Citrus Sinensis ID: 008851

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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-
Protein Sequence
MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQMQPS
Secondary Structure (PSIPRED)
cccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEcccccccccccEEEEEccHHHHHHHHHHHcccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccHHHHHHHHHHHHcccccHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHcccHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEcccccccHHHHHHHHHHHccEEEEEccEccccccEccEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEccccHHHHHHHHHHccccccEEEEccccccccccccccccccccHHccHcccccccccccEEcccccccccccccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccHHHHHHHHHHccHHHHHHHHHHHHHHcccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccHHHHHcccHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
massqhrcvfvgnipydatEEQLIEICREVGPVVSFRLVidretgkpkgygfceykdEETALSARRNLqgyeingrqlrvdfaendkgadrnreqgrggpgmaaivdpqkqlggpaihgesvhhqpiGLHIAITAAAVMTGALGAAqvgvqsnqngiqsqlaspndpltLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLgmatpqvlqmpilrqgpghpaqplfqdgqqqvaqlpglpplaqkmqlmPKVQEAQIQLHNQfsaatqptlhpqiqlpqnAKNQALQqaslpgqsgipmlpsmhpsvrpqiqlanssslnqqvhppslenqVQVSasnlgqntwtklpnsamrssflphppssdagfqpgpstsagigqtvsrdaersarvpedgtrahrnnaytnmsmglaskrstvndpldsishpskivktedgsgtsfsvgalnvskpigsapsqafgaglvpvnqvpkveevqysekqipqispDVESALLQQVLSltpeqlnslppeQRQQVIQLQQALLRDQMQPS
Flexible Loop (DISEMBL)
massqhrcvFVGNIPYDATEEQLIEICREVGPVVSfrlvidretgkpkgygfceYKDEETALSARRNLQgyeingrqlrvdfaendkgadrnreqgrggpGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQtvsrdaersarvpedgtrahrnnaytnmsmglaSKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQMQPS
Low Complexity Region (SEG)
MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAItaaavmtgalgaaQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQlllakppllkalFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEqrqqviqlqqallRDQMQPS
Disordered region (IsUnstruct)
******RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL**************************************IHGESVHHQPIGLHIAITAAAVMTGALGAAQVGV**************************************************LLLAKPPLLKALFQAQIMLGMATPQVLQMPIL********************************************************************************************************************************************************************************************************************************************************AGLVPV*****************************************************************
Disordered Region (DISOPRED)
*****HR**FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR***********************************************************************************************************************RQLLLAKPPLLKALFQAQIMLGM******************************************************************************************************************************************************************************************************************************************************************************************************QVLSLTPEQLNSLPP**************R******
Disordered Region (DISEMBL)
MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPST*********************GTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQAL********
Disordered Region (DISPRO)
****QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSN**GIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPP***********QEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLN**********************************************************************************************************************************************************************ISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRD*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQMQPS
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	551	2.2.26 [Sep-21-2011]
Q8BIQ5	580	Cleavage stimulation fact	yes	no	0.304	0.289	0.412	2e-36
Q8HXM1	572	Cleavage stimulation fact	no	no	0.304	0.293	0.408	2e-36
P33240	577	Cleavage stimulation fact	yes	no	0.304	0.291	0.408	4e-36
Q5RDA3	577	Cleavage stimulation fact	yes	no	0.304	0.291	0.408	4e-36
Q9H0L4	616	Cleavage stimulation fact	no	no	0.299	0.267	0.420	1e-34
Q8C7E9	632	Cleavage stimulation fact	no	no	0.299	0.261	0.411	2e-34
Q9P6P7	422	Uncharacterized RNA-bindi	yes	no	0.368	0.481	0.366	5e-27
O43040	363	Cleavage and termination	no	no	0.415	0.630	0.315	2e-25
P25299	296	mRNA 3'-end-processing pr	yes	no	0.143	0.266	0.455	2e-18
Q8R0F5	326	RNA-binding motif protein	no	no	0.139	0.236	0.402	1e-10

>sp|Q8BIQ5|CSTF2_MOUSE Cleavage stimulation factor subunit 2 OS=Mus musculus GN=Cstf2 PE=1 SV=2

 Score =  154 bits (389), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/223 (41%), Positives = 120/223 (53%), Gaps = 55/223 (24%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 16  RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           NL G E +GR LRVD A ++K  +  +  G G P    I  P         +GES+    
Sbjct: 76  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESP---------YGESI---- 119

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDP---LTLHLAKMSRNQLNEI 183
                                               SP D    ++  +A +   Q+ E+
Sbjct: 120 ------------------------------------SPEDAPESISKAVASLPPEQMFEL 143

Query: 184 MSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQV 226
           M +MKL    + ++AR +LL  P L  AL QAQ+++ +  P++
Sbjct: 144 MKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQVVMRIVDPEI 186

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.
Mus musculus (taxid: 10090)

>sp|Q8HXM1|CSTF2_BOVIN Cleavage stimulation factor subunit 2 OS=Bos taurus GN=CSTF2 PE=2 SV=1

 Score =  154 bits (388), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 120/223 (53%), Gaps = 55/223 (24%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 16  RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           NL G E +GR LRVD A ++K  +  +  G G P    I  P         +GE++    
Sbjct: 76  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESP---------YGETI---- 119

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDP---LTLHLAKMSRNQLNEI 183
                                               SP D    ++  +A +   Q+ E+
Sbjct: 120 ------------------------------------SPEDAPESISKAVASLPPEQMFEL 143

Query: 184 MSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQV 226
           M +MKL    + ++AR +LL  P L  AL QAQ+++ +  P++
Sbjct: 144 MKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQVVMRIVDPEI 186

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.

Bos taurus (taxid: 9913)

>sp|P33240|CSTF2_HUMAN Cleavage stimulation factor subunit 2 OS=Homo sapiens GN=CSTF2 PE=1 SV=1

 Score =  153 bits (386), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 120/223 (53%), Gaps = 55/223 (24%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 16  RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           NL G E +GR LRVD A ++K  +  +  G G P    I  P         +GE++    
Sbjct: 76  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESP---------YGETI---- 119

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDP---LTLHLAKMSRNQLNEI 183
                                               SP D    ++  +A +   Q+ E+
Sbjct: 120 ------------------------------------SPEDAPESISKAVASLPPEQMFEL 143

Query: 184 MSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQV 226
           M +MKL    + ++AR +LL  P L  AL QAQ+++ +  P++
Sbjct: 144 MKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQVVMRIVDPEI 186

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.

Homo sapiens (taxid: 9606)

>sp|Q5RDA3|CSTF2_PONAB Cleavage stimulation factor subunit 2 OS=Pongo abelii GN=CSTF2 PE=2 SV=1

 Score =  153 bits (386), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 120/223 (53%), Gaps = 55/223 (24%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 16  RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           NL G E +GR LRVD A ++K  +  +  G G P    I  P         +GE++    
Sbjct: 76  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESP---------YGETI---- 119

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDP---LTLHLAKMSRNQLNEI 183
                                               SP D    ++  +A +   Q+ E+
Sbjct: 120 ------------------------------------SPEDAPESISKAVASLPPEQMFEL 143

Query: 184 MSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQV 226
           M +MKL    + ++AR +LL  P L  AL QAQ+++ +  P++
Sbjct: 144 MKQMKLCVQNSPQEARNMLLQNPQLAYALLQAQVVMRIVDPEI 186

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.

Pongo abelii (taxid: 9601)

>sp|Q9H0L4|CSTFT_HUMAN Cleavage stimulation factor subunit 2 tau variant OS=Homo sapiens GN=CSTF2T PE=1 SV=1

 Score =  148 bits (373), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 95/226 (42%), Positives = 120/226 (53%), Gaps = 61/226 (26%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVG VVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 16  RSVFVGNIPYEATEEQLKDIFSEVGSVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           NL G E +GR LRVD A ++K    N+E+              K L GPA         P
Sbjct: 76  NLNGREFSGRALRVDNAASEK----NKEE-------------LKSL-GPAA--------P 109

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDP------LTLHLAKMSRNQL 180
           I                             I S    P DP      +T  +A +   Q+
Sbjct: 110 I-----------------------------IDSPYGDPIDPEDAPESITRAVASLPPEQM 140

Query: 181 NEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQV 226
            E+M +MKL    + ++AR +LL  P L  AL QAQ+++ +  P++
Sbjct: 141 FELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQVVMRIMDPEI 186

May play a significant role in AAUAAA-independent mRNA polyadenylation in germ cells. Directly involved in the binding to pre-mRNAs.

Homo sapiens (taxid: 9606)

>sp|Q8C7E9|CSTFT_MOUSE Cleavage stimulation factor subunit 2 tau variant OS=Mus musculus GN=Cstf2t PE=1 SV=2

 Score =  147 bits (372), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/226 (41%), Positives = 119/226 (52%), Gaps = 61/226 (26%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVG VVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 16  RSVFVGNIPYEATEEQLKDIFSEVGSVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           NL G E +GR LRVD A ++K    N+E+              K LG             
Sbjct: 76  NLNGREFSGRALRVDNAASEK----NKEE-------------LKSLG------------- 105

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDP------LTLHLAKMSRNQL 180
                   AA +                  I S    P DP      +T  +A +   Q+
Sbjct: 106 -------PAAPI------------------IDSPYGDPIDPEDAPESITRAVASLPPEQM 140

Query: 181 NEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQV 226
            E+M +MKL    + ++AR +LL  P L  AL QAQ+++ +  P++
Sbjct: 141 FELMKQMKLCVQNSHQEARNMLLQNPQLAYALLQAQVVMRIMDPEI 186

May play a significant role in AAUAAA-independent mRNA polyadenylation in germ cells. Directly involved in the binding to pre-mRNAs.

Mus musculus (taxid: 10090)

>sp|Q9P6P7|YKCG_SCHPO Uncharacterized RNA-binding protein C644.16 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC644.16 PE=4 SV=1

 Score =  122 bits (307), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 77/210 (36%), Positives = 109/210 (51%), Gaps = 7/210 (3%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           V+VGNIPY+  EEQ+I+I ++ GPV SF+LVID E+G+PKGYGFCEY D  TA SA RNL
Sbjct: 7   VYVGNIPYEMAEEQVIDIFKQSGPVKSFQLVIDPESGQPKGYGFCEYHDPATAASAVRNL 66

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIG 128
             Y+   R+LRVDF   D+    ++  G    G      PQ        +G +    P  
Sbjct: 67  NNYDAGTRRLRVDFPTADQIRRLDKLLGPSRYGYY----PQSYANQSYTYGNNFGSYP-P 121

Query: 129 LHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMK 188
              +        G       G +         LA  ND +   LA+++ N+++ ++S +K
Sbjct: 122 TQPSTQPLPQSYGYPSYPPAGYRGGSARPSGVLA--NDEVYRVLAQLAPNEIDYMLSAIK 179

Query: 189 LMATQNKEQARQLLLAKPPLLKALFQAQIM 218
            +  +  EQA QL    P L  A+FQA +M
Sbjct: 180 ALCLEAPEQAAQLFETNPQLSYAVFQAMLM 209

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

>sp|O43040|CTF1_SCHPO Cleavage and termination factor 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ctf1 PE=1 SV=1

 Score =  118 bits (295), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 133/285 (46%), Gaps = 56/285 (19%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           M+ +    VFVGNIPYD +E+Q+ EI  +VGPV +F+LV+D ETG  KGYGFCE+ D ET
Sbjct: 1   MSMTAGNVVFVGNIPYDVSEQQMTEIFNQVGPVKTFKLVLDPETGSGKGYGFCEFFDSET 60

Query: 61  ALSARRNLQGYEINGRQLRVDFAEND----------KGADRNREQ---------GRGGPG 101
              A R L   E+  R++RV+F  ND          +  DR  EQ          R  P 
Sbjct: 61  TAMAVRKLNNSELGPRKIRVEFPSNDPRRNQSYEYTERTDRYMEQQNAHESSYNSRFIPP 120

Query: 102 MAAIVD--PQKQLGG---PAIHGESVHHQPIGLHIAITAAAV--------MTGALGAA-- 146
           +       P  Q GG   PAI+  S+      L+  I + +V        MT    +A  
Sbjct: 121 VLHSTSSLPASQGGGMPSPAIYSSSM---ATNLNKNINSTSVPAYNFHNSMTSDFDSASQ 177

Query: 147 -----------QVGVQSNQNGIQSQLASPNDPLTLHLA--------KMSRNQLNEIMSEM 187
                      Q    S   G  +   S ++P ++ LA          S  +L  ++S++
Sbjct: 178 PHTDAYNARTFQYNKSSQNKGDYTSGTSISNPTSIPLAPSVVQVLSTFSAQELLNMLSKL 237

Query: 188 KLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPIL 232
           + +     E+AR+LL+A P L  A FQA +++ +    VLQ  ++
Sbjct: 238 QTVVHIAPEEARRLLIANPALPYAAFQAMLLMNLVDANVLQQVVV 282

Component of the cleavage factor I (CF I) involved in pre-mRNA 3'-end processing.

