90 (43%), Gaps = 7/90 (7%)

Query: 62  KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHF------AYIEYSKPEE 115
             D   +++ V N+    T EQL+ +FS  G VV   +   +         + EY   E 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 116 ATAAL-ALNNMDVGGRPLNVEMAKSFPQKP 144
           A +A+  LN  +  GR L V+ A S   K 
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAAL-A 121
            L + +L      + L Q+F   G VV   +        SK F ++ Y  P  A AA+ +
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 122 LNNMDVGGRPLNVEMAKS 139
           +N   +G + L V++ +S
Sbjct: 80  MNGFQIGMKRLKVQLKRS 97

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 68  KTLQVSNLSPLLTVE-QLRQLFSFCGTVVECTITDSKHFAYIEYSKP---EEATAALALN 123
           + + + +      +  QL QL    G +    I +  + A+IE +     + A       
Sbjct: 9   RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 124 NMDVGGRPLNVEMAKSFPQ 142
              V G+P+ V +++ + +
Sbjct: 69  PALVFGKPVRVHLSQKYKR 87

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 82  EQLRQLFSFCGTVVECTITDSKH--FAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
           E LR   S  G + +  + D      A + +  PEEA   +  L+    GGR +  +   
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 74  NLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV-GGRP 131
            L   ++  QL  +   CG V    +  +K +++  Y   EE+  A   LN  +V     
Sbjct: 27  GLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLG 86

Query: 132 LNVEMAKSFPQK 143
             + +  +F +K
Sbjct: 87  QKITLYLNFVEK 98

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMD 126
             + V NL      +++  L         C +  +K  A++     E+A  A+   +   
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLK-YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 127 VGGRPLNVEMAKS 139
             G+ L V++  +
Sbjct: 65  FRGKDLIVQLQPT 77

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 3e-06
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 68  KTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTITDS-KHFAYIEYSKPEEATAAL-ALNN 124
             L VSNL+P  +T + L  LF   G V    I  + K  A ++ +   +A  A+  LN 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 62

Query: 125 MDVGGRPLNVEMAKSFPQKPSHLNSSLAGSS 155
             + G+P+ + ++K    +         G +
Sbjct: 63  HKLHGKPIRITLSKHQNVQLPREGQEDQGLT 93

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (103), Expect = 4e-06
 Identities = 12/94 (12%), Positives = 29/94 (30%), Gaps = 6/94 (6%)

Query: 61  GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPE 114
           G  ++ K    ++N+   +T   + Q                         A +++   +
Sbjct: 2   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 115 EATAALALNNMDVGGRPLNVEMAKSFPQKPSHLN 148
           +A  +  L+   + GR   V +      +    N
Sbjct: 62  DARKSERLHRKKLNGREAFVHVVTLEDMREIEKN 95

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 7/83 (8%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKHFAYIEYSKPEEATAAL- 120
           K L + NLSP +T   L  LF+         I         +  A+I +   E A  AL 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 121 ALNNMDVGGRPLNVEMAKSFPQK 143
            +N   + G+ L +E  K+  Q+
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQR 101

>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 = 43.6 bits (102), Expect = 4e-06
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 13/85 (15%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVVEC------TITDSKHFAYIEYSKPEEATAALA 121
           KT+ + NLS     E L ++    G +             SK  A+ ++   E A   LA
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 122 -------LNNMDVGGRPLNVEMAKS 139
                     + + GR L V++A +
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVT 93

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 7e-06
 Identities = 18/109 (16%), Positives = 35/109 (32%), Gaps = 21/109 (19%)

Query: 37  LQAHAAQVQ-AQQSAKDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGT-- 93
           L+A   Q Q A+Q  +D                 L +SNL   +  ++L  +    G   
Sbjct: 1   LKASGVQAQMAKQQEQD--------------PTNLYISNLPLSMDEQELENMLKPFGQVI 46

Query: 94  ---VVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
              ++  +   S+   +      E+  A +   N   +   P      +
Sbjct: 47  STRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 7/68 (10%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNN 124
           +  L P  T + L +L    G +V             K + ++++  P  A  A+ AL  
Sbjct: 3   IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 62

Query: 125 MDVGGRPL 132
             V  +  
Sbjct: 63  SGVQAQMA 70

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 11/75 (14%), Positives = 22/75 (29%), Gaps = 9/75 (12%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTI--------TDSKHFAYIEYSKPEEATAAL-AL 122
           + +      VE +R   S  G V    I               ++E++   +   A+  L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 123 NNMDVGGRPLNVEMA 137
                  R +  +  
Sbjct: 79  TGRKFANRVVVTKYC 93

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS------KHFAYIEYSKPEEATAAL-A 121
            L V  LS     + L Q+FS  G + E  +         + F ++ +   ++A  A+ A
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 122 LNNMDVGGRPLNVEMAKS 139
           +N   V GR + V+ A  
Sbjct: 67  MNGKSVDGRQIRVDQAGK 84

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (92), Expect = 4e-05
 Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 72  VSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGR 130
           +  L   +T +++  L S             K  A++     E+A AA+   +   +  R
Sbjct: 3   IRGLPGDVTNQEVHDLLSDYELKYCFVDKY-KGTAFVTLLNGEQAEAAINTFHQSRLRER 61

Query: 131 PLNVEMAKS 139
            L+V++  +
Sbjct: 62  ELSVQLQPT 70

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.5 bits (91), Expect = 7e-05
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 68  KTLQVSNLSPLLTVEQLRQLFSFCGTVV-ECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           + L ++NL        L  LF+          + +    A++E++   ++ AA  AL   
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGF 68

Query: 126 DV-GGRPLNVEMAK 138
            +     + +  AK
Sbjct: 69  KITPTHAMKITFAK 82

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (92), Expect = 9e-05
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 2/78 (2%)

Query: 69  TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDV 127
            + VS L P  + + L+         V            +EY + E+   AL  L++   
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREA-GDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKF 75

Query: 128 GGRPLNVEMAKSFPQKPS 145
                     + +P++ S
Sbjct: 76  RSHEGETSYIRVYPERSS 93

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (86), Expect = 7e-04
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM 125
           K  +   NL       ++++ FS  G++    + +    A +E+ +P EA  A   L   
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69

Query: 126 DVGGRPLNVEMAKSFPQKPS 145
                PL +E A       +
Sbjct: 70  KFHHVPLYLEWAPIGVFGAA 89

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 0.001
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 13/81 (16%)

Query: 67  KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------------SKHFAYIEYSKPE 114
           K  + V  LS  L   ++ +   + G   +                     AY+ Y + E
Sbjct: 8   KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 115 EATAAL-ALNNMDVGGRPLNV 134
           +A  A+  +NN+ V GR L  
Sbjct: 68  DALRAIQCVNNVVVDGRTLKA 88