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

>sp|P25299|RNA15_YEAST mRNA 3'-end-processing protein RNA15 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RNA15 PE=1 SV=1

 Score = 94.7 bits (234), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 36/79 (45%), Positives = 59/79 (74%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R V++G+IPYD TEEQ++++C  VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 18 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 77

Query: 67 NLQGYEINGRQLRVDFAEN 85
          NL GY++  R L+  ++ N
Sbjct: 78 NLNGYQLGSRFLKCGYSSN 96

RNA-binding component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with the cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex. Binds to A-rich RNA sequence elements.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q8R0F5|RBMX2_MOUSE RNA-binding motif protein, X-linked 2 OS=Mus musculus GN=Rbmx2 PE=1 SV=1

 Score = 68.6 bits (166), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 48/77 (62%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FVG +PY+ TE  +I +  + G +V+  LV D++TGK KG+ F  Y+D+ + + A  N 
Sbjct: 38  IFVGGLPYELTEGDIICVFSQYGEIVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNF 97

Query: 69  QGYEINGRQLRVDFAEN 85
            G +I GR +RVD   N
Sbjct: 98  NGIKIKGRTIRVDHVSN 114

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	551
255572355	509	mRNA splicing factor, putative [Ricinus	0.891	0.964	0.638	1e-173
359495190	562	PREDICTED: uncharacterized protein LOC10	0.949	0.930	0.612	1e-164
356574567	544	PREDICTED: uncharacterized protein LOC10	0.940	0.952	0.583	1e-154
356535727	545	PREDICTED: uncharacterized protein LOC10	0.940	0.950	0.577	1e-150
449494200	527	PREDICTED: uncharacterized protein LOC10	0.925	0.967	0.563	1e-145
449446484	527	PREDICTED: uncharacterized protein LOC10	0.925	0.967	0.561	1e-144
224066585	561	predicted protein [Populus trichocarpa]	0.898	0.882	0.588	1e-142
22330574	461	cleavage stimulating factor 64 [Arabidop	0.818	0.978	0.477	1e-112
297839015	460	predicted protein [Arabidopsis lyrata su	0.814	0.976	0.476	1e-112
21591633	461	cleavage stimulation factor 64 [Arabidop	0.818	0.978	0.475	1e-112

>gi|255572355|ref|XP_002527116.1| mRNA splicing factor, putative [Ricinus communis] gi|223533539|gb|EEF35279.1| mRNA splicing factor, putative [Ricinus communis]

 Score =  615 bits (1587), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 331/518 (63%), Positives = 382/518 (73%), Gaps = 27/518 (5%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           +SSQ RCVFVGNIPYDATEEQLI+ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA
Sbjct: 3   SSSQQRCVFVGNIPYDATEEQLIDICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 62

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGES 121
           LSARRNLQGYEINGRQLRVDFAENDK ADRNREQGRGGPG+A I DPQKQ+GGPAI GES
Sbjct: 63  LSARRNLQGYEINGRQLRVDFAENDKNADRNREQGRGGPGLANI-DPQKQIGGPAILGES 121

Query: 122 VHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLN 181
             HQPIGLHIAITAA VM GALG  Q G+QSN NG+QSQ A  +DPLTLHLAKMSR+QLN
Sbjct: 122 AQHQPIGLHIAITAATVMAGALGGVQTGMQSNLNGLQSQSALASDPLTLHLAKMSRSQLN 181

Query: 182 EIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQ 241
           +IMSE+K+MATQNKE AR LLL KP L KALFQAQIMLGM TPQVLQMP +RQ PG PA 
Sbjct: 182 DIMSELKVMATQNKESARHLLLTKPQLPKALFQAQIMLGMVTPQVLQMPNIRQPPGQPAV 241

Query: 242 PLFQDGQQ----QVAQLPGLPPLAQKMQ--LMPKVQEAQIQ-------LHNQFSAATQPT 288
              +D QQ     +  +PGLPP +Q++Q  L+PK+QE Q         + NQFS   Q  
Sbjct: 242 RPLEDSQQGQRPAIQNVPGLPPFSQRIQSSLVPKLQEGQFSSVSQNSLVQNQFSVPPQ-L 300

Query: 289 LHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLEN 348
           + P+ Q+ Q++ +   QQA L GQSG+P +P +HPSVRPQIQ+ANSSSLNQQ  PPSL  
Sbjct: 301 VQPRTQIQQHSNSHIPQQAILSGQSGVPPIPHVHPSVRPQIQVANSSSLNQQT-PPSLLQ 359

Query: 349 Q--VQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERS 406
           Q   QV  +N G+ +   LPN AM SS  P P   DA FQPGP   +GI  +V R A+RS
Sbjct: 360 QPGKQVRTANFGRASHIVLPNVAMESSIFPRPLQPDAAFQPGPPILSGISDSVGRGADRS 419

Query: 407 ARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALN 466
            +VP+D  + HRNNAY  M   +      VND  + I+ PSK++K +DG   SFS  ALN
Sbjct: 420 TQVPDDTAQVHRNNAYFKMQTNM------VNDSKEPINRPSKMLKLDDGRSMSFSSSALN 473

Query: 467 VSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQ 504
           VSK   S P+Q+     VP N +PK EE+Q SEKQ+ Q
Sbjct: 474 VSK---SGPTQSHAISSVPANSLPKPEELQTSEKQVSQ 508

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495190|ref|XP_002264617.2| PREDICTED: uncharacterized protein LOC100256296 [Vitis vinifera] gi|297739347|emb|CBI29337.3| unnamed protein product [Vitis vinifera]

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 341/557 (61%), Positives = 406/557 (72%), Gaps = 34/557 (6%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           MASSQHRCVFVGNIPYDATEEQLI+IC EVGPVVSFRLVIDRETGKPKGYGFCEYKDEET
Sbjct: 1   MASSQHRCVFVGNIPYDATEEQLIQICEEVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGE 120
           ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM A V+PQKQ+GGPAI G+
Sbjct: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMVANVEPQKQVGGPAILGD 120

Query: 121 SVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQL 180
           +  HQP+GL +A+ A++VM GALG AQ G +SNQNG QSQ    +DPLTLHLAKMSRNQL
Sbjct: 121 AALHQPVGLPLAMAASSVMAGALGGAQAGSKSNQNGFQSQAMLGSDPLTLHLAKMSRNQL 180

Query: 181 NEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPA 240
           NE++S++K+MAT+NKE ARQLLL  P L KALFQAQIMLGM TPQVLQMP +RQ    P 
Sbjct: 181 NEVISDLKVMATKNKELARQLLLTSPQLPKALFQAQIMLGMVTPQVLQMPNIRQASVPPT 240

Query: 241 QPLFQDGQQQ----VAQLPGLPPLAQ-KMQ--LMPKVQEAQIQ-------LHNQFSAATQ 286
           QP+ QDGQQ     V  L GLPPLAQ KMQ  LMPK QE Q+        +H+QFSA  Q
Sbjct: 241 QPVLQDGQQGQQLAVQTLSGLPPLAQSKMQLGLMPKGQEGQVSAMPHNSLVHSQFSALPQ 300

Query: 287 PTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPS------VRPQIQLANSSSLNQQ 340
               PQIQLP    NQALQQA+  GQSG+  LPS+ P       VRPQIQ+A+SSSL  Q
Sbjct: 301 QPAQPQIQLPPQGHNQALQQATFAGQSGVTALPSVRPQPPAKLPVRPQIQVASSSSLKHQ 360

Query: 341 VHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVS 400
           + PP L+   Q  ++  G N+   +PN+ +R + +  P   D+GFQPG ST + I +T +
Sbjct: 361 MQPPLLQQPGQFGSAKSGNNSQLVIPNATLRPTLMTRPSFPDSGFQPGSSTFSSIPETTN 420

Query: 401 RDAERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSF 460
            +A+RS++V         NN Y+NM  GL+ K+S   D  + ++HPSK+VK +DG    F
Sbjct: 421 NNADRSSQV--------TNNTYSNMPSGLSMKKSMARDTSEPMNHPSKMVKLDDGRRAPF 472

Query: 461 SVGALNV----SKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQIS--PDVESALL 514
           S   LN+    +    S PSQ  G G V  NQ+ K EEVQ+ +K+ PQ+   P++ESALL
Sbjct: 473 STVGLNLSTSSASASASGPSQVLGIGSVSANQISKAEEVQHMDKKAPQLQLPPEIESALL 532

Query: 515 QQVLSLTPEQLNSLPPE 531
           QQVL+LTPEQL+SLPPE
Sbjct: 533 QQVLNLTPEQLSSLPPE 549

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356574567|ref|XP_003555417.1| PREDICTED: uncharacterized protein LOC100806489 [Glycine max]

 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 332/569 (58%), Positives = 391/569 (68%), Gaps = 51/569 (8%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
           SQHRCVFVGNIPYDATEEQLIEIC+EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS
Sbjct: 6   SQHRCVFVGNIPYDATEEQLIEICQEVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 65

Query: 64  ARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVH 123
           ARRNLQGYEINGRQLRVDFAENDKG DRNREQGRGGPGM   VD QKQ+G PA+HGE+V 
Sbjct: 66  ARRNLQGYEINGRQLRVDFAENDKGNDRNREQGRGGPGMTTNVDHQKQVGVPAVHGEAVQ 125

Query: 124 HQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEI 183
           HQPIGLHIAITAAAVMT ALG AQ G+QSNQN +QSQ A  +DPLTLHLAKMSR+QL EI
Sbjct: 126 HQPIGLHIAITAAAVMTAALGGAQFGIQSNQNSLQSQSALAHDPLTLHLAKMSRSQLTEI 185

Query: 184 MSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPL 243
           +SE+K MATQNKE ARQLLL++P L KALFQAQIMLGM T QVLQMP LR      +Q  
Sbjct: 186 ISELKGMATQNKELARQLLLSRPQLPKALFQAQIMLGMVTSQVLQMPNLRLVSDQTSQSS 245

Query: 244 FQDGQ----QQVAQLPGLPPLAQKMQ--LMPKVQEAQIQL--HN-----QFSAATQPTLH 290
             +GQ      V  L GLP    K+Q  L P  QE Q+    HN     Q +A  +P + 
Sbjct: 246 MNEGQLGQASLVQTLSGLPHGQDKLQPGLTPYAQEGQVNTIPHNPLVPSQLTAHPKPPVQ 305

Query: 291 PQIQLPQNAKNQALQQASLPGQSGIPMLPSMHP------SVRPQIQLANSSSLNQQVHPP 344
           P+I L QN  N  L   +L GQS + MLPS         SVRP IQLA S++LNQQ+H  
Sbjct: 306 PRIPLQQNPNNLVL-PGTLSGQSNL-MLPSARSPGLGSLSVRPPIQLATSTALNQQMHAS 363

Query: 345 SLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAE 404
            L++ V V  S +G N                         +PGPS S    Q +S+  +
Sbjct: 364 LLQHSVHVGNSTVGHNVQ-----------------------KPGPSMSTTNSQLLSK-GD 399

Query: 405 RSARVPEDGTRAHRNNAY--TNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSV 462
           +S++V ED   A R N Y  +N+ +G+  K + V D  +S + PSK++K ++G  T  S 
Sbjct: 400 KSSKVIEDLNWAKRTNTYSKSNIPLGV-EKTNMVRDSSESFTRPSKVMKLDEGRSTPLSA 458

Query: 463 GALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTP 522
           G L++  P+    S   G   +PV+  PK E  QYSE+Q  Q+ PDVES LLQQVL+LTP
Sbjct: 459 GILDM--PVTDGSSHILGRSSLPVHAAPKAEG-QYSEQQSSQLPPDVESVLLQQVLNLTP 515

Query: 523 EQLNSLPPEQRQQVIQLQQALLRDQMQPS 551
           EQL+SLPP+Q+QQV+QLQQAL RDQ+QPS
Sbjct: 516 EQLSSLPPDQQQQVLQLQQALRRDQIQPS 544

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535727|ref|XP_003536395.1| PREDICTED: uncharacterized protein LOC100794399 [Glycine max]

 Score =  540 bits (1390), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 329/570 (57%), Positives = 389/570 (68%), Gaps = 52/570 (9%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
           SQHRCVFVGNIPYDATEEQLIEIC+EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS
Sbjct: 6   SQHRCVFVGNIPYDATEEQLIEICQEVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 65

Query: 64  ARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVH 123
           ARRNLQGYEINGRQLRVDFAENDKG DRNREQGRGGPGM   VD QKQ+G PA+ GE+V 
Sbjct: 66  ARRNLQGYEINGRQLRVDFAENDKGNDRNREQGRGGPGMTTNVDHQKQVGIPAVLGEAVQ 125

Query: 124 HQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEI 183
           HQPIGLHIAITAAAVMT ALG AQ G+QSNQN +QSQ A  +DPLTLHLAKMSR+QL EI
Sbjct: 126 HQPIGLHIAITAAAVMTAALGGAQFGIQSNQNSLQSQSALAHDPLTLHLAKMSRSQLTEI 185

Query: 184 MSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPL 243
           +SE+K MATQNKE ARQLLL++P L KALFQAQIMLGM T QVLQMP LR      +Q L
Sbjct: 186 ISELKGMATQNKELARQLLLSRPQLPKALFQAQIMLGMVTSQVLQMPNLRLVSDQTSQSL 245

Query: 244 FQDGQ----QQVAQLPGLPPLAQ-KMQ--LMPKVQEAQIQL--H-----NQFSAATQPTL 289
             +GQ      V  L GLPP  Q K+Q  L P  QE Q+    H     NQ +A  +P +
Sbjct: 246 MNEGQLGQPSLVQTLSGLPPPGQGKLQPGLTPYAQEGQVNTIPHNPLAPNQLTAHPKPPV 305