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 0.002
 Identities = 17/98 (17%), Positives = 34/98 (34%), Gaps = 6/98 (6%)

Query: 54  SGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAY 107
           S          A    +++  L    + E++ Q FS    V             S   A+
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 108 IEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQKPS 145
           ++++  E A  AL  +   +G R + +  +     + S
Sbjct: 62  VQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTS 99

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	682
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.73
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.71
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.7
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.7
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.7
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.7
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.69
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.69
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.69
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.69
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.69
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.68
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.68
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.67
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.67
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.66
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.65
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.65
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.65
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.65
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.65
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.65
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.64
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.64
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.64
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.64
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.63
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.63
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.63
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.63
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.62
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.6
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.59
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.59
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.58
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.55
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.54
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.45
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.37
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	99.3
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.27
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.21
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.1
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.52
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.14
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.84
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	90.7

>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=99.73  E-value=4.1e-18  Score=143.12  Aligned_cols=73  Identities=26%  Similarity=0.452  Sum_probs=68.9

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||+.+|+++|.++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.||++
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            5789999999999999999999999999999986      35789999999999999999 8999999999999999975

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.1e-17  Score=143.27  Aligned_cols=78  Identities=31%  Similarity=0.464  Sum_probs=71.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      +...++|||+|||+.+|+++|+++|..||.|..|.|+    ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.||.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            4457899999999999999999999999999999986    46789999999999999999 899999999999999997


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      ...
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.72  E-value=6.1e-18  Score=141.95  Aligned_cols=73  Identities=27%  Similarity=0.555  Sum_probs=68.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||+.+++++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.||++
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            4689999999999999999999999999999986      35689999999999999999 8999999999999999875

>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=99.72  E-value=2e-17  Score=142.55  Aligned_cols=79  Identities=28%  Similarity=0.427  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .....++|||+|||+.+++++|.++|..||+|..|.|+    ..+|||||+|.+.++|..|| .|||..|+|+.|.|.||
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            44557899999999999999999999999999999987    46799999999999999999 89999999999999999


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      .+..
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8754

>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=99.72  E-value=9.2e-18  Score=145.72  Aligned_cols=76  Identities=24%  Similarity=0.380  Sum_probs=71.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..++|||+|||+.+++++|+++|.+||.|..|.|+..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|++..+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            3679999999999999999999999999999999988999999999999999999 899999999999999987643

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=9.9e-18  Score=143.27  Aligned_cols=75  Identities=24%  Similarity=0.398  Sum_probs=70.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..+|||+|||+.+|+++|+++|..||.|..|.|+    ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|.++....
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            4689999999999999999999999999999997    35799999999999999999 899999999999999998654

>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=99.71  E-value=1.6e-17  Score=143.21  Aligned_cols=76  Identities=28%  Similarity=0.385  Sum_probs=70.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||+.+|+++|.++|.+||+|..|.|+      ..+|||||+|.+.++|+.|| .|||..|+|+.|.|.|+
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            457899999999999999999999999999999986      35679999999999999999 79999999999999998


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>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=99.71  E-value=1.7e-17  Score=142.99  Aligned_cols=77  Identities=22%  Similarity=0.409  Sum_probs=71.2

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||..+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            346799999999999999999999999999999986      46789999999999999999 89999999999999999


Q ss_pred             ccCC
Q 005698          138 KSFP  141 (682)
Q Consensus       138 ~~~~  141 (682)
                      .+..
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8654

>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=99.71  E-value=9.7e-18  Score=143.32  Aligned_cols=76  Identities=28%  Similarity=0.472  Sum_probs=70.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|+++|++||+|..|.|+      ..+|||||+|.+.++|+.|| .|||..|+|+.|.|.||.
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            46899999999999999999999999999999986      46899999999999999999 899999999999999997


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      +..
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.71  E-value=1.2e-17  Score=147.94  Aligned_cols=75  Identities=23%  Similarity=0.245  Sum_probs=71.3

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      .++|||+|||+.+++++|++||..||+|+.|.|...+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+....
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            579999999999999999999999999999999988999999999999999999 899999999999999997543

>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=99.70  E-value=2.4e-17  Score=138.96  Aligned_cols=76  Identities=20%  Similarity=0.311  Sum_probs=69.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceec-CceEEEEecc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVG-GRPLNVEMAK  138 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~-Gr~L~V~~a~  138 (682)
                      ..++.++|||+|||..+|+++|.++|..||.|..|.|+ ..+|||||+|.+.++|..|| .|||+.|. |+.|.|.||+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            45568899999999999999999999999999999997 46699999999999999999 89999885 6899999986

>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=99.70  E-value=1.3e-17  Score=142.71  Aligned_cols=76  Identities=30%  Similarity=0.415  Sum_probs=70.4

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||+.+|+++|.++|..||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.||
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            356799999999999999999999999999999987      25679999999999999999 79999999999999999


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      ++.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            864

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.7e-17  Score=146.66  Aligned_cols=74  Identities=23%  Similarity=0.354  Sum_probs=69.9

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..++|||+|||+.+|+++|.++|.+||.|..|.|.   ..+|||||+|.+.++|..|| .|||+.|.|+.|.|.|+..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999997   46899999999999999999 8999999999999999864

>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=99.70  E-value=2.1e-17  Score=140.91  Aligned_cols=76  Identities=22%  Similarity=0.291  Sum_probs=69.8

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ....+|||+|||+.+|+++|.++|..||+|..|.|+      .++|||||+|.+.++|+.|| .|||+.|.|+.|.|+||
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            346899999999999999999999999999999986      25789999999999999999 79999999999999999


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      .+.
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            764

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=4.6e-17  Score=141.76  Aligned_cols=78  Identities=29%  Similarity=0.336  Sum_probs=71.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      ...++|||+|||+.+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.++
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            346789999999999999999999999999999996      36789999999999999999 79999999999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .....
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87543

>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=99.70  E-value=4.3e-17  Score=150.47  Aligned_cols=83  Identities=25%  Similarity=0.436  Sum_probs=74.1

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .....++|||+|||+++|+++|++||..||.|+.|.|+      ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999986      25789999999999999999 799999999999999


Q ss_pred             ecccCCCCCC
Q 005698          136 MAKSFPQKPS  145 (682)
Q Consensus       136 ~a~~~~~~~~  145 (682)
                      |+.....++.
T Consensus       118 ~a~~~~~~p~  127 (139)
T d1u6fa1         118 LAASGHQRPG  127 (139)
T ss_dssp             ESSCCCCCCC
T ss_pred             EcCCCCCCCC
Confidence            9987665543

>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=99.70  E-value=2.1e-17  Score=140.52  Aligned_cols=75  Identities=33%  Similarity=0.444  Sum_probs=71.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..++|||+|||+.+++++|.++|.+||+|..|.|...+|||||+|.+.++|+.|| .|||..|.|+.|.|.||...
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            4578999999999999999999999999999999988999999999999999999 89999999999999999764

>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=99.69  E-value=3.6e-17  Score=138.69  Aligned_cols=76  Identities=26%  Similarity=0.366  Sum_probs=71.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..+.+...+|||||+|.+.++|..|| .|||+.|.|+.|.|.|+++..
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            3579999999999999999999999999998888888999999999999999999 899999999999999998643

>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=99.69  E-value=2.2e-17  Score=144.76  Aligned_cols=79  Identities=27%  Similarity=0.422  Sum_probs=71.6

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEe
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEM  136 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~  136 (682)
                      .++.++|||+|||+.+|+++|.++|..||.|+.|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999886      35689999999999999999 8999999999999999


Q ss_pred             cccCCC
Q 005698          137 AKSFPQ  142 (682)
Q Consensus       137 a~~~~~  142 (682)
                      +.+...
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            987543

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.4e-17  Score=139.80  Aligned_cols=76  Identities=24%  Similarity=0.437  Sum_probs=70.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ...++|||+|||+.+|+++|++||..||.|..|.+.   ..++||||+|.+.++|+.|| .|||+.|.|+.|.|.|++..
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            346789999999999999999999999999999986   56899999999999999999 89999999999999998764

>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=99.69  E-value=4e-17  Score=141.00  Aligned_cols=77  Identities=23%  Similarity=0.383  Sum_probs=70.6

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-------cCCCeEEEEeCCHHHHHHHH-Hc-CCceecCceEEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-------DSKHFAYIEYSKPEEATAAL-AL-NNMDVGGRPLNVE  135 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-------~~kg~aFVeF~s~e~A~~Al-~L-ng~~l~Gr~L~V~  135 (682)
                      ...++|||+|||+.+++++|.++|.+||.|..|.|+       ..+|||||+|.+.++|+.|| .| ||..|+|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            356789999999999999999999999999999985       35799999999999999999 77 8999999999999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      ||....
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998654

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.4e-17  Score=145.90  Aligned_cols=74  Identities=24%  Similarity=0.389  Sum_probs=69.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ..++|||+|||+.+|+++|++||..||+|..|.|+      .++|||||+|.+.++|+.||.|||+.|.|+.|.|.++..
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCC
Confidence            35799999999999999999999999999999997      478999999999999999999999999999999998764

>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=99.69  E-value=2.6e-17  Score=137.82  Aligned_cols=70  Identities=27%  Similarity=0.497  Sum_probs=66.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      .|||+|||+.+|+++|.++|..||+|..|.|+      .++|||||+|.+.++|..|| .|||..|.|+.|.|.|++
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            69999999999999999999999999999997      24689999999999999999 899999999999999986

>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=99.69  E-value=3e-17  Score=137.11  Aligned_cols=74  Identities=30%  Similarity=0.437  Sum_probs=69.6

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ..++|||+||+  +|+++|+++|++||.|..|.|...+|||||+|.+.++|..|| .|||..|+|+.|.|.|+++.+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            46899999995  999999999999999999999988999999999999999999 899999999999999997543

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3.3e-17  Score=144.03  Aligned_cols=76  Identities=25%  Similarity=0.403  Sum_probs=70.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+.+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.||.++|..|+|+.|.|.+|.+.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            4799999999999999999999999999999996      4789999999999999999999999999999999998865


Q ss_pred             CC
Q 005698          141 PQ  142 (682)
Q Consensus       141 ~~  142 (682)
                      ..
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.69  E-value=3.2e-17  Score=140.09  Aligned_cols=76  Identities=28%  Similarity=0.416  Sum_probs=70.4

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...+|||+|||+.+|+++|++||.+||.|..|.++      ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|.||.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            46789999999999999999999999999999876      47899999999999999999 899999999999999997


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      ...
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.68  E-value=3.2e-17  Score=138.57  Aligned_cols=71  Identities=38%  Similarity=0.582  Sum_probs=66.1

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe---------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT---------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v~i~---------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      |||+|||+.+|+++|+++|++||.|..|.|+         .++|||||+|.+.++|+.|| .|||..|+|+.|.|.|+..
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            8999999999999999999999999999986         14689999999999999999 8999999999999999864


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.68  E-value=3.2e-17  Score=138.71  Aligned_cols=73  Identities=30%  Similarity=0.441  Sum_probs=68.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|+      .++|||||+|.+.++|+.||.++|+.|+|+.|.|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            45799999999999999999999999999999986      36799999999999999999889999999999998874

>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=99.68  E-value=3.3e-17  Score=137.29  Aligned_cols=72  Identities=26%  Similarity=0.403  Sum_probs=66.3

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      +||||+|||+.+|+++|.++|..||.|..+.++      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.++.+
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            699999999999999999999999999877764      46899999999999999999 8999999999999999875

>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=99.68  E-value=4.7e-17  Score=135.63  Aligned_cols=70  Identities=26%  Similarity=0.442  Sum_probs=66.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecc
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~  138 (682)
                      .|||+|||+.+++++|.++|.+||.|..|.|.     ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999999999997     46789999999999999999 799999999999999985

>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=99.68  E-value=1.4e-17  Score=139.63  Aligned_cols=75  Identities=25%  Similarity=0.398  Sum_probs=69.4

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCc-eecCceEEEEecccCCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNM-DVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~-~l~Gr~L~V~~a~~~~~  142 (682)
                      ++|||+|||+.+|+++|+++|.+||.|..+.+...+|||||+|.+.++|+.|| .|||. .|+|+.|.|.|+.+...
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            47999999999999999999999999988888878999999999999999999 89995 69999999999987543

>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=99.68  E-value=3.2e-17  Score=139.18  Aligned_cols=75  Identities=24%  Similarity=0.348  Sum_probs=68.2

Q ss_pred             CCCEEEEeCCCCCCC-HHHHHHHHhcCCCeEEEEEe-------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           66 LKKTLQVSNLSPLLT-VEQLRQLFSFCGTVVECTIT-------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        66 ~~~tL~V~NLp~~vt-eedL~~~F~~~G~V~~v~i~-------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ..++|||+|||+.+| +++|+++|++||.|..|.|.       ..+|||||+|.+.++|+.||.|||+.|+|+.|.|.|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            378999999999876 56699999999999999985       3678999999999999999999999999999999999


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      .+.
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.67  E-value=6.3e-17  Score=136.93  Aligned_cols=73  Identities=37%  Similarity=0.563  Sum_probs=67.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVE  135 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~  135 (682)
                      ...++|||+|||+.+++++|.++|.+||.|..|.|+      .++|||||+|.+.++|+.|| .|||..|.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            456789999999999999999999999999999987      35689999999999999999 899999987  889999