Query: 290 HPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHP------SVRPQIQLANSSSLNQQVHP 343
            P+I L Q+  N  L   +L GQS + MLPS  P      SVRP IQ   S++LNQQ+HP
Sbjct: 306 QPRIPLQQHPNNLVL-PGTLSGQSNL-MLPSARPPGLGSLSVRPLIQPGTSTALNQQMHP 363

Query: 344 PSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDA 403
             L++ V V  S +G N                            PS S+   Q +S+  
Sbjct: 364 SLLQHSVHVGNSTVGHNIQMHC-----------------------PSMSSANSQLLSK-G 399

Query: 404 ERSARVPEDGTRAHRNNAY--TNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFS 461
           ++S++V ED   A R N +  +N+ +G+  K + V+D  +S + PSK++K ++G     S
Sbjct: 400 DKSSKVIEDLNWAKRANTHSKSNIPLGV-EKTNMVHDSSESFTRPSKVMKLDEGRSAPLS 458

Query: 462 VGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLT 521
            G  ++  P     S   G   +PV+  PK E  QYSE+Q  Q+ PDVES LLQQVL+LT
Sbjct: 459 SGISDM--PFTDGSSHILGRSSLPVHAAPKAEG-QYSEQQFSQLPPDVESVLLQQVLNLT 515

Query: 522 PEQLNSLPPEQRQQVIQLQQALLRDQMQPS 551
           PEQL+SLPP+Q+QQVIQLQQAL RDQ+QPS
Sbjct: 516 PEQLSSLPPDQQQQVIQLQQALRRDQIQPS 545

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449494200|ref|XP_004159476.1| PREDICTED: uncharacterized protein LOC101225147 [Cucumis sativus]

 Score =  520 bits (1340), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 320/568 (56%), Positives = 373/568 (65%), Gaps = 58/568 (10%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           MAS+QHRCVFVGNIPYDATEEQLIEIC+EVGPVVSFRLVIDRETGKPKGYGFCEYKDEET
Sbjct: 1   MASTQHRCVFVGNIPYDATEEQLIEICQEVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGE 120
           ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG+ A        GGP  HGE
Sbjct: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGLVA------NAGGPTPHGE 114

Query: 121 SVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQL 180
           S  HQPIGLHIAITAAAVM GA         SNQN +QS    PNDPLTLHLAK+SR+QL
Sbjct: 115 SSQHQPIGLHIAITAAAVMAGA--LGGAQAASNQNNLQSA-TMPNDPLTLHLAKLSRSQL 171

Query: 181 NEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPA 240
            E+MS +K MATQNK+ ARQLLLA+P L KALFQ+QIMLGM TPQVLQ P L+Q   HP 
Sbjct: 172 TEVMSGLKAMATQNKDLARQLLLARPQLSKALFQSQIMLGMVTPQVLQKPNLQQSATHPQ 231

Query: 241 QPLFQDGQQQVAQL---PGLPPLA-QKMQ--LMPKVQEAQIQLH-------NQFSAATQP 287
            PL +  Q Q + L   PGLPPLA  +MQ   +PK +E Q  L        +QFSA+ +P
Sbjct: 232 LPLHESQQGQPSSLQIQPGLPPLAPNRMQTGFVPK-KETQSSLMPQNPLAPHQFSASQRP 290

Query: 288 TLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSM----HPSVRPQIQLANSSSLNQQVHP 343
           +L  QIQ           Q SL G  G   LPS+    + S+R Q+Q  +SSSL Q + P
Sbjct: 291 SLQSQIQPSHTL------QGSLTGIPGGSSLPSISLQGNISIRQQVQAPSSSSLKQHMRP 344

Query: 344 PSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDA 403
           P  +      A   G NT   + N   + S LPHP  SDA FQPGPST+    Q V  D 
Sbjct: 345 PPQQYLGHGGALIPGHNTH--ITNPEAKPSLLPHPSLSDADFQPGPSTAYSTPQIVGSDV 402

Query: 404 ERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVG 463
           ++S+ VP                +G+  KR+ ++    + + P K +K EDG G+SF  G
Sbjct: 403 DKSSPVP----------------LGVDGKRTMLHGFSGTTNRPVKQIKLEDGKGSSFLAG 446

Query: 464 ALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPE 523
            L+ S  IG+      G+G + +   P V   Q SEK    +  +VES LLQQVL+LTPE
Sbjct: 447 GLSTS--IGTN-----GSGQLGIASDPNVTGTQLSEKPTSLLPQNVESVLLQQVLNLTPE 499

Query: 524 QLNSLPPEQRQQVIQLQQALLRDQMQPS 551
           QLNSLP EQR QVI+LQ AL RDQM+PS
Sbjct: 500 QLNSLPLEQRLQVIELQHALRRDQMRPS 527

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446484|ref|XP_004141001.1| PREDICTED: uncharacterized protein LOC101211663 [Cucumis sativus]

 Score =  519 bits (1337), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 319/568 (56%), Positives = 373/568 (65%), Gaps = 58/568 (10%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           MAS+QHRCVFVGNIPYDATEEQLIEIC+EVGPVVSFRLVIDRETGKPKGYGFCEYKDEET
Sbjct: 1   MASTQHRCVFVGNIPYDATEEQLIEICQEVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGE 120
           ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG+ A        GGP  HGE
Sbjct: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGLVA------NAGGPTPHGE 114

Query: 121 SVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQL 180
           +  HQPIGLHIAITAAAVM GA         SNQN +QS    PNDPLTLHLAK+SR+QL
Sbjct: 115 ASQHQPIGLHIAITAAAVMAGA--LGGAQAASNQNNLQSA-TMPNDPLTLHLAKLSRSQL 171

Query: 181 NEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPA 240
            E+MS +K MATQNK+ ARQLLLA+P L KALFQ+QIMLGM TPQVLQ P L+Q   HP 
Sbjct: 172 TEVMSGLKAMATQNKDLARQLLLARPQLSKALFQSQIMLGMVTPQVLQKPNLQQSATHPQ 231

Query: 241 QPLFQDGQQQVAQL---PGLPPLA-QKMQ--LMPKVQEAQIQLH-------NQFSAATQP 287
            PL +  Q Q + L   PGLPPLA  +MQ   +PK +E Q  L        +QFSA+ +P
Sbjct: 232 LPLHESQQGQPSSLQIQPGLPPLAPNRMQTGFVPK-KETQSSLMPQNPLAPHQFSASQRP 290

Query: 288 TLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSM----HPSVRPQIQLANSSSLNQQVHP 343
           +L  QIQ           Q SL G  G   LPS+    + S+R Q+Q  +SSSL Q + P
Sbjct: 291 SLQSQIQPSHTL------QGSLTGIPGGSSLPSISLQGNISIRQQVQAPSSSSLKQHMRP 344

Query: 344 PSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDA 403
           P  +      A   G NT   + N   + S LPHP  SDA FQPGPST+    Q V  D 
Sbjct: 345 PPQQYLGHGGALIPGHNTH--ITNPEAKPSLLPHPSLSDADFQPGPSTAYSTPQIVGSDV 402

Query: 404 ERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVG 463
           ++S+ VP                +G+  KR+ ++    + + P K +K EDG G+SF  G
Sbjct: 403 DKSSPVP----------------LGVDGKRTMLHGFSGTTNRPVKQIKLEDGKGSSFLAG 446

Query: 464 ALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPE 523
            L+ S  IG+      G+G + +   P V   Q SEK    +  +VES LLQQVL+LTPE
Sbjct: 447 GLSTS--IGTN-----GSGQLGIASDPNVTGTQLSEKPTSLLPQNVESVLLQQVLNLTPE 499

Query: 524 QLNSLPPEQRQQVIQLQQALLRDQMQPS 551
           QLNSLP EQR QVI+LQ AL RDQM+PS
Sbjct: 500 QLNSLPLEQRLQVIELQHALRRDQMRPS 527

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224066585|ref|XP_002302149.1| predicted protein [Populus trichocarpa] gi|222843875|gb|EEE81422.1| predicted protein [Populus trichocarpa]

 Score =  510 bits (1313), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 310/527 (58%), Positives = 367/527 (69%), Gaps = 32/527 (6%)

Query: 38  LVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
           LVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDK ADRNREQGR
Sbjct: 54  LVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKNADRNREQGR 113

Query: 98  GGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGI 157
           GGP +AA  DPQKQ GGPAI  E   HQPIGLHIAITAA VM G LG AQ  +QSNQNG+
Sbjct: 114 GGPRLAANNDPQKQAGGPAILEEPAQHQPIGLHIAITAATVMAGTLGGAQTVMQSNQNGL 173

Query: 158 QSQLASPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQI 217
           QSQ A  +DPLTLHLAKMSRNQLNEIMSE+K MATQN+E A QLLL KP L KALFQAQI
Sbjct: 174 QSQPALASDPLTLHLAKMSRNQLNEIMSELKGMATQNREAAHQLLLGKPQLSKALFQAQI 233

Query: 218 MLGMATPQVLQMPILRQGPGHPAQPLFQDGQQ----QVAQLPGLPPLAQKMQL------- 266
           MLGM TPQVLQ+P +RQ  G PA    QD QQ     V  LPGLPP AQ+MQL       
Sbjct: 234 MLGMVTPQVLQLPNIRQSTGQPALSSLQDSQQVQRPAVPNLPGLPPTAQRMQLGLGQFSA 293

Query: 267 --MPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPS 324
              P VQ  +  +HNQFSA  QP++  Q Q+P +  N     A+L GQS    LP++ PS
Sbjct: 294 GPQPSVQPQKSLVHNQFSATPQPSVQAQTQIPHHVNNHVPHHATLLGQSAP--LPAVLPS 351

Query: 325 VRPQIQLANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAG 384
           VRP +Q+ANS+ LNQQ+ P  +++  QV  +N   N    LPN AM+SS L  PP++ + 
Sbjct: 352 VRPPVQMANSAPLNQQMQPSLVQHTRQVGNTNARHNPQVVLPNKAMQSSLLSRPPATGS- 410

Query: 385 FQPGPSTSAGIGQTVSRDAERSARVPEDGTRAHRNNAYTNMSMGLASKRSTVNDPLDSIS 444
           FQ    + +      + +A+RS           R+NAY NM      + ST +D  + ++
Sbjct: 411 FQQSGLSVSSGLSDAA-NADRSTL---------RSNAYLNM------QTSTAHDSKEPVN 454

Query: 445 HPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKVEEVQYSEKQIPQ 504
            PSK++K +DG   S  +G  N+    GS PSQA     VP N +P+ E++Q+S KQ PQ
Sbjct: 455 RPSKVLKLDDGRSMSVPMGGSNLFSATGSGPSQAPAVNSVPPNPLPRPEDLQHSGKQAPQ 514

Query: 505 ISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQMQPS 551
           +  D+ESALLQQVL+LTPEQL+SLPP+Q+QQVIQLQQALLRDQMQPS
Sbjct: 515 LPADIESALLQQVLNLTPEQLSSLPPDQQQQVIQLQQALLRDQMQPS 561

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330574|ref|NP_177325.2| cleavage stimulating factor 64 [Arabidopsis thaliana] gi|7239507|gb|AAF43233.1|AC012654_17 Contains similarity to the polyadenylation factor 64 kDa subunit from Xenopus laevis gb|U17394; It contains RNA recognition motif PF|00076. ESTs gb|AI993960 and T42211 come from this gene [Arabidopsis thaliana] gi|110738120|dbj|BAF00992.1| cleavage stimulation factor like protein [Arabidopsis thaliana] gi|332197113|gb|AEE35234.1| cleavage stimulating factor 64 [Arabidopsis thaliana]

 Score =  412 bits (1060), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 266/557 (47%), Positives = 338/557 (60%), Gaps = 106/557 (19%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           +SSQ RCVFVGNIPYDATEEQL EIC EVGPVVSFRLV DRETGKPKGYGFCEYKDEETA
Sbjct: 4   SSSQRRCVFVGNIPYDATEEQLREICGEVGPVVSFRLVTDRETGKPKGYGFCEYKDEETA 63

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM---AAIVDPQKQLGGPAIH 118
           LSARRNLQ YEINGRQLRVDFAENDKG D+ R+Q +GGPG+     + + QKQ+GGP   
Sbjct: 64  LSARRNLQSYEINGRQLRVDFAENDKGTDKTRDQSQGGPGLPSTTTVTESQKQIGGPV-- 121

Query: 119 GESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRN 178
            +S  HQP+GLH+A TAA+V+ GALG  QVG Q  Q+ +Q      +DPL LHLAKMSR+
Sbjct: 122 -DSNMHQPVGLHLATTAASVIAGALGGPQVGSQFTQSNLQ---VPASDPLALHLAKMSRS 177

Query: 179 QLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGH 238
           QL EI+S +KLMATQNKE ARQLL+++P LLKA+F AQ+MLG+ +PQVLQ P + Q P H
Sbjct: 178 QLTEIISSIKLMATQNKEHARQLLVSRPQLLKAVFLAQVMLGIVSPQVLQSPNIVQAPSH 237

Query: 239 PAQPLFQDGQQQVAQLPG---LPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQL 295
                 QD     AQL G   LPPLAQ+ Q + +        H+Q+    Q +  P  Q+
Sbjct: 238 MTGSSIQD-----AQLSGQNLLPPLAQRSQQLSRAP------HSQY-PVQQSSKQPFSQI 285

Query: 296 PQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSAS 355
           P        Q  + PG S      S++P  R Q+++ N+    QQV P         +++
Sbjct: 286 P--------QLVAQPGPS------SVNPPPRSQVKVENAPFQRQQVVP---------AST 322