Q ss_pred             ec
Q 005698          136 MA  137 (682)
Q Consensus       136 ~a  137 (682)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            87

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=8.8e-17  Score=139.99  Aligned_cols=74  Identities=23%  Similarity=0.498  Sum_probs=68.1

Q ss_pred             CCCCEEEEeCCC-CCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           65 ALKKTLQVSNLS-PLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        65 ~~~~tL~V~NLp-~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ....+|||+||+ ..+++++|+++|.+||.|+.|.|.  +|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+...
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            445789999997 578899999999999999999996  899999999999999999 79999999999999999754

>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=99.67  E-value=5.4e-17  Score=137.55  Aligned_cols=73  Identities=26%  Similarity=0.392  Sum_probs=68.5

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .+|||+|||+.+|+++|.++|.+||+|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.||...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            369999999999999999999999999999997      35799999999999999999 79999999999999999754

>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=99.67  E-value=5.8e-17  Score=137.29  Aligned_cols=72  Identities=33%  Similarity=0.503  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEEe
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEM  136 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~  136 (682)
                      ..++|||+|||+.+|+++|+++|++||+|..|.|+      ..+|||||+|.+.++|+.|| .|||..|.|  .+|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            35789999999999999999999999999999997      35689999999999999999 899999998  5599988


Q ss_pred             c
Q 005698          137 A  137 (682)
Q Consensus       137 a  137 (682)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.67  E-value=5.7e-17  Score=136.50  Aligned_cols=70  Identities=30%  Similarity=0.467  Sum_probs=65.0

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEE
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNV  134 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V  134 (682)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|+|+.|.|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            346799999999999999999999999999999986      34689999999999999999 89999999999987

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=7.5e-17  Score=134.31  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=66.4

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .++|||+|||+.+|+++|+++|.+||.|..+.++      ..+|||||+|.+.++|++||.|||..|+|+.|.|..|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            4789999999999999999999999999999987      3578999999999999999999999999999999876

>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=99.67  E-value=2.3e-16  Score=138.43  Aligned_cols=78  Identities=23%  Similarity=0.270  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      .+...++|||+|||+.+|+++|.++|..||.|..|.|+      .++|||||+|.+.++|+.|| .+|+ .|+|+.|.|.
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            44456889999999999999999999999999999997      36899999999999999999 5665 7999999999


Q ss_pred             ecccCC
Q 005698          136 MAKSFP  141 (682)
Q Consensus       136 ~a~~~~  141 (682)
                      |+....
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            997643

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.4e-16  Score=135.52  Aligned_cols=75  Identities=36%  Similarity=0.463  Sum_probs=68.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCcee-cCceEEEEeccc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDV-GGRPLNVEMAKS  139 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l-~Gr~L~V~~a~~  139 (682)
                      ++.++|||+|||+.+|+++|.++|..||.|..+.+.  ..+|||||+|.+.++|..|| .|||..| +|+.|.|.|++.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            457899999999999999999999999999888776  56899999999999999999 8999988 589999999875

>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=99.67  E-value=9.4e-17  Score=141.76  Aligned_cols=74  Identities=30%  Similarity=0.461  Sum_probs=68.6

Q ss_pred             CCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+||++ .||+++|.++|..||.|..|.|+ ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|++..
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57999999965 69999999999999999999998 56799999999999999999 89999999999999998754

>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=99.66  E-value=2e-17  Score=142.11  Aligned_cols=77  Identities=22%  Similarity=0.363  Sum_probs=70.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .+....+|||+|||+.+|+++|+++|..||.|..|.|+     .++|||||+|.+.++|+.||.|||..|.|+.|.|.+|
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            34456799999999999999999999999998887775     5789999999999999999999999999999999998


Q ss_pred             cc
Q 005698          138 KS  139 (682)
Q Consensus       138 ~~  139 (682)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.66  E-value=7.3e-17  Score=137.55  Aligned_cols=77  Identities=18%  Similarity=0.306  Sum_probs=70.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccCCCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      ..++|||+|||+.+|+++|+++|.+||.|..|.+. ..++||||+|.+.++|+.||. +++.|+|+.|.|.++.+....
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCCCCCC
Confidence            47899999999999999999999999999999887 578999999999999999985 789999999999999765433

>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=99.66  E-value=1.7e-16  Score=137.76  Aligned_cols=78  Identities=31%  Similarity=0.463  Sum_probs=72.1

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecC--ceEEEEecccC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGG--RPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~G--r~L~V~~a~~~  140 (682)
                      ..+.++|||+|||+.+++++|+++|.+||.|..|.|...++||||+|.+.++|+.|| .|||..|.|  +.|.|+|++..
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            345789999999999999999999999999999999988999999999999999999 899999987  58999999864


Q ss_pred             C
Q 005698          141 P  141 (682)
Q Consensus       141 ~  141 (682)
                      +
T Consensus        94 ~   94 (97)
T d1whya_          94 P   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.65  E-value=1.2e-16  Score=132.23  Aligned_cols=70  Identities=24%  Similarity=0.412  Sum_probs=65.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ++|||+|||+.+++++|++||..||.|..|.|.    ...+||||+|.+.++|++||.|||..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            589999999999999999999999999999997    3567999999999999999999999999999999864

>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=99.65  E-value=1.3e-16  Score=136.14  Aligned_cols=74  Identities=18%  Similarity=0.266  Sum_probs=66.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..++|||+|||+.++++||+++|.+|| |..+.+...+|||||+|.+.++|+.|| .|||+.|.|+.|.|+|++..
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            367999999999999999999999999 444555567999999999999999999 89999999999999999754

>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=99.65  E-value=9.9e-17  Score=132.66  Aligned_cols=69  Identities=23%  Similarity=0.444  Sum_probs=64.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .|||+|||+.+|+++|.++|.+||+|..|.|+      ..+|||||+|.+.++|+.||.+++..|+|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999987      4689999999999999999988999999999998643

>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=99.65  E-value=6.2e-17  Score=142.08  Aligned_cols=74  Identities=34%  Similarity=0.486  Sum_probs=68.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||+.+|+++|++||++||+|..|.|+      ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+..
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            5789999999999999999999999999999986      24689999999999999999 8999999999999999875


Q ss_pred             C
Q 005698          140 F  140 (682)
Q Consensus       140 ~  140 (682)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.65  E-value=4e-17  Score=135.92  Aligned_cols=70  Identities=23%  Similarity=0.405  Sum_probs=66.2

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ++|||+|||+.+|+++|+++|.+||.|..|.|+      .++|||||+|.+.++|+.||.+|++.|+|+.|.|.+|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999986      4789999999999999999988999999999999876

>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=99.65  E-value=7.7e-17  Score=132.71  Aligned_cols=69  Identities=16%  Similarity=0.327  Sum_probs=65.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .|||+|||+++|+++|.++|..||.|..|.++      ..+|||||+|.+.++|+.||.|||+.|+|+.|.|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            49999999999999999999999999999886      4679999999999999999999999999999999876

>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=99.65  E-value=3.2e-16  Score=137.39  Aligned_cols=78  Identities=23%  Similarity=0.352  Sum_probs=68.7

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .+..+|||+|||+.+|+++|++||..|| |+.|.|+       ..+|||||+|.+.++|++|+.|||+.|+|+.|.|.|+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3568999999999999999999999999 7777665       3578999999999999877799999999999999999


Q ss_pred             ccCCCC
Q 005698          138 KSFPQK  143 (682)
Q Consensus       138 ~~~~~~  143 (682)
                      ......
T Consensus        92 ~~~~~~   97 (104)
T d1wi8a_          92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            865443

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1e-16  Score=139.60  Aligned_cols=79  Identities=29%  Similarity=0.445  Sum_probs=68.9

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEE--------EEe------cCCCeEEEEeCCHHHHHHHH-HcCCcee
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVEC--------TIT------DSKHFAYIEYSKPEEATAAL-ALNNMDV  127 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v--------~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l  127 (682)
                      .+...++|||+|||+.+|+++|.+||..||.|..+        .+.      ..+|||||+|.+.++|..|| .|||+.|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            44567899999999999999999999999998543        222      35689999999999999999 8999999


Q ss_pred             cCceEEEEecccCC
Q 005698          128 GGRPLNVEMAKSFP  141 (682)
Q Consensus       128 ~Gr~L~V~~a~~~~  141 (682)
                      +|+.|.|.||+...
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998644

>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=99.65  E-value=1e-16  Score=134.85  Aligned_cols=73  Identities=27%  Similarity=0.454  Sum_probs=66.0

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEE-EEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVEC-TIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v-~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      |||+|||+++|+++|.++|.+||.|..+ .|+      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.||.+..
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999999765 454      35799999999999999999 799999999999999998654


Q ss_pred             C
Q 005698          142 Q  142 (682)
Q Consensus       142 ~  142 (682)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.65  E-value=7.4e-17  Score=139.68  Aligned_cols=79  Identities=23%  Similarity=0.289  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFP  141 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~  141 (682)
                      ....++|||+|||+.+|+++|+++|..||.|..|.+. ..+|||||+|.+.++|+.|| .|||+.|.|+.|.|.|+.+..
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            3457899999999999999999999999999887765 57899999999999999999 899999999999999998765


Q ss_pred             C
Q 005698          142 Q  142 (682)
Q Consensus       142 ~  142 (682)
                      .
T Consensus        93 ~   93 (96)
T d1fjca_          93 G   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.64  E-value=4.6e-17  Score=138.54  Aligned_cols=74  Identities=18%  Similarity=0.217  Sum_probs=67.7

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQ  142 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~  142 (682)
                      ++|||+|||+.+|+++|+++|++||.|+.|.|. ..|||||+|.+.++|+.|| .|||..|.|+.|.|.++.....
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC-TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccc-ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcC
Confidence            369999999999999999999999999999986 3599999999999999999 8999999999999988765443

>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=99.64  E-value=4.1e-16  Score=132.66  Aligned_cols=78  Identities=17%  Similarity=0.209  Sum_probs=72.0

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-H--cCCceecCceEEEEecccC
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-A--LNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~--Lng~~l~Gr~L~V~~a~~~  140 (682)
                      ..+.++|||+|||+.+++++|.++|..||.|..|.|...++||||+|.+.++|+.|| .  +++..|.|+.|.|.|++..
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            457899999999999999999999999999999999988999999999999999999 4  5788999999999999765


Q ss_pred             C
Q 005698          141 P  141 (682)
Q Consensus       141 ~  141 (682)
                      .
T Consensus        85 ~   85 (88)
T d2cq1a1          85 E   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.64  E-value=3e-16  Score=135.73  Aligned_cols=76  Identities=26%  Similarity=0.326  Sum_probs=68.8

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcC------CceecCceE
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALN------NMDVGGRPL  132 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Ln------g~~l~Gr~L  132 (682)
                      ..++|||+|||+.+|+++|+++|.+||.|..+.|+      ..+|||||+|.+.++|..|| .||      |..|.|+.|
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            46799999999999999999999999999999886      36899999999999999999 676      678999999


Q ss_pred             EEEecccCC
Q 005698          133 NVEMAKSFP  141 (682)
Q Consensus       133 ~V~~a~~~~  141 (682)
                      .|.|+.+..
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999998643

>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=99.64  E-value=1e-16  Score=140.20  Aligned_cols=78  Identities=17%  Similarity=0.237  Sum_probs=70.0

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVE  135 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~  135 (682)
                      ..+...++|||+|||+.+|+++|+++|+.||.|..+.+.     ..+|||||+|.+.++|+.|| .|||..|.|++|.|.
T Consensus        13 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            344557899999999999999999999999999999886     35789999999999999999 899999999999987


Q ss_pred             eccc
Q 005698          136 MAKS  139 (682)
Q Consensus       136 ~a~~  139 (682)
                      ++.+
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7654

>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=99.64  E-value=3.2e-16  Score=134.28  Aligned_cols=76  Identities=21%  Similarity=0.314  Sum_probs=67.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|+      .++|||||+|.+.++|+.||. ++..|+|+.|.|.++.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeCC
Confidence            356899999999999999999999999999999987      357899999999999999995 3458999999999987


Q ss_pred             cCC
Q 005698          139 SFP  141 (682)
Q Consensus       139 ~~~  141 (682)
                      +..
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.5e-16  Score=134.96  Aligned_cols=75  Identities=20%  Similarity=0.418  Sum_probs=68.7

Q ss_pred             CCCEEEEeCCCCCCCHHHHH----HHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           66 LKKTLQVSNLSPLLTVEQLR----QLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~----~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      +.++|||+|||+.++++||+    .+|++||+|..|.|.   ..+|||||+|.+.++|..|| .|||+.|.|+.|.|.||
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            46899999999999999886    468999999999987   46899999999999999999 89999999999999999


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      +..
T Consensus        82 k~~   84 (91)
T d1nu4a_          82 KTD   84 (91)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

>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=99.63  E-value=4.2e-16  Score=128.88  Aligned_cols=70  Identities=20%  Similarity=0.293  Sum_probs=66.0

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccC
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      |||+|||+.+++++|+++|.+|| |..+.+...+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            89999999999999999999999 777777788999999999999999999 89999999999999999753