Query: 356 NLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERSARVPEDGTR 415
           N+G ++   +PN+A++ S +PH    ++  Q G       GQTVS               
Sbjct: 323 NIGYSSQNSVPNNAIQPSQVPHQALPNSVMQQG-------GQTVS--------------- 360

Query: 416 AHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAP 475
                    ++ G   KR     P  S++ PSK++K ED   TS   G ++ S      P
Sbjct: 361 ---------LNFG---KRINEGPPHQSMNRPSKMMKVEDRRTTSLPGGHVSNSM----LP 404

Query: 476 SQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQ 535
           +QA         Q P+             ISPDV+S LLQQV++LTPEQL  L PEQ+Q+
Sbjct: 405 NQA---------QAPQTH-----------ISPDVQSTLLQQVMNLTPEQLRLLTPEQQQE 444

Query: 536 VIQLQQALLRDQ-MQPS 551
           V++LQQAL +D  MQPS
Sbjct: 445 VLKLQQALKQDHMMQPS 461

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839015|ref|XP_002887389.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297333230|gb|EFH63648.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  412 bits (1059), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 263/552 (47%), Positives = 336/552 (60%), Gaps = 103/552 (18%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           +SSQ RCVFVGNIPYDATEEQL EIC EVGPVVSFRLV DRETGKPKGYGFCEYKDEETA
Sbjct: 3   SSSQRRCVFVGNIPYDATEEQLREICGEVGPVVSFRLVTDRETGKPKGYGFCEYKDEETA 62

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM---AAIVDPQKQLGGPAIH 118
           LSARRNLQ YEINGRQLRVDFAENDKG D+ R+QG+GGPG+   + + + QKQ+GGP   
Sbjct: 63  LSARRNLQSYEINGRQLRVDFAENDKGTDKTRDQGQGGPGLPSTSVMTESQKQIGGPV-- 120

Query: 119 GESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRN 178
            ++  HQP+GL++AITAA+VM GALG  QVG Q  Q+ +Q      +DPLTLHLAKMSR+
Sbjct: 121 -DTNMHQPVGLNVAITAASVMAGALGGPQVGSQFTQSNLQ---VPASDPLTLHLAKMSRS 176

Query: 179 QLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGH 238
           QL EI+S +KLMATQNKEQARQLL+++P LLKA+F AQIMLG+ +PQVLQ P + Q P H
Sbjct: 177 QLTEIISSIKLMATQNKEQARQLLVSRPQLLKAVFLAQIMLGIVSPQVLQSPNIVQAPSH 236

Query: 239 PAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQN 298
                 QD Q     L  LPPLAQ+ Q + +  ++Q  +        Q +  P  Q+P  
Sbjct: 237 MTGSSIQDTQLSGQNL--LPPLAQRSQQLSRAPQSQYPVQ-------QSSKQPFSQIP-- 285

Query: 299 AKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSASNLG 358
                 Q  + PG S      S++P  R Q++   +    QQ  P         +++N+G
Sbjct: 286 ------QLVAQPGPS------SVNPPPRSQVKGETAPFQRQQGVP---------ASTNIG 324

Query: 359 QNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERSARVPEDGTRAHR 418
            ++ T +PN+A++ S +PHP  +++  Q G       GQTVS +                
Sbjct: 325 YSSQTSVPNNAIQPSQVPHPALTNSVMQQG-------GQTVSLN---------------- 361

Query: 419 NNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQA 478
                        KR     P  S++ PSK++K +D   TS   G  + S          
Sbjct: 362 -----------YGKRINEGPPHQSMNRPSKMMKVDDRRTTSHPGGHASNS---------- 400

Query: 479 FGAGLVPVNQVPKVEEVQYSEKQIPQ--ISPDVESALLQQVLSLTPEQLNSLPPEQRQQV 536
               ++P NQV           Q PQ  ISPDV+  LLQQV++LTPEQL  L PEQ+Q+V
Sbjct: 401 ----MLP-NQV-----------QAPQTRISPDVQPTLLQQVMNLTPEQLRLLTPEQQQEV 444

Query: 537 IQLQQALLRDQM 548
           ++LQQAL +D M
Sbjct: 445 LKLQQALKQDHM 456

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21591633|gb|AAM64164.1|AF515695_1 cleavage stimulation factor 64 [Arabidopsis thaliana]

 Score =  411 bits (1057), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 265/557 (47%), Positives = 338/557 (60%), Gaps = 106/557 (19%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           +SSQ RCVFVGNIPYDATEEQL EIC EVGPVVSFRLV DRETGKPKGYGFCEYKDEETA
Sbjct: 4   SSSQRRCVFVGNIPYDATEEQLREICGEVGPVVSFRLVTDRETGKPKGYGFCEYKDEETA 63

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM---AAIVDPQKQLGGPAIH 118
           LSARRNLQ YEINGRQLRVDFAENDKG D+ R+Q +GGPG+     + + QKQ+GGP   
Sbjct: 64  LSARRNLQSYEINGRQLRVDFAENDKGTDKTRDQSQGGPGLPSTTTVTESQKQIGGPV-- 121

Query: 119 GESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRN 178
            +S  HQP+GLH+A TAA+V+ GA+G  QVG Q  Q+ +Q      +DPL LHLAKMSR+
Sbjct: 122 -DSNMHQPVGLHLATTAASVIAGAIGGPQVGSQFTQSNLQ---VPASDPLALHLAKMSRS 177

Query: 179 QLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGH 238
           QL EI+S +KLMATQNKE ARQLL+++P LLKA+F AQ+MLG+ +PQVLQ P + Q P H
Sbjct: 178 QLTEIISSIKLMATQNKEHARQLLVSRPQLLKAVFLAQVMLGIVSPQVLQSPNIVQAPSH 237

Query: 239 PAQPLFQDGQQQVAQLPG---LPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQL 295
                 QD     AQL G   LPPLAQ+ Q + +        H+Q+    Q +  P  Q+
Sbjct: 238 MTGSSIQD-----AQLSGQNLLPPLAQRSQQLSRAP------HSQY-PVQQSSKQPFSQI 285

Query: 296 PQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLANSSSLNQQVHPPSLENQVQVSAS 355
           P        Q  + PG S      S++P  R Q+++ N+    QQV P         +++
Sbjct: 286 P--------QLVAQPGPS------SVNPPPRSQVKVENAPFQRQQVVP---------AST 322

Query: 356 NLGQNTWTKLPNSAMRSSFLPHPPSSDAGFQPGPSTSAGIGQTVSRDAERSARVPEDGTR 415
           N+G ++   +PN+A++ S +PH    ++  Q G       GQTVS               
Sbjct: 323 NIGYSSQNSVPNNAIQPSQVPHQALPNSVMQQG-------GQTVS--------------- 360

Query: 416 AHRNNAYTNMSMGLASKRSTVNDPLDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAP 475
                    ++ G   KR     P  S++ PSK++K ED   TS   G ++ S      P
Sbjct: 361 ---------LNFG---KRINEGPPHQSMNRPSKMMKVEDRRTTSLPGGHVSNSM----LP 404

Query: 476 SQAFGAGLVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQ 535
           +QA         Q P+             ISPDV+S LLQQV++LTPEQL  L PEQ+Q+
Sbjct: 405 NQA---------QAPQTH-----------ISPDVQSTLLQQVMNLTPEQLRLLTPEQQQE 444

Query: 536 VIQLQQALLRDQ-MQPS 551
           V++LQQAL +D  MQPS
Sbjct: 445 VLKLQQALKQDHMMQPS 461

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	551
TAIR|locus:2013016	461	CSTF64 "cleavage stimulating f	0.604	0.722	0.501	1.6e-79
UNIPROTKB|Q5ZLS0	475	CSTF2 "Uncharacterized protein	0.170	0.197	0.691	9.8e-40
UNIPROTKB|E2R1C1	435	CSTF2T "Uncharacterized protei	0.170	0.216	0.670	4.4e-39
UNIPROTKB|F1S1L9	551	LOC100515986 "Uncharacterized	0.205	0.205	0.603	1.2e-37
UNIPROTKB|K7GQE7	555	LOC100515986 "Uncharacterized	0.205	0.203	0.603	1.7e-37
UNIPROTKB|E1BVJ6	592	CSTF2 "Uncharacterized protein	0.170	0.158	0.691	2.9e-37
FB|FBgn0027841	437	CstF-64 "Cleavage stimulation	0.147	0.185	0.740	3.4e-37
UNIPROTKB|E1C8T0	608	CSTF2 "Uncharacterized protein	0.170	0.154	0.691	4e-37
UNIPROTKB|Q8HXM1	572	CSTF2 "Cleavage stimulation fa	0.205	0.197	0.603	1.2e-36
UNIPROTKB|E9PID8	438	CSTF2 "Cleavage stimulation fa	0.205	0.257	0.603	1.3e-36

TAIR|locus:2013016 CSTF64 "cleavage stimulating factor 64" [Arabidopsis thaliana (taxid:3702)]

 Score = 799 (286.3 bits), Expect = 1.6e-79, P = 1.6e-79
 Identities = 179/357 (50%), Positives = 219/357 (61%)

Query:     2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
             +SSQ RCVFVGNIPYDATEEQL EIC EVGPVVSFRLV DRETGKPKGYGFCEYKDEETA
Sbjct:     4 SSSQRRCVFVGNIPYDATEEQLREICGEVGPVVSFRLVTDRETGKPKGYGFCEYKDEETA 63

Query:    62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAA---IVDPQKQLGGPAIH 118
             LSARRNLQ YEINGRQLRVDFAENDKG D+ R+Q +GGPG+ +   + + QKQ+GGP   
Sbjct:    64 LSARRNLQSYEINGRQLRVDFAENDKGTDKTRDQSQGGPGLPSTTTVTESQKQIGGPV-- 121

Query:   119 GESVHHQPIGLHIAIXXXXXXXXXXXXXQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRN 178
              +S  HQP+GLH+A              QVG Q  Q+ +Q      +DPL LHLAKMSR+
Sbjct:   122 -DSNMHQPVGLHLATTAASVIAGALGGPQVGSQFTQSNLQ---VPASDPLALHLAKMSRS 177

Query:   179 QLNEIMSEMKLMATQNKEQARQXXXXXXXXXXXXFQAQIMLGMATPQVLQMPILRQGPGH 238
             QL EI+S +KLMATQNKE ARQ            F AQ+MLG+ +PQVLQ P + Q P H
Sbjct:   178 QLTEIISSIKLMATQNKEHARQLLVSRPQLLKAVFLAQVMLGIVSPQVLQSPNIVQAPSH 237

Query:   239 PAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQN 298
                   QD Q     L  LPPLAQ+ Q + +        H+Q+    Q +  P  Q+PQ 
Sbjct:   238 MTGSSIQDAQLSGQNL--LPPLAQRSQQLSRAP------HSQYPVQ-QSSKQPFSQIPQL 288

Query:   299 AKNQALQQASLPGQSGIPM--LPSMHPSVRP---QIQLANSSSL-NQQVHPPSLENQ 349
                      + P +S + +   P     V P    I  ++ +S+ N  + P  + +Q
Sbjct:   289 VAQPGPSSVNPPPRSQVKVENAPFQRQQVVPASTNIGYSSQNSVPNNAIQPSQVPHQ 345

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:0003729 "mRNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0031123 "RNA 3'-end processing" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP

GO:0048589 "developmental growth" evidence=IMP

UNIPROTKB|Q5ZLS0 CSTF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 332 (121.9 bits), Expect = 9.8e-40, Sum P(3) = 9.8e-40
 Identities = 65/94 (69%), Positives = 74/94 (78%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             NL G E +GR LRVD A ++K  +  +  G G P
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2R1C1 CSTF2T "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 317 (116.6 bits), Expect = 4.4e-39, Sum P(3) = 4.4e-39
 Identities = 63/94 (67%), Positives = 72/94 (76%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVG VVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    20 RSVFVGNIPYEATEEQLKDIFSEVGSVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 79

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             NL G E +GR LRVD A ++K  +  +  G   P
Sbjct:    80 NLNGREFSGRALRVDNAASEKNKEELKSLGPAAP 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1S1L9 LOC100515986 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 333 (122.3 bits), Expect = 1.2e-37, Sum P(3) = 1.2e-37
 Identities = 70/116 (60%), Positives = 81/116 (69%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESV 122
             NL G E +GR LRVD A ++K  +  +  G G P    I  P  +   P    ES+
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESPYGETISPEDAPESI 128

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|K7GQE7 LOC100515986 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 333 (122.3 bits), Expect = 1.7e-37, Sum P(4) = 1.7e-37
 Identities = 70/116 (60%), Positives = 81/116 (69%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESV 122
             NL G E +GR LRVD A ++K  +  +  G G P    I  P  +   P    ES+
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESPYGETISPEDAPESI 128

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1BVJ6 CSTF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 332 (121.9 bits), Expect = 2.9e-37, Sum P(3) = 2.9e-37
 Identities = 65/94 (69%), Positives = 74/94 (78%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             NL G E +GR LRVD A ++K  +  +  G G P
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

FB|FBgn0027841 CstF-64 "Cleavage stimulation factor 64 kilodalton subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 308 (113.5 bits), Expect = 3.4e-37, Sum P(3) = 3.4e-37
 Identities = 60/81 (74%), Positives = 68/81 (83%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEE+L EI  EVGPV+S +LV DRE+GKPKG+GFCEYKD+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEKLKEIFSEVGPVLSLKLVFDRESGKPKGFGFCEYKDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDK 87
             NL GYEI GR LRVD A  +K
Sbjct:    76 NLNGYEIGGRTLRVDNACTEK 96

GO:0006379 "mRNA cleavage" evidence=ISS;NAS

GO:0005848 "mRNA cleavage stimulating factor complex" evidence=ISS;NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|E1C8T0 CSTF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 332 (121.9 bits), Expect = 4.0e-37, Sum P(3) = 4.0e-37
 Identities = 65/94 (69%), Positives = 74/94 (78%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             NL G E +GR LRVD A ++K  +  +  G G P
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q8HXM1 CSTF2 "Cleavage stimulation factor subunit 2" [Bos taurus (taxid:9913)]

 Score = 333 (122.3 bits), Expect = 1.2e-36, Sum P(3) = 1.2e-36
 Identities = 70/116 (60%), Positives = 81/116 (69%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESV 122
             NL G E +GR LRVD A ++K  +  +  G G P    I  P  +   P    ES+
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESPYGETISPEDAPESI 128

GO:0071920 "cleavage body" evidence=ISS

GO:0005847 "mRNA cleavage and polyadenylation specificity factor complex" evidence=ISS

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PID8 CSTF2 "Cleavage stimulation factor subunit 2" [Homo sapiens (taxid:9606)]

 Score = 333 (122.3 bits), Expect = 1.3e-36, Sum P(2) = 1.3e-36
 Identities = 70/116 (60%), Positives = 81/116 (69%)

Query:     7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct:    16 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 75

Query:    67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESV 122
             NL G E +GR LRVD A ++K  +  +  G G P    I  P  +   P    ES+
Sbjct:    76 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP---VIESPYGETISPEDAPESI 128

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_II000576	hypothetical protein (561 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00030785	hypothetical protein (770 aa)					•	•	•		0.514

---

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	551
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-51
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-47
smart00360	73	smart00360, RRM, RNA recognition motif	4e-28
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-25
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-25
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-22
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-20
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-19
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-19
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	9e-19
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-18
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-18
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-17
pfam14327	84	pfam14327, CSTF2_hinge, Hinge domain of cleavage s	2e-17
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-17
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-17
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-16
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-15
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-15
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-15
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-15
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-15
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-15
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-14
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-14
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-14
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	5e-14
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-14
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-14
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-13
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-13
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-13
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-13
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-13
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-13
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-13
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-13
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-13
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-13
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-13
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-12
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-12
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	4e-12
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-12
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	4e-12
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	7e-12
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-12
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-11
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-11
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-11
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-11
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	8e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	9e-11
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-10
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-10
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-10
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-10
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-10
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-10
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	2e-10
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	3e-10
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-10
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-10
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	7e-10
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	1e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-09
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-09
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-09
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-09
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-09
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	2e-09
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	3e-09
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-09
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-09
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-09
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-08
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-08
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-08
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-08
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	3e-08
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-08
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-08
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	4e-08
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-08
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	5e-08
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	5e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-08
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	6e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	8e-08
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	8e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-07
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-07
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-07
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-07
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-07
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	4e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	5e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-07
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	7e-07
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	7e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	9e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-06
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	1e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-06
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	1e-06
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	1e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-06
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	3e-06
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	4e-06
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	6e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	6e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-06
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	6e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-06
cd12432	90	cd12432, RRM_ACINU, RNA recognition motif in apopt	7e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	7e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	9e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	9e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	1e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-05
cd12489	85	cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in v	2e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-05
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	4e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	6e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	6e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	6e-05
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	6e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	7e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	7e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	7e-05
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	7e-05
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	7e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	8e-05
cd12488	85	cd12488, RRM2_hnRNPR, RNA recognition motif 2 in v	8e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	8e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	1e-04
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	1e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	1e-04
cd12492	85	cd12492, RRM2_RBM46, RNA recognition motif 2 found	1e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	2e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-04
cd12434	75	cd12434, RRM_RCAN_like, RNA recognition motif in r	2e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	2e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	3e-04
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	3e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	4e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	5e-04
cd12686	81	cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif	5e-04
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	5e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	5e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	6e-04
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	7e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-04
cd12491	89	cd12491, RRM2_RBM47, RNA recognition motif 2 in ve	7e-04
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	7e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	7e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	8e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	9e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	9e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	9e-04
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12445	81	cd12445, RRM2_CPEBs, RNA recognition motif 2 in cy	0.001
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.001
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	0.001
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.001
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.001
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.002
pfam14304	44	pfam14304, CSTF_C, Transcription termination and c	0.002
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.002
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.003
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.003
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.004
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	0.004
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.004
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.004
cd12295	74	cd12295, RRM_YRA2, RNA recognition motif in yeast	0.004
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.004
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.004
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.004
cd12521	74	cd12521, RRM3_MRN1, RNA recognition motif 3 of RNA	0.004

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score =  168 bits (427), Expect = 6e-51
 Identities = 64/75 (85%), Positives = 68/75 (90%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEYKD+ETALSA RNL
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 69 QGYEINGRQLRVDFA 83
           GYE+NGRQLRVD A
Sbjct: 61 NGYELNGRQLRVDNA 75

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

>gnl|CDD|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 =  158 bits (402), Expect = 3e-47
 Identities = 63/75 (84%), Positives = 66/75 (88%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVGNIPYDATEEQLIEI  EVGPVVSFRLV DR+TGKPKGYGFCE++D ETA SA RNL
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 69 QGYEINGRQLRVDFA 83
           GYE NGR LRVDFA
Sbjct: 61 NGYEFNGRALRVDFA 75

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

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

 Score =  106 bits (267), Expect = 4e-28
 Identities = 37/73 (50%), Positives = 49/73 (67%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           +FVGN+P D TEE+L E+  + G V S RLV D+ETGK KG+ F E++ EE A  A   
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 68 LQGYEINGRQLRV 80
          L G E++GR L+V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 98.8 bits (247), Expect = 2e-25
 Identities = 35/71 (49%), Positives = 48/71 (67%), Gaps = 1/71 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P D TEE L ++  + GP+ S R+V D ETG+ KG+ F E++DEE A  A   L
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 69 QGYEINGRQLR 79
           G E+ GR+LR
Sbjct: 60 NGKELGGRELR 70

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

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

 Score = 98.1 bits (245), Expect = 6e-25
 Identities = 32/75 (42%), Positives = 47/75 (62%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          +VGN+PY+ TEE L ++  + G V S R++ DRETG+ +G+GF E +  E A +A   L 
Sbjct: 3  YVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLN 62

Query: 70 GYEINGRQLRVDFAE 84
          G +  GR L V+ A 
Sbjct: 63 GTDFGGRTLTVNEAR 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 89.3 bits (222), Expect = 5e-22
 Identities = 32/73 (43%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P D TEE L E+  + G + S R+V D+  GK KG+ F E++  E A  A   L
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 69 QGYEINGRQLRVD 81
           G E++GR+L+V 
Sbjct: 60 NGKELDGRKLKVS 72

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

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

 Score = 83.8 bits (208), Expect = 6e-20
 Identities = 34/82 (41%), Positives = 50/82 (60%), Gaps = 5/82 (6%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA---LS 63
          R VF+ N+P+DATEE+L E+  + G V   R+V D+ TG  KG  F ++K +E+A   L 
Sbjct: 1  RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 64 ARRNLQ--GYEINGRQLRVDFA 83
          A  N +  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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 88.9 bits (219), Expect = 2e-19
 Identities = 40/82 (48%), Positives = 52/82 (63%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             +FVGN+PYD TEE L E+ ++ GPV   RLV DRETGK +G+ F E++ EE+A  A  
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 67  NLQGYEINGRQLRVDFAENDKG 88
            L G E+ GR LRV  A+    
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQ 197

Length = 306

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

 Score = 82.3 bits (204), Expect = 2e-19
 Identities = 28/77 (36%), Positives = 48/77 (62%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++G +PY+ TE  ++ +  + G +V   LV D++TGK KG+ F  Y+D+ + + A  NL
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 69 QGYEINGRQLRVDFAEN 85
           G ++ GR +RVD   N
Sbjct: 72 NGIKLLGRTIRVDHVRN 88

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

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

 Score = 80.3 bits (199), Expect = 9e-19
 Identities = 29/72 (40%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVGN+P+D  EE+L +   + G V + R+V DR+TG  KG+G+  +K +++   A   L
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA-LKL 60

Query: 69 QGYEINGRQLRV 80
           G ++ GR++RV
Sbjct: 61 NGIKLKGRKIRV 72

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

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

 Score = 78.8 bits (195), Expect = 4e-18
 Identities = 32/72 (44%), Positives = 48/72 (66%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVGNIP   +++ + ++  + G V+S++ V D  TGK K +GFCE++D E AL A R L
Sbjct: 3  VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 69 QGYEINGRQLRV 80
           G E+ G++L V
Sbjct: 63 NGLELGGKKLLV 74

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

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

 Score = 78.5 bits (194), Expect = 4e-18
 Identities = 33/77 (42%), Positives = 47/77 (61%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           + VGN+P + T+EQ  E+    G V    LV    TG+ KGYGF EY  + +AL A+  
Sbjct: 1  LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 68 LQGYEINGRQLRVDFAE 84
          L G +I GR+L+VD+A+
Sbjct: 61 LDGKQIGGRKLQVDWAD 77

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

 Score = 77.7 bits (192), Expect = 1e-17
 Identities = 30/75 (40%), Positives = 46/75 (61%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          + +FV  + YD TE +L     E GP+   RLV D++TGKP+GY F E++ E    +A +
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 67 NLQGYEINGRQLRVD 81
             G +I+GR++ VD
Sbjct: 62 YADGKKIDGRRVLVD 76

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

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

 Score = 76.7 bits (189), Expect = 2e-17
 Identities = 27/75 (36%), Positives = 46/75 (61%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+ +   +E L     + G VV  R++ DRETG+ +G+G+ +++  E A  A   +
Sbjct: 2  LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 69 QGYEINGRQLRVDFA 83
           G E++GR + VDF+
Sbjct: 62 DGKELDGRPINVDFS 76

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

>gnl|CDD|222683 pfam14327, CSTF2_hinge, Hinge domain of cleavage stimulation factor subunit 2

 Score = 76.9 bits (190), Expect = 2e-17
 Identities = 27/67 (40%), Positives = 44/67 (65%)

Query: 165 NDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATP 224
            D ++  L+K+   QL E++S+MK +A QN +QARQLL   P L  AL QA +++G+  P
Sbjct: 16  PDAISQTLSKLPPEQLLELISQMKTLAQQNPDQARQLLQQNPQLAYALLQALLLMGLVDP 75

Query: 225 QVLQMPI 231
           +V+ + +
Sbjct: 76  EVITLVL 82

The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localisation. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex. Length = 84

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

 Score = 75.5 bits (186), Expect = 5e-17
 Identities = 29/73 (39%), Positives = 47/73 (64%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+ +DA E+ + E   E G + S RL  D ++G+PKG+G+ E+  +E A +A   L
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 69 QGYEINGRQLRVD 81
           G ++ GR +R+D
Sbjct: 61 GGTDLLGRPVRLD 73

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

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

 Score = 75.3 bits (186), Expect = 5e-17
 Identities = 26/72 (36%), Positives = 39/72 (54%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G +P   +E+Q+ E+    G + +F LV D  TG  KGY FCEY D      A   L
Sbjct: 3  IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 69 QGYEINGRQLRV 80
           G ++  ++L V
Sbjct: 63 NGMQLGDKKLTV 74

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

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

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 29/76 (38%), Positives = 46/76 (60%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+PYD T+EQL E   EVGP+    +V D+ + K +G+G+  +  EE A  A    
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 69 QGYEINGRQLRVDFAE 84
          +  +  GR++ V+FA+
Sbjct: 62 KKTKFGGRKIHVEFAK 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 28/71 (39%), Positives = 42/71 (59%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          +VGN+ ++ TE+ L  I    G +   +L  D ETG+ KGYGF ++ D E A  A   L 
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 70 GYEINGRQLRV 80
          G+E+ GR ++V
Sbjct: 62 GFELAGRPIKV 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 71.0 bits (174), Expect = 2e-15
 Identities = 28/76 (36%), Positives = 44/76 (57%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+ +  T+E L +   +V P+    +V D ETG+ +GYGF  +   E A  A   L
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 69 QGYEINGRQLRVDFAE 84
          +  +++GR LR+D AE
Sbjct: 62 KNKKLHGRILRLDIAE 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|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 = 70.8 bits (174), Expect = 2e-15
 Identities = 26/71 (36%), Positives = 37/71 (52%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          FV N+P+  TEE+L E+    G +    L +D+ET + KG+ F  +   E A+ A   L 
Sbjct: 3  FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 70 GYEINGRQLRV 80
          G    GR L V
Sbjct: 63 GSIFQGRLLHV 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 71.1 bits (175), Expect = 3e-15
 Identities = 31/77 (40%), Positives = 41/77 (53%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          +  +FVG +    TEE L E+    G +   RLV D  TG  KGY F EY+ E  AL A 
Sbjct: 3  YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 66 RNLQGYEINGRQLRVDF 82
          R+     I+G ++ VDF
Sbjct: 63 RDAHKLVIDGSEIFVDF 79