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.9e-16  Score=132.97  Aligned_cols=73  Identities=10%  Similarity=0.168  Sum_probs=68.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .++|||+|||..+|+++|.++|..||.|..|.|.     ..+|||||+|.+.++|+.||.++|..|.|+.|.|.|...
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcCC
Confidence            6799999999999999999999999999999997     356899999999999999999999999999999998653

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=4.5e-16  Score=135.39  Aligned_cols=77  Identities=18%  Similarity=0.305  Sum_probs=71.0

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEecccCCCC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKSFPQK  143 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~~~~~  143 (682)
                      ...+|||+|||+.+++++|++||.+||+|+.|.|. .+|||||+|.+.++|+.|| .|||..|.|+.|.|.++......
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~~   91 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPER   91 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCCC
Confidence            46789999999999999999999999999999987 5699999999999999999 89999999999999998865543

>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=99.63  E-value=7.9e-17  Score=140.64  Aligned_cols=78  Identities=29%  Similarity=0.319  Sum_probs=71.1

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .+.++|||+|||..+++++|.++|..||.|..|.|.      ..+|||||+|.+.++|+.|| .|||..|.|+.|.|.|+
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            457899999999999999999999999999887765      47899999999999999999 89999999999999999


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      +....
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87543

>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=99.63  E-value=1.5e-16  Score=131.73  Aligned_cols=69  Identities=22%  Similarity=0.370  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .|||||||+.+|+++|+++|++||.|..|.|+      .++|||||+|.+.++|+.||.+++..|+|+.|.|..|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999987      4789999999999999999988889999999999765

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=1.6e-15  Score=133.13  Aligned_cols=79  Identities=14%  Similarity=0.157  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc--CCceecCceEEEEeccc
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL--NNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L--ng~~l~Gr~L~V~~a~~  139 (682)
                      ...+..+|||+|||+.+|+++|.++|..||.|..|.|...++||||+|.+.++|+.|| .|  ++..|.|+.|.|.|+..
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            4456889999999999999999999999999999999999999999999999999999 55  66788999999999976


Q ss_pred             CC
Q 005698          140 FP  141 (682)
Q Consensus       140 ~~  141 (682)
                      ..
T Consensus        91 ~~   92 (104)
T d1wexa_          91 KR   92 (104)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>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=99.60  E-value=4.8e-16  Score=136.74  Aligned_cols=82  Identities=18%  Similarity=0.185  Sum_probs=72.5

Q ss_pred             CCCEEEEeCCCCCC-CH----HHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           66 LKKTLQVSNLSPLL-TV----EQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        66 ~~~tL~V~NLp~~v-te----edL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      ...+|||+||+..+ ++    ++|+++|..||.|+.|.+...++||||+|.+.++|..|| .|||+.|+|+.|.|.|++.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   83 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeeccc
Confidence            47899999999876 33    579999999999999999999999999999999999999 8999999999999999987


Q ss_pred             CCCCCCCC
Q 005698          140 FPQKPSHL  147 (682)
Q Consensus       140 ~~~~~~~~  147 (682)
                      .......+
T Consensus        84 ~~~~~~~~   91 (104)
T d1weya_          84 LHIGSSHL   91 (104)
T ss_dssp             SSCCSCCS
T ss_pred             CCCCCccc
Confidence            65544433

>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=99.59  E-value=1.3e-15  Score=132.76  Aligned_cols=79  Identities=20%  Similarity=0.303  Sum_probs=71.6

Q ss_pred             CCCCCCCEEEEeCCCC-CCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH---HcCCceecCceEEEEec
Q 005698           62 KADALKKTLQVSNLSP-LLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL---ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~-~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al---~Lng~~l~Gr~L~V~~a  137 (682)
                      ......++|||+|||. .+|+++|.++|..||.|..|.|...+|||||+|.+.++|..||   .+++..|+|+.|.|.|+
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            3455678999999997 4899999999999999999999988999999999999999998   37899999999999999


Q ss_pred             ccC
Q 005698          138 KSF  140 (682)
Q Consensus       138 ~~~  140 (682)
                      +..
T Consensus        93 ~~~   95 (99)
T d1x4fa1          93 EKY   95 (99)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            753

>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=99.59  E-value=1.5e-15  Score=131.20  Aligned_cols=76  Identities=17%  Similarity=0.276  Sum_probs=67.0

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCC-eEEEEEe-------cCCCeEEEEeCCHHHHHHHH-HcC--CceecCceEEEEe
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGT-VVECTIT-------DSKHFAYIEYSKPEEATAAL-ALN--NMDVGGRPLNVEM  136 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~-V~~v~i~-------~~kg~aFVeF~s~e~A~~Al-~Ln--g~~l~Gr~L~V~~  136 (682)
                      +.|||+|||..+|+++|+++|..||+ |..|.|+       ..+|||||+|.+.++|..|| .|+  +..+.|+.|.|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 8999986       36789999999999999999 775  4567899999999


Q ss_pred             cccCCCC
Q 005698          137 AKSFPQK  143 (682)
Q Consensus       137 a~~~~~~  143 (682)
                      |.+....
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9875543

>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=99.59  E-value=1e-15  Score=135.29  Aligned_cols=76  Identities=25%  Similarity=0.343  Sum_probs=68.5

Q ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCcee--cCceEEEEecccC
Q 005698           66 LKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDV--GGRPLNVEMAKSF  140 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l--~Gr~L~V~~a~~~  140 (682)
                      +..+|||+|||+.||+++|.++|.+||.|..|.|.  ..+|||||+|.+.++|+.|| .|||..|  .|..|.|.|++..
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            45689999999999999999999999999999987  46789999999999999999 8999988  4688999998764


Q ss_pred             C
Q 005698          141 P  141 (682)
Q Consensus       141 ~  141 (682)
                      .
T Consensus        86 ~   86 (108)
T d2adba1          86 S   86 (108)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=99.59  E-value=4.5e-15  Score=130.14  Aligned_cols=79  Identities=19%  Similarity=0.153  Sum_probs=69.8

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      .....+|||+|||+.+||+||++||..||.|..+.++      ..+|||||+|.+.++|++||.||+..|+|+.|.|.++
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            3456689999999999999999999999998875544      4779999999999999999999999999999999998


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .....
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            86543

>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=99.59  E-value=5.8e-16  Score=132.25  Aligned_cols=70  Identities=29%  Similarity=0.435  Sum_probs=63.6

Q ss_pred             CCCEEEEeCCCCCCCHHHH---HHHHhcCCCeEEEEEec---------CCCeEEEEeCCHHHHHHHH-HcCCceecCceE
Q 005698           66 LKKTLQVSNLSPLLTVEQL---RQLFSFCGTVVECTITD---------SKHFAYIEYSKPEEATAAL-ALNNMDVGGRPL  132 (682)
Q Consensus        66 ~~~tL~V~NLp~~vteedL---~~~F~~~G~V~~v~i~~---------~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L  132 (682)
                      ..++|||+|||+.+++++|   .++|++||.|..|.|+.         ..|||||+|.+.++|+.|| .|||+.|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3578999999999999999   77899999999999971         3489999999999999999 899999999999