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 70.5 bits (173), Expect = 3e-15
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+PYD T E L+   +  G   S RL+ D++TGK KG  F E+   E A++    L
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAE-AMTKALKL 61

Query: 69 QGYEINGRQLRVD 81
              + GR++ V+
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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 69.4 bits (170), Expect = 7e-15
 Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +P+  T+E+L ++ ++ G V S RLV +R +GKPKG  + EY++E +A  A   +
Sbjct: 5  LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63

Query: 69 QGYEINGRQLRV 80
           G EI  + + V
Sbjct: 64 DGTEIKEKTISV 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 4/76 (5%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVI--DRETGKPKGYGFCEYKDEETALSARR 66
          ++VGN+ +  TEEQ+ E+    G +   R+++  DR T  P G+ F EY   E A +A +
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 67 NLQGYEINGRQLRVDF 82
           L G +++ R +RVD+
Sbjct: 59 YLNGTKLDDRIIRVDW 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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVG IP D  E++L+ +  + GP+   RL++D  +G  +GY F  Y ++E A  A + L
Sbjct: 4  VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 69 QGYEIN-GRQLRV 80
            YEI  G++L V
Sbjct: 63 HNYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 67.0 bits (164), Expect = 4e-14
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+ + A ++ L E  +E G VV  R+  D + G+ KG+G  E+  EE A  A    
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALE-K 59

Query: 69 QGYEINGRQLRVDFAE 84
           G E+ GR++RVD A 
Sbjct: 60 SGEELLGREIRVDLAT 75

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

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

 Score = 66.8 bits (164), Expect = 5e-14
 Identities = 28/72 (38%), Positives = 42/72 (58%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VGN+    TEE L E+  + GPVV+  +  DR T   +GYGF E+  EE A  A + +
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 69 QGYEINGRQLRV 80
             ++ G+ +RV
Sbjct: 61 NMIKLYGKPIRV 72

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

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

 Score = 66.9 bits (164), Expect = 6e-14
 Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +PY  T++ L +   + G +    ++ DR+TGK +GYGF  +KD+E+A  A ++ 
Sbjct: 3  IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 69 QGYEINGRQLRVDFA 83
              I+GR+  V+ A
Sbjct: 63 NPI-IDGRKANVNLA 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 66.6 bits (163), Expect = 6e-14
 Identities = 30/73 (41%), Positives = 45/73 (61%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V  +P D T+E+L  +   +GP+ S ++V DR TG+  GYGF +Y DE  A  A   L G
Sbjct: 5  VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

Query: 71 YEINGRQLRVDFA 83
          +EI  ++L+V +A
Sbjct: 65 FEIRNKRLKVSYA 77

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

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

 Score = 66.5 bits (163), Expect = 7e-14
 Identities = 25/65 (38%), Positives = 42/65 (64%)

Query: 19 TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL 78
          TE  L E+    GP+   ++V D++TG+ +G+GF  ++  E A  A+  L G EI+GR++
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71

Query: 79 RVDFA 83
          RVD++
Sbjct: 72 RVDYS 76

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 26/77 (33%), Positives = 45/77 (58%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +    TE++L  +  + G V    L+ D ETG+ +G+GF  ++  E A +A R+L
Sbjct: 4  LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 69 QGYEINGRQLRVDFAEN 85
           G E+ GR ++V+ A+ 
Sbjct: 64 NGKELEGRVIKVEKAKR 80

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

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

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 25/72 (34%), Positives = 44/72 (61%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V ++  D +E+ +  +    G + S  L  D ETGK KGYGF EY++ ++A  A  ++
Sbjct: 3  IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 69 QGYEINGRQLRV 80
            +++ G+QLRV
Sbjct: 63 NLFDLGGQQLRV 74

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

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

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+V N+  D  +E+L E+  + G + S +++ D + GK KG+GF  +++ E A  A   L
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 69 QGYEINGRQLRV 80
           G E+NG++L V
Sbjct: 63 NGKEVNGKKLYV 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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 66.1 bits (162), Expect = 1e-13
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +A EE + +   E G + +  L +DR TG  KGY   EY+ ++ A +A   L
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 69 QGYEINGRQLRVDFA 83
           G E+ G+ + VD+A
Sbjct: 69 NGKELLGQTISVDWA 83

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V N+  DA E+ L E+ R  GP+    L  D+ETG+ +G+ F  +   E A  A   L G
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 71 YEINGRQLRVDFAE 84
          +  +   L V++A+
Sbjct: 64 FGYDNLILSVEWAK 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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 31/73 (42%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 9  VFVGNIPYDATEEQLIEICRE-VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          VF+ NIPYD   + L ++ RE VG V    L  D E GK +G G  E+KD+E+   A   
Sbjct: 2  VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALET 60

Query: 68 LQGYEINGRQLRV 80
          +  YE+ GR+L V
Sbjct: 61 MNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 7/75 (9%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE---ETALSAR 65
          +FVGN+ Y  T E+L E  +  G +    ++ D+ TG+PKG+ + E+ D+   E AL   
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-- 59

Query: 66 RNLQGYEINGRQLRV 80
            L   E  GRQ++V
Sbjct: 60 --LNESEFRGRQIKV 72

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

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

 Score = 64.8 bits (158), Expect = 2e-13
 Identities = 27/76 (35%), Positives = 48/76 (63%), Gaps = 3/76 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+ ++ TE++L      VG +   R++   ++GK KG+ F ++++ E A +A   L
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57

Query: 69 QGYEINGRQLRVDFAE 84
          +G  +NGR LRV++ E
Sbjct: 58 KGKHLNGRALRVEYGE 73

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

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

 Score = 66.6 bits (162), Expect = 4e-13
 Identities = 31/93 (33%), Positives = 51/93 (54%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+G + +   +  L +     G VV  ++++DRETG+ +G+GF  + DE  A +A   +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            G E+NGR +RV+ A +   A R    G G  G
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSG 129

Length = 144

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 64.3 bits (157), Expect = 4e-13
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 8/76 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREV---GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          V++GN+ +D TE+ +    RE      + S RL  D+ETG+ KG+G  ++ DEE +L A 
Sbjct: 2  VYIGNLAWDITEDDV----REFFKGCEITSVRLATDKETGEFKGFGHVDFADEE-SLDAA 56

Query: 66 RNLQGYEINGRQLRVD 81
            L G  + GR +R+ 
Sbjct: 57 LKLDGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 70.7 bits (173), Expect = 6e-13
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
           S+ R +++GN+P    E+Q+ E+    G + +F L+ D  TG  KGY FCEYKD      
Sbjct: 294 SKDR-IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352

Query: 64  ARRNLQGYEINGRQLRVDFA 83
           A   L G +    +L V  A
Sbjct: 353 AIAALNGKDTGDNKLHVQRA 372

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

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 21/72 (29%), Positives = 39/72 (54%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VG +  +  E+ L       G +   ++ +D ET K +G+ F E+++ E A +A  N+
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 69 QGYEINGRQLRV 80
             E+ GR +RV
Sbjct: 61 NESELFGRTIRV 72

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

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVV-SFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +FVG++  D T+  L E  R   P V   ++V+D  TG+ KGYGF  + DE+    A   
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 68 LQGYEINGRQLRVDFA 83
          + G   + R +RV  A
Sbjct: 64 MNGVYCSSRPMRVSPA 79

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 61.5 bits (150), Expect = 4e-12
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          ++VGN+ +  T+E L     E G   V S +    +  GK KG+ + E+  E  A + + 
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 67 NLQGYEINGRQLRV 80
           L+G E NG++  V
Sbjct: 61 KLEGREFNGKKCVV 74

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 24/80 (30%), Positives = 41/80 (51%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           ++VG++  D TE  L EI    GPV+S R+  D  T +  GY +  +++   A  A   
Sbjct: 1  SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 68 LQGYEINGRQLRVDFAENDK 87
          L    I G+ +R+ +++ D 
Sbjct: 61 LNFDVIKGKPIRIMWSQRDP 80

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          FVGN+P++  +  L  I +++  V S RLV D+ET K KG+ + E++D E+ L       
Sbjct: 5  FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVES-LKEALEYD 62

Query: 70 GYEINGRQLRVDFA 83
          G   + R LRVD A
Sbjct: 63 GALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 60.7 bits (148), Expect = 7e-12
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 8/77 (10%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA--- 64
           VFV N+ Y   E++L ++  + G +   RLV + + GK KGY + E+++EE+   A   
Sbjct: 1  TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKL 59

Query: 65 RRNLQGYEINGRQLRVD 81
           R L    I GR + V 
Sbjct: 60 DREL----IKGRPMFVS 72

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

 Score = 60.4 bits (147), Expect = 9e-12
 Identities = 31/75 (41%), Positives = 43/75 (57%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+FV N+P DA E  L ++    G V + +++ D  T K KGYGF    + E A SA  +
Sbjct: 3  CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 68 LQGYEINGRQLRVDF 82
          L GY + GR L+V F
Sbjct: 63 LNGYRLGGRVLQVSF 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +FVGN+    TEE L E+  + GP+   ++  D   GKPK + F  +K E +   A +
Sbjct: 2  RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQ 60

Query: 67 NLQGYEINGRQLRVD 81
           L G  + GR+LR+ 
Sbjct: 61 LLNGIRLFGRELRIK 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|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 59.9 bits (145), Expect = 1e-11
 Identities = 24/75 (32%), Positives = 45/75 (60%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G + +D  E+ L ++  + G +    +V DRET + +G+GF  +++ + A  A   +
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 69 QGYEINGRQLRVDFA 83
           G  ++GRQ+RVD A
Sbjct: 63 NGKSVDGRQIRVDQA 77

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

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

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V N+P   TEE L E     G V   RLV +++  +P+G+ F E+   E A +A + L
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 69 QGYEINGRQLR 79
           G  ++GR LR
Sbjct: 59 NGLVLDGRTLR 69

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

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 21/72 (29%), Positives = 48/72 (66%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ ++P + T++ L ++    G V+S ++ +D+ TG+ K +GF  Y + E+A +A + +
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 69 QGYEINGRQLRV 80
           G+++ G++L+V
Sbjct: 61 NGFQVGGKRLKV 72

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

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 60.0 bits (145), Expect = 3e-11
 Identities = 26/59 (44%), Positives = 35/59 (59%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +FV N+PYDATEE L     + G V     VID+ TG+ KG GF  +KD+ T  +  +N
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

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

 Score = 58.9 bits (143), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 40/79 (50%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V N+      + L  +  + GP+V   + +D  T +P+G+ + +++D   A  A   L
Sbjct: 3  LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 69 QGYEINGRQLRVDFAENDK 87
                GR++ + FA+ D+
Sbjct: 63 DRTRFLGREIEIQFAQGDR 81

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

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

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VGN+   AT+ +L +   + GP+ S  + + R    P G+ F E++D   A  A R L
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPLRS--VWVAR---NPPGFAFVEFEDPRDAEDAVRAL 56

Query: 69 QGYEINGRQLRVDFAEN 85
           G  I G ++RV+ +  
Sbjct: 57 DGRRICGNRVRVELSRG 73

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

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

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPK-----GYGFCEYKDEETA 61
            +FV N+ +  TEE L +   + G V S  +   ++   P      GYGF E+K +E A
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 62 LSARRNLQGYEINGRQL 78
            A + LQG  ++G  L
Sbjct: 61 QKALKRLQGTVLDGHAL 77

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

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

 Score = 58.1 bits (141), Expect = 8e-11
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA--LSARR 66
          +FVG IP D TEE+L +     G V   +++ DR  G  KGYGF  ++ +E A  + A  
Sbjct: 5  IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMG 63

Query: 67 NLQGYEINGRQLRV 80
          NL      G++L +
Sbjct: 64 NL---NFRGKKLNI 74

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

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 57.7 bits (140), Expect = 9e-11
 Identities = 21/53 (39%), Positives = 30/53 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          +FVG +  D TEE L E   + G V S  +V D+ETGK +G+ F  + D +  
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPV 54

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 27/72 (37%), Positives = 38/72 (52%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ N+ Y  TEE L ++  + GP+    L ID+ T KPKG+ F  Y   E A+ A   L
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 69 QGYEINGRQLRV 80
           G    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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 27/75 (36%), Positives = 38/75 (50%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+V N+P+  T   L +I  + G VV   +V D+ET K KG  F  + D E A    + L
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 69 QGYEINGRQLRVDFA 83
             E+ GR L+   A
Sbjct: 64 NNKELFGRTLKCSIA 78

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

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 57.3 bits (138), Expect = 1e-10
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 3/78 (3%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          + +FV  +  D TEE L E        ++ R+V DR+TG  KG+GF ++  EE A +A+ 
Sbjct: 1  KTLFVKGLSEDTTEETLKE---SFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57

Query: 67 NLQGYEINGRQLRVDFAE 84
           ++  EI+G ++ +DFA+
Sbjct: 58 AMEDGEIDGNKVTLDFAK 75

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 22/63 (34%), Positives = 39/63 (61%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V++  +P + T+E L ++C+  G ++S + ++D++T K KGYGF ++   E AL A   L
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 69 QGY 71
           G 
Sbjct: 63 NGR 65

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

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R ++V N+P+  + E+L ++  + G +   R+   +ET   +G  F  Y+D   A +A  
Sbjct: 3  RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACD 59