Q ss_pred             EEE
Q 005698          133 NVE  135 (682)
Q Consensus       133 ~V~  135 (682)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            983

>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=99.58  E-value=2.2e-15  Score=128.67  Aligned_cols=76  Identities=22%  Similarity=0.268  Sum_probs=69.8

Q ss_pred             CCCCCEEEEeCCCCC-CCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-Hc--CCceecCceEEEEeccc
Q 005698           64 DALKKTLQVSNLSPL-LTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-AL--NNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~-vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~L--ng~~l~Gr~L~V~~a~~  139 (682)
                      ....++|||+|||.. +|++||.+||..||.|..|.|...++||||+|.+.++|..|| .|  ++..|.|++|.|.|++.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            346889999999986 889999999999999999999988999999999999999999 54  78899999999999974

>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=99.58  E-value=1.2e-15  Score=133.48  Aligned_cols=79  Identities=16%  Similarity=0.192  Sum_probs=68.7

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEec
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a  137 (682)
                      ......+|||+|||+++|++||++||..||.| .|.|+     ..+|||||+|.+.++|+.||.||++.|+|+.|.|.|+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34456799999999999999999999999854 55554     3578999999999999999999999999999999998


Q ss_pred             ccCCC
Q 005698          138 KSFPQ  142 (682)
Q Consensus       138 ~~~~~  142 (682)
                      .....
T Consensus        90 ~~~~~   94 (102)
T d1weza_          90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.57  E-value=1.5e-15  Score=132.89  Aligned_cols=76  Identities=13%  Similarity=0.174  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-EEEe-----cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           63 ADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTIT-----DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        63 ~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~-v~i~-----~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .+....+|||+|||+.+|+++|.+||..||.|.. +.|.     ..+|||||+|.+.++|+.||.|||..|+|+.|.|.+
T Consensus         4 v~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           4 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   83 (103)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEE
Confidence            3445678999999999999999999999999876 4443     468999999999999999999999999999999988


Q ss_pred             cc
Q 005698          137 AK  138 (682)
Q Consensus       137 a~  138 (682)
                      +.
T Consensus        84 ~~   85 (103)
T d2cpya1          84 VT   85 (103)
T ss_dssp             EC
T ss_pred             CC
Confidence            75

>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=99.55  E-value=1.8e-15  Score=127.87  Aligned_cols=73  Identities=18%  Similarity=0.309  Sum_probs=64.9

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEE-EEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~-v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      +...+|||+|||+.++++||++||..||.|.. +.|.     .++|||||+|.+.++|+.|| .|||..|.|+.|.|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34678999999999999999999999999865 3443     45789999999999999999 89999999999999875

>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=99.54  E-value=1.3e-15  Score=124.43  Aligned_cols=64  Identities=23%  Similarity=0.386  Sum_probs=60.2

Q ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEE
Q 005698           70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLN  133 (682)
Q Consensus        70 L~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~  133 (682)
                      |||+|||+.+|+++|.++|..||.|..+.+.      ..+|||||+|.+.++|+.|| .|||..|.|+.|+
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            8999999999999999999999999999886      47899999999999999999 8999999998763

>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=99.52  E-value=2.3e-16  Score=134.72  Aligned_cols=73  Identities=23%  Similarity=0.368  Sum_probs=64.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEE
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVE  135 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~  135 (682)
                      .++|||+|||+.+|+++|.++|..||.|..+.|.           ..+|||||+|.+.++|+.||.|||+.|.|+.|.|.
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCB
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEEC
Confidence            3689999999999999999999999987655442           57899999999999999999999999999999997


Q ss_pred             eccc
Q 005698          136 MAKS  139 (682)
Q Consensus       136 ~a~~  139 (682)
                      .++.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            5543

>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=99.51  E-value=4.9e-15  Score=131.75  Aligned_cols=74  Identities=14%  Similarity=0.151  Sum_probs=65.3

Q ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecc
Q 005698           65 ALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAK  138 (682)
Q Consensus        65 ~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~  138 (682)
                      ....+|||+|||+.+|+++|.+||..||.|..+.++      ...|||||+|.+.++|+.||.|||..|+|+.|.|.++.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            346799999999999999999999999988654332      46789999999999999999999999999999998765

>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=99.45  E-value=6.5e-14  Score=124.61  Aligned_cols=73  Identities=19%  Similarity=0.089  Sum_probs=65.8

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCH-HHHHHHH-HcCCceecCceEEEEeccc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKP-EEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~-e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      .-.+||||||+.+|+++|+++|.+||+|.+|.|+..+|||||.|.+. ++|..|+ .||+..|.++.+.|.|+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            45669999999999999999999999999999999999999999985 7788888 8999999988888877653

>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=99.42  E-value=1.7e-13  Score=119.55  Aligned_cols=65  Identities=26%  Similarity=0.390  Sum_probs=59.7

Q ss_pred             CCCCCEEEEeC--CCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH-HcCCceec
Q 005698           64 DALKKTLQVSN--LSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVG  128 (682)
Q Consensus        64 ~~~~~tL~V~N--Lp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al-~Lng~~l~  128 (682)
                      ..+..+|||+|  ||+.+|+++|+++|.+||.|..|.+...++||||+|.+.++|..|+ .|||..|.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            34578899955  9999999999999999999999999988999999999999999999 89998873

>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=99.40  E-value=2.9e-13  Score=129.00  Aligned_cols=78  Identities=19%  Similarity=0.266  Sum_probs=70.5

Q ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEE
Q 005698           62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVE  135 (682)
Q Consensus        62 ~~~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~  135 (682)
                      ......++|||+|||+.+|+++|.++|..||.|..|.|+      ..+|||||+|.+.++|..||.+++..|+|+.|.|.
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            344567899999999999999999999999999999887      35689999999999999999889999999999999


Q ss_pred             eccc
Q 005698          136 MAKS  139 (682)
Q Consensus       136 ~a~~  139 (682)
                      +|.+
T Consensus       172 ~A~~  175 (183)
T d1u1qa_         172 KALS  175 (183)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            9864

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.37  E-value=5.4e-13  Score=111.70  Aligned_cols=71  Identities=15%  Similarity=0.199  Sum_probs=63.1

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCce-EEEEecc
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRP-LNVEMAK  138 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~-L~V~~a~  138 (682)
                      .+.|||+|||+.++++.| .+|.+||+|+.|.+...+|||||+|.+.++|+.||.|||..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            567999999999986655 5899999999999988899999999999999999999999999985 5677654

>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=99.30  E-value=1.5e-13  Score=120.57  Aligned_cols=69  Identities=20%  Similarity=0.328  Sum_probs=63.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe-----cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEec
Q 005698           69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMA  137 (682)
Q Consensus        69 tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~-----~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a  137 (682)
                      .|+|.+++..+++++|.++|++||.|..|.|+     ..+|||||+|.+.++|..|| .|||.+|+|+.|.|+|+
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46677888889999999999999999999997     46799999999999999999 89999999999999985

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=5.5e-12  Score=109.34  Aligned_cols=77  Identities=19%  Similarity=0.273  Sum_probs=66.6

Q ss_pred             CCCCEEEEeCC--CCCC---------CHHHHHHHHhcCCCeEEEEEe--cCCCeEEEEeCCHHHHHHHH-HcCCceecCc
Q 005698           65 ALKKTLQVSNL--SPLL---------TVEQLRQLFSFCGTVVECTIT--DSKHFAYIEYSKPEEATAAL-ALNNMDVGGR  130 (682)
Q Consensus        65 ~~~~tL~V~NL--p~~v---------teedL~~~F~~~G~V~~v~i~--~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr  130 (682)
                      ...++|+|.||  |..+         .++||.+.|++||.|..|.|.  ..+|||||+|.+.++|..|| .|||..|+|+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr   85 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   85 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCE
Confidence            45789999999  4332         126899999999999999987  46799999999999999999 8999999999


Q ss_pred             eEEEEecccCC
Q 005698          131 PLNVEMAKSFP  141 (682)
Q Consensus       131 ~L~V~~a~~~~  141 (682)
                      .|.|.++.+..
T Consensus        86 ~i~v~~~~g~~   96 (99)
T d2dita1          86 QITAQAWDGTT   96 (99)
T ss_dssp             ECEEEECCSCC
T ss_pred             EEEEEEeCCcC
Confidence            99999987543

>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=99.21  E-value=8.2e-12  Score=118.67  Aligned_cols=74  Identities=31%  Similarity=0.438  Sum_probs=66.6

Q ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEe------cCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEecccC
Q 005698           67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEMAKSF  140 (682)
Q Consensus        67 ~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~------~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~a~~~  140 (682)
                      .++|||+|||+.+|+++|.++|.+||.|..|.|+      ..+|||||+|.+.++|..|+.+++..|.+..|.+.+....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            4799999999999999999999999999999986      3578999999999999999988888899998888776543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=4.4e-11  Score=104.37  Aligned_cols=74  Identities=19%  Similarity=0.230  Sum_probs=63.6

Q ss_pred             CCCEEEEeCC--CCCC--------CHHHHHHHHhcCCCeEEEEEe--------cCCCeEEEEeCCHHHHHHHH-HcCCce
Q 005698           66 LKKTLQVSNL--SPLL--------TVEQLRQLFSFCGTVVECTIT--------DSKHFAYIEYSKPEEATAAL-ALNNMD  126 (682)
Q Consensus        66 ~~~tL~V~NL--p~~v--------teedL~~~F~~~G~V~~v~i~--------~~kg~aFVeF~s~e~A~~Al-~Lng~~  126 (682)
                      +.++|+|.||  +..+        ..+||++.|.+||.|..|.|.        ...||+||+|.+.++|..|+ .|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            5789999999  4333        236799999999999999986        23589999999999999999 899999


Q ss_pred             ecCceEEEEeccc
Q 005698          127 VGGRPLNVEMAKS  139 (682)
Q Consensus       127 l~Gr~L~V~~a~~  139 (682)
                      |+|+.|.|.++..
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998753

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.52  E-value=7.4e-05  Score=61.77  Aligned_cols=53  Identities=23%  Similarity=0.382  Sum_probs=49.0

Q ss_pred             HHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHHHcCCceecCceEEEEe
Q 005698           82 EQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGGRPLNVEM  136 (682)
Q Consensus        82 edL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al~Lng~~l~Gr~L~V~~  136 (682)
                      .+|.+.|..||+|+-|+++  .+-.+|+|.+-..|..||.|+|+.|+|+.|.|..
T Consensus        39 ~~Llq~l~~~GeViLvRFv--~d~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN--QGQMLVTFADSHSALSVLDVDGMKVKGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE--TTEEEEECSCSHHHHHHHHGGGSEETTEEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEEEe--CCeEEEEECCcHHHHHHhccCCeEEcceEEEEec
Confidence            4788899999999999998  6789999999999999999999999999999964

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=0.00073  Score=56.24  Aligned_cols=62  Identities=18%  Similarity=0.146  Sum_probs=53.8

Q ss_pred             CEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEec--------CCCeEEEEeCCHHHHHHHH-HcCCceecC
Q 005698           68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD--------SKHFAYIEYSKPEEATAAL-ALNNMDVGG  129 (682)
Q Consensus        68 ~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~--------~kg~aFVeF~s~e~A~~Al-~Lng~~l~G  129 (682)
                      +.|.|.+||+.+||+++.+.++..|++..+....        .-.-|||.|.+.+++..-. .++|+.|.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            5799999999999999999999999998877651        2246999999999998888 899999865

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.84  E-value=0.002  Score=50.60  Aligned_cols=58  Identities=21%  Similarity=0.377  Sum_probs=51.4

Q ss_pred             HHHHHHHhcCCCeEEEEEe---cCCCeEEEEeCCHHHHHHHH-HcCCceecCceEEEEeccc
Q 005698           82 EQLRQLFSFCGTVVECTIT---DSKHFAYIEYSKPEEATAAL-ALNNMDVGGRPLNVEMAKS  139 (682)
Q Consensus        82 edL~~~F~~~G~V~~v~i~---~~kg~aFVeF~s~e~A~~Al-~Lng~~l~Gr~L~V~~a~~  139 (682)
                      +-|..+|.++|.|..|.|.   +..-.|-|...+..+|..|| .|+-..|++++|.|.++.+
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4567889999999999996   45568999999999999999 8999999999999998764

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.70  E-value=0.33  Score=40.01  Aligned_cols=55  Identities=22%  Similarity=0.299  Sum_probs=46.3

Q ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEecCCCeEEEEeCCHHHHHHHH
Q 005698           64 DALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL  120 (682)
Q Consensus        64 ~~~~~tL~V~NLp~~vteedL~~~F~~~G~V~~v~i~~~kg~aFVeF~s~e~A~~Al  120 (682)
                      .+...-||.-.+|......||.++|..||.|.--.|.  .--|||...+.++|+.++
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId--dTSa~V~L~~~e~~~~v~   66 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID--DTSAFVSLSQPEQVQIAV   66 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE--TTEEEEECSCHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEec--CceEEEEecCHHHHHHHH
Confidence            3445678888999999999999999999988655554  457999999999999888