Query: 67 NLQGYEINGRQLRV 80
          +L G+ +  R L V
Sbjct: 60 HLSGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 22/72 (30%), Positives = 40/72 (55%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+PY   E+ L ++  + G +    + ID+++GK KG+ +  + D E A+ A + L
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 69 QGYEINGRQLRV 80
           G    GR + +
Sbjct: 65 DGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 56.8 bits (137), Expect = 2e-10
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +FV N+PY+ T ++L E+  +    V  RL   ++ G  KG  + E+K E  A  A  
Sbjct: 4  RTLFVKNLPYNITVDELKEVFEDA---VDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALE 59

Query: 67 NLQGYEINGRQLRVDF 82
            QG E++GR + VD+
Sbjct: 60 EKQGAEVDGRSIVVDY 75

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 30/77 (38%), Positives = 46/77 (59%), Gaps = 7/77 (9%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP---KGYGFCEYKDEETALSARR 66
          ++GN+PYD TEE + E  R +  V S RL   RE G P   +G+G+ E++D ++ L A  
Sbjct: 5  YLGNLPYDVTEEDIKEFFRGL-NVSSVRL--PREPGDPGRLRGFGYAEFEDRDSLLQA-L 60

Query: 67 NLQGYEINGRQLRVDFA 83
          +L    +  R++RVD A
Sbjct: 61 SLNDESLKNRRIRVDIA 77

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 56.5 bits (136), Expect = 3e-10
 Identities = 31/73 (42%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVG IP D  E++L+ +   VG +   RL++D + GK +GY F  Y  +  A  A R L
Sbjct: 4  VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVREL 62

Query: 69 QGYEIN-GRQLRV 80
            YEI  GR L V
Sbjct: 63 NNYEIRPGRLLGV 75

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 56.1 bits (135), Expect = 3e-10
 Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G +P D  E++LI +C ++G +   R+++D   G  +GY F  + +++ A +A + L
Sbjct: 4  IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 69 QGYEI-NGRQLRV 80
            YEI NGR L V
Sbjct: 63 NNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 23/72 (31%), Positives = 38/72 (52%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VG+I ++  E+ + +     GP+ S  +  D  T K KG+ F EY+  E A  A   +
Sbjct: 3  VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 69 QGYEINGRQLRV 80
           G  + GR ++V
Sbjct: 63 NGVMLGGRNIKV 74

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

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V N+P   TEEQL E+  E G V   R+       K K Y F  +++ + A+ A   +
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVE--RVK------KIKDYAFVHFEERDDAVKAMEEM 55

Query: 69 QGYEINGRQLRVDFAE 84
           G E+ G  + V  A+
Sbjct: 56 NGKELEGSPIEVSLAK 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 23/70 (32%), Positives = 41/70 (58%)

Query: 14 IPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI 73
          +P   T+E+   +   VGPV + ++V D+ TG   G+GF +Y+  E A  A R L G ++
Sbjct: 8  LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 74 NGRQLRVDFA 83
            ++++V +A
Sbjct: 68 QNKRIKVAYA 77

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

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

 Score = 55.3 bits (134), Expect = 6e-10
 Identities = 21/67 (31%), Positives = 34/67 (50%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          +G++     E  +     E G V S +++ +++TGK  GYGF E+   E A  A ++L G
Sbjct: 4  MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

Query: 71 YEINGRQ 77
            I   Q
Sbjct: 64 KPIPNTQ 70

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

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

 Score = 61.1 bits (148), Expect = 6e-10
 Identities = 27/80 (33%), Positives = 49/80 (61%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++VGN+ ++ TE++L +I    G +   +L  D ETG+ KG+GF ++ D E A  A   +
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 69  QGYEINGRQLRVDFAENDKG 88
            G+E+ GR ++V +A++   
Sbjct: 249 NGFELAGRPIKVGYAQDSTY 268

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

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 54.8 bits (132), Expect = 7e-10
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETG-KPKGYGFCEYKDEETALSARRN 67
          V+VGN+P D  E ++ ++  + GP+V     ID +   +P GY F E++D   A  A R 
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVD----IDLKLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 68 LQGYEINGRQLRVD 81
            GY+ +G++LRV+
Sbjct: 58 RDGYDFDGQRLRVE 71

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 54.6 bits (131), Expect = 1e-09
 Identities = 30/73 (41%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 9  VFVGNIPYDATEEQLIEICRE-VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          VF+ NIPYD   + + ++ RE VG V    L  D E GK +G G  E+KDEE    A   
Sbjct: 2  VFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKKALEV 60

Query: 68 LQGYEINGRQLRV 80
          +  Y++NGR L +
Sbjct: 61 MNKYDLNGRPLNI 73

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +P D TEE+  E   + G VV  +L+ D +TG+ +G+GF  + D E+A+    + 
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSA 60

Query: 69 QGYEINGRQLRV 80
             E+ G+Q+ V
Sbjct: 61 GMLELGGKQVEV 72

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

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

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +FVGN+    TEE + E+  + GPV+  ++  D++ GKPK + F  +K E +   A  
Sbjct: 2  RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMN 60

Query: 67 NLQGYEINGRQLRV 80
           L G ++ GR L +
Sbjct: 61 LLNGIKLYGRPLNI 74

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

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 53.9 bits (130), Expect = 2e-09
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+P D  E  + ++  + GP+ +  L  +R  G P  + F E++D   A  A R  
Sbjct: 2  IYVGNLPGDIRERDIEDLFYKYGPIKAIDLK-NRRRGPP--FAFVEFEDPRDAEDAVRGR 58

Query: 69 QGYEINGRQLRVDF 82
           GY+ +G +LRV+F
Sbjct: 59 DGYDFDGYRLRVEF 72

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 22/72 (30%), Positives = 37/72 (51%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V++G++P+   E +L +   + G V   RL   ++TGK KGY F E++  E A      +
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 69 QGYEINGRQLRV 80
            Y +  R L+ 
Sbjct: 62 NNYLLFERLLKC 73

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

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

 Score = 53.9 bits (130), Expect = 2e-09
 Identities = 24/71 (33%), Positives = 39/71 (54%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG++  +   E L       G +   R+V D +TGK KGYGF  +  +E A +A +++
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 69 QGYEINGRQLR 79
           G  + GR +R
Sbjct: 62 NGQWLGGRAIR 72

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

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 11 VGNIPYDATEEQLIEI---CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          V N+ Y  T + L  +     EVG V   R   DR T + +G+ F  + D+  A  A   
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPR---DRYTRESRGFAFVRFYDKRDAEDAMDA 59

Query: 68 LQGYEINGRQLRVD 81
          + G E++GR+LRV 
Sbjct: 60 MDGKELDGRELRVQ 73

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

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

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 23/72 (31%), Positives = 40/72 (55%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + VG +  +  ++ L EI    G V    L IDRE   P+GY + E++  E A  A +++
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 69 QGYEINGRQLRV 80
           G +I+G+++ V
Sbjct: 61 DGGQIDGQEVTV 72

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

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVG IP D  E++L+ +    G +  FRL+++  +G+ +GY F  Y  +E A  A R L
Sbjct: 4  VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 69 QGYEI 73
            YEI
Sbjct: 63 NNYEI 67

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 53.4 bits (128), Expect = 3e-09
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVG IP D  E++L+ +  + GP+   RL++D  +G+ +GY F  +  +E A  A +  
Sbjct: 4  VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 69 QGYEI-NGRQLRV 80
            YEI  G+ L V
Sbjct: 64 DNYEIRPGKHLGV 76

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 53.0 bits (127), Expect = 3e-09
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +FVGN+     EE L E+  + GP+    +  D+E GKPK +GF  +K  E+   A  
Sbjct: 2  RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA 60

Query: 67 NLQGYEINGRQLRV 80
           L G  + GR ++V
Sbjct: 61 LLNGIRLYGRPIKV 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 7/77 (9%)

Query: 7  RC-VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          RC +FVGN+P D TEE+  E+  + G V    + +++E    KG+GF        A  A+
Sbjct: 1  RCRLFVGNLPNDITEEEFKELFSKYGEVS--EVFLNKE----KGFGFIRLDTRTNAEKAK 54

Query: 66 RNLQGYEINGRQLRVDF 82
            L G    GRQLRV F
Sbjct: 55 AELDGIMRKGRQLRVRF 71

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

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

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P   T E+L  +  + G V    +V        K YGF   ++EE A  A + L
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKAL 53

Query: 69 QGYEINGRQLRV 80
           GYE  G+++ V
Sbjct: 54 NGYEFMGKRINV 65

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

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 52.7 bits (126), Expect = 6e-09
 Identities = 22/76 (28%), Positives = 42/76 (55%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+ V  +    TE  L E+    GP+    +V D+ TG+ +G+ F  ++  + +  A  +
Sbjct: 1  CLGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60

Query: 68 LQGYEINGRQLRVDFA 83
            G E++GR++RVD++
Sbjct: 61 ANGMELDGRRIRVDYS 76

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 52.4 bits (126), Expect = 7e-09
 Identities = 23/73 (31%), Positives = 36/73 (49%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P+D TE++L E  +E G V+  R+      G+   +GF  + D E       N 
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 69 QGYEINGRQLRVD 81
            Y     +L V+
Sbjct: 66 PIYFRGDHRLNVE 78

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 52.7 bits (126), Expect = 8e-09
 Identities = 22/76 (28%), Positives = 44/76 (57%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+  
Sbjct: 11 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 68 LQGYEINGRQLRVDFA 83
            G E++GR++RVDF+
Sbjct: 71 ANGMELDGRRIRVDFS 86

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+P+  T + L ++ RE G V+   +  D + G+ KG+G   ++  E A  A    
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 69 QGYEINGRQLRV 80
           GY++ GR+L V
Sbjct: 60 NGYDLEGRELEV 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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 25/74 (33%), Positives = 40/74 (54%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          + N+P   T++Q  E+ R  G +    LV    TG  KGYGF EY  +++A  A+ +L G
Sbjct: 4  IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 71 YEINGRQLRVDFAE 84
           ++  R L V + +
Sbjct: 64 KQLGSRTLYVHWTD 77

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|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 = 51.5 bits (124), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VGN+P+  TEE+L       G +   R+  D      KGY F  +   E A +A   +
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 69 QGYEINGRQLRV 80
           G  ING+ ++ 
Sbjct: 57 NGTSINGQTVKC 68

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 51.4 bits (123), Expect = 1e-08
 Identities = 25/74 (33%), Positives = 36/74 (48%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V N+P   T E+  E+ R  G +    LV    TG  KGYGF EY  +++A  AR  L G
Sbjct: 4  VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 71 YEINGRQLRVDFAE 84
           ++    L   + +
Sbjct: 64 KQLGESTLFAQWMD 77

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V  +P + T++++  +   +G + S +L+ D+ TG+  GYGF  Y D E A  A   L G
Sbjct: 6  VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65

Query: 71 YEINGRQLRVDFA 83
            +  + ++V +A
Sbjct: 66 LRLQNKTIKVSYA 78

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

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 20/72 (27%), Positives = 43/72 (59%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++G++P+   E++L +   + G V + R+   ++TG  K YGF ++ + E A  A +++
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 69 QGYEINGRQLRV 80
            Y + G+ L+V
Sbjct: 62 NNYLLMGKVLQV 73

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRE-TGKPKGYGFCEYKDEETALSARRN 67
          + V N+P+  TE  L ++    G V    + I R+  GK KG+ F ++  +  A  A + 
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFVWE--VTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 68 LQGYEINGRQLRVDFA 83
          + G +I GR + VD+A
Sbjct: 60 VNGKKIKGRPVAVDWA 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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR---ETGKPKGYGFCEYKDEETALSAR 65
          +++GN+    TE  L+++  + G +  F  +  +     G+P+GY F  ++ +E A  A 
Sbjct: 2  LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 66 RNLQGYEINGRQLRVDFA 83
          ++L G    G++L V +A
Sbjct: 62 KSLNGKTALGKKLVVRWA 79

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

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 51.6 bits (123), Expect = 2e-08
 Identities = 25/78 (32%), Positives = 41/78 (52%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+F+ N+  DA E  L ++    G V + +++ D  T K KG+GF    + E A  A  +
Sbjct: 3  CIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIAS 62

Query: 68 LQGYEINGRQLRVDFAEN 85
          L GY +  + L+V F  +
Sbjct: 63 LNGYRLGDKILQVSFKTS 80

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

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

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEY---KDEETA 61
            + +  +    TEE +++    +   P+   RL+ D+ TG  +G+ F E+   +D    
Sbjct: 3  NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62

Query: 62 LSARRNLQGYEINGRQLRVDFA 83
          + A  NL  + I+GR +RV +A
Sbjct: 63 MDALNNLDPFVIDGRVVRVSYA 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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 56.5 bits (136), Expect = 2e-08
 Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           VFVG IP D  E++L+ +  + GP+   RL++D   G+ +GY F  +  +E A  A + L
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAFVTFCGKEEAKEAVKLL 119

Query: 69  QGYEI-NGRQLRV 80
             YEI  GR L V
Sbjct: 120 NNYEIRPGRLLGV 132

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +P + TE  L +   + G V    ++ D E  +P+G+GF  ++ E+ ++    N 
Sbjct: 5  IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED-SVDQVVNE 63

Query: 69 QGYEINGRQLRVDFAE 84
            ++ING+++ V  AE
Sbjct: 64 HFHDINGKKVEVKRAE 79

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V N+ YD TEE L E+   VG V   ++  DR +G+ +G     ++  E A  A +  
Sbjct: 3  LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQF 61

Query: 69 QGYEINGRQLRVDF 82
           G  ++G+ ++V+ 
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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 50.9 bits (121), Expect = 3e-08
 Identities = 26/75 (34%), Positives = 40/75 (53%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+FV N+  DA E  L ++    G V + +++ D  T K KG+GF    + + A  A  +
Sbjct: 5  CIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64

Query: 68 LQGYEINGRQLRVDF 82
          L GY +  R L+V F
Sbjct: 65 LNGYRLGDRVLQVSF 79

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

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

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VG IPY +TE+++       G +    L+   +TG+ +G  F  +K EE A      L
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAK-RALAL 59

Query: 69 QGYEINGRQLRV 80
           G ++ GR L+V
Sbjct: 60 DGEDMGGRFLKV 71

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

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

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VGNIP   T+  LI + +  G ++ FR   DR      G+ F +    E A  A   L
Sbjct: 3  VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIVQL 56

Query: 69 QGYEINGRQLRVDFAEN 85
          QG+ ++GR LR  + ++
Sbjct: 57 QGFPVHGRPLRCGWGKD 73

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

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 7  RCVFVGNIPYDATE-EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          RC+FV  +P    +   L ++  +VG     +L I    G+P+G+ F EY   E A  A+
Sbjct: 3  RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQ 61

Query: 66 RNLQGYEINGRQLRVDF 82
          + L G+ + G  +RV F
Sbjct: 62 QALNGHSLQGSPIRVSF 78

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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR---ETGKPKGYGFCEYKDEETALSAR 65
          ++VGN+    TEE L +     GP+ S +++  R   E  + +  GF  + +   A  A 
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 66 RNLQGYEINGRQLRVDFA 83
            L G ++ G +L++ + 
Sbjct: 64 DELDGKDVMGYELKLGWG 81

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  + TEE++ E   + G +V   L +D++T K +G+ F  +  EE         
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET- 60

Query: 69 QGYEINGRQLRVDFA 83
          Q + I G+++ V  A
Sbjct: 61 QFHVIGGKKVEVKKA 75

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 50.5 bits (120), Expect = 4e-08
 Identities = 26/78 (33%), Positives = 41/78 (52%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+FV N+  D+ E  L ++    G V + +++ D  T K KG+GF    + + A  A  +
Sbjct: 5  CIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64

Query: 68 LQGYEINGRQLRVDFAEN 85
          L GY +  R L+V F  N
Sbjct: 65 LNGYRLGDRVLQVSFKTN 82

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

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

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 18/56 (32%), Positives = 27/56 (48%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          VFV  +     E  L E   + G V   R++ DR + + KG  + E+ DEE+   A
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 19/64 (29%), Positives = 32/64 (50%)

Query: 19 TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL 78
          T+E L  I    G + S  ++ D++TG    Y F E++ +E    A   +    I+ R++
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75

Query: 79 RVDF 82
           VDF
Sbjct: 76 HVDF 79

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 50.0 bits (119), Expect = 5e-08
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+P+D T + L +   E G V+     I  E GK KG G   ++  E A  A R +
Sbjct: 2  IFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVRFESPEVAERACRMM 59

Query: 69 QGYEINGRQLRVDFAEN 85
           GY++NGR++ V    N
Sbjct: 60 NGYKLNGREIDVRIDRN 76

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            +FVG +  D T+E+L E     G ++   L I R       + F +++ E+ A  A  
Sbjct: 4  YSIFVGQLSPDVTKEELNERFSRHGKILEVNL-IKRANHTN-AFAFIKFEREQAAARAVE 61

Query: 67 NLQGYEINGRQLRVDFAE 84
          +     +  + + V + E
Sbjct: 62 SENHSMLKNKTMHVQYKE 79

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 49.0 bits (118), Expect = 6e-08
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 23 LIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF 82
          L ++    G V   +L+  +      G+ F E+  EE A  A + L G    GR LRVD+
Sbjct: 1  LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 83 A 83
          +
Sbjct: 56 S 56

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

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 55.2 bits (133), Expect = 6e-08
 Identities = 32/171 (18%), Positives = 46/171 (26%), Gaps = 2/171 (1%)

Query: 214 QAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEA 273
           Q    L     QVL   +  +    P Q   +          G P   Q  Q +P   +A
Sbjct: 167 QQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQA 226

Query: 274 QIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQL-- 331
             Q         QP    Q Q P  ++         P Q   P  P   P  + Q     
Sbjct: 227 PAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHP 286

Query: 332 ANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSD 382
                 N  + PP     + +     GQ    +     ++ S       S 
Sbjct: 287 GLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQQREALSQ 337

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 49.2 bits (118), Expect = 7e-08
 Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 3/75 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+    TE+ L E+  ++GP+ S +L+ +        Y F EY D  +A +A + +
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57

Query: 69 QGYEINGRQLRVDFA 83
           G  I G++++V++A
Sbjct: 58 NGRLILGQEIKVNWA 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|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 49.2 bits (118), Expect = 8e-08
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P+    ++L E   + G V S  +  D+ETG  KGYGF  +   +   +A +  
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK- 60

Query: 69 QGYEINGRQLRV 80
          Q + + G +L+V
Sbjct: 61 QKHILEGNKLQV 72

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 49.3 bits (117), Expect = 8e-08
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 9  VFVGNIPYDATEEQLIEICRE-VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           F+ NIP+D   + L ++ +E VG V    L++D E GK +G    E+K EE+   A   
Sbjct: 2  AFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAE-GKSRGCAVVEFKMEESMKKAVEV 60

Query: 68 LQGYEINGRQLRV 80
          L  + +NGR L+V
Sbjct: 61 LNKHVLNGRPLKV 73

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 23/68 (33%), Positives = 35/68 (51%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V N+P   TE++L +I    G +V   L+ D+ TG P+G  F  Y   E A +A  +L
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 69 QGYEINGR 76
           G    G 
Sbjct: 63 NGTIPPGS 70

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

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 27/78 (34%), Positives = 43/78 (55%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          H  VFVG++  + T E +       G +   R+V D  TGK KGYGF  + ++  A +A 
Sbjct: 1  HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60

Query: 66 RNLQGYEINGRQLRVDFA 83
           ++ G  + GRQ+R ++A
Sbjct: 61 VHMGGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 48.8 bits (116), Expect = 2e-07
 Identities = 26/79 (32%), Positives = 41/79 (51%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV NI  D   E L       GP+V   + +D  T +P+G+ + +++D   A  A  NL
Sbjct: 3  LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 69 QGYEINGRQLRVDFAENDK 87
              I GRQ+ + FA+ D+
Sbjct: 63 DRKWICGRQIEIQFAQGDR 81

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

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

 Score = 53.3 bits (128), Expect = 2e-07
 Identities = 56/277 (20%), Positives = 96/277 (34%), Gaps = 42/277 (15%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V N+    T+E+L E+  E G + S ++++D E G  +G+GF  + + E A  A   +
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIG 128
            G  + G+ L V  A+  K   R   Q +           Q Q     +   S      G
Sbjct: 347 HGRMLGGKPLYVALAQR-KEQRRAHLQDQFM---------QLQPRMRQLPMGSPM---GG 393

Query: 129 LHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEIMSEMK 188
                       G     Q   Q       S + +P  P           + N +     
Sbjct: 394 AM----GQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGP-------GGPLRPNGLAP--- 439

Query: 189 LMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQ 248
           + A +   +  Q    KPP         +   M  P    +P+ +  P   +        
Sbjct: 440 MNAVRAPSRNAQNAAQKPP---------MQPVMYPPNYQSLPLSQDLPQPQSTASQGGQN 490

Query: 249 QQVAQ-LPGLPPLAQKM----QLMPKVQEAQIQLHNQ 280
           +++AQ L    P  QK     +L P V+  +  L  +
Sbjct: 491 KKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAK 527

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

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+    T ++L  +  E G VV        E  K K Y F   + EE AL+A   L
Sbjct: 3  IFVGNVSATCTSDELRGLFEEFGRVV--------ECDKVKDYAFVHMEREEEALAAIEAL 54

Query: 69 QGYEINGRQLRVD 81
           G E+ GR++ V+
Sbjct: 55 NGKEVKGRRINVE 67

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 23/65 (35%), Positives = 37/65 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG IP D  E++L+ +  + GP+   RL++D  TG  +GY F  +  +E A  A +  
Sbjct: 4  IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 69 QGYEI 73
            +EI
Sbjct: 64 NNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ N+      + L +     G ++S ++  D E G  KGYGF  ++ EE A+ A   +
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 69 QGYEINGRQLRV 80
           G  +N +++ V
Sbjct: 64 NGMLLNDKKVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+P+D T ++L E   + G V+     I  E GK KG G   +   E+A  A R +
Sbjct: 2  IFVRNLPFDLTWQKLKEKFSQCGHVMFAE--IKMENGKSKGCGTVRFDSPESAEKACRLM 59

Query: 69 QGYEINGRQLRVDFAEN 85
           G +INGR++ V    N
Sbjct: 60 NGIKINGREIDVRLDRN 76

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 9/76 (11%)

Query: 9  VFVGNIPYDATEEQLIE-ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +FV       T E+ IE +    GP+V   +         K + F E++D E A  A   
Sbjct: 2  LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53

Query: 68 LQGYEINGRQLRVDFA 83
          L G  I+G  L V+F 
Sbjct: 54 LHGSRIDGSVLTVEFV 69

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

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

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 17/74 (22%), Positives = 38/74 (51%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG++  + T+  L             R++ D ++G+ +GYGF  ++ ++ A +A   +
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 69 QGYEINGRQLRVDF 82
           G  +  R +R ++
Sbjct: 62 NGKWLGSRPIRCNW 75

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

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

 Score = 48.2 bits (114), Expect = 3e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+FV N+  +A E  L ++    G V + +++ D  T K KG+GF    + + A  A  +
Sbjct: 3  CIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS 62

Query: 68 LQGYEINGRQLRVDF 82
          L GY +  R L+V F
Sbjct: 63 LNGYRLGDRVLQVSF 77

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

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

 Score = 47.8 bits (113), Expect = 3e-07
 Identities = 26/78 (33%), Positives = 43/78 (55%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          H  VFVG++  + T + +       G +   R+V D  TGK KGYGF  + ++  A +A 
Sbjct: 1  HFHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

Query: 66 RNLQGYEINGRQLRVDFA 83
          + + G  + GRQ+R ++A
Sbjct: 61 QQMGGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 47.2 bits (112), Expect = 3e-07
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V N+ Y A+E+ L E+  +     S R  I +  G+PKGY F E++  E A  A  +   
Sbjct: 6  VNNLSYSASEDSLQEVFEKA---TSIR--IPQNNGRPKGYAFVEFESAEDAKEALNSCNN 60

Query: 71 YEINGRQLRVDF 82
           EI GR +R++F
Sbjct: 61 TEIEGRSIRLEF 72

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

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VF+G IP D  E++LI + + VG +  FRL++   +G  +G+ + +Y D   A +A   L
Sbjct: 4  VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTF-SGLNRGFAYAKYSDRRGASAAIATL 62

Query: 69 QGYEI 73
            YE+
Sbjct: 63 HNYEL 67

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V N+P++AT+++L E+    G V S RL    + G  +G+ F E+  ++ A +A   L+ 
Sbjct: 5  VRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEALKS 63

Query: 71 YEINGRQLRVDFA 83
            + GR L +++A
Sbjct: 64 THLYGRHLVLEYA 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 47.2 bits (112), Expect = 4e-07
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  D  E  L E   + GPV    ++ D++TGK +G+GF  +++ ++A  A   +
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV-V 60

Query: 69 QGYEINGRQLRVDFA 83
          + + ING ++ V  A
Sbjct: 61 KFHPINGHRVEVKKA 75

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 47.2 bits (113), Expect = 5e-07
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG++  + T+E L     +       ++V D+ TGK KGYGF  + D    L A + +
Sbjct: 9  IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 69 QGYEINGRQLRV 80
           G  +  R +++
Sbjct: 69 NGKYVGNRPIKL 80

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

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

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEETALSARR 66
           +F+GN+  +  E+ L +     G ++   +++ D +TG  KG+ F  Y   E + +A  
Sbjct: 3  NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 67 NLQGYEINGRQLRVDFA 83
           + G  +  R + V +A
Sbjct: 63 AMNGQYLCNRPITVSYA 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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 46.7 bits (111), Expect = 5e-07
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+  D ++E+L  +    G V+S  ++        + + F   + E  A  A   L
Sbjct: 3  IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEEL 54

Query: 69 QGYEINGRQLRVD 81
           G E++GR+L V+
Sbjct: 55 NGRELHGRKLVVE 67

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

 Score = 46.4 bits (111), Expect = 7e-07
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALSARR 66
          F+G + +D TEE L E   + G VV   ++ D  TG+ +G+GF  + D       L+A+ 
Sbjct: 2  FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61

Query: 67 NLQGYEINGRQ 77
          ++    ++GR+
Sbjct: 62 HV----LDGRE 68

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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 46.8 bits (111), Expect = 7e-07
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VGN+ Y +T E+L       GP+    ++ D+ +G PKGY + E+     ++ A   L
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVAL 60

Query: 69 QGYEINGRQLRV 80
                GR ++V
Sbjct: 61 DESSFRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 46.7 bits (111), Expect = 7e-07
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 7/75 (9%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALSAR 65
          V+VGN+ Y AT E+L       G V    ++ D+ +G PKG+ + E+ D+E   TAL+  
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 66 RNLQGYEINGRQLRV 80
           +L      GRQ++V
Sbjct: 62 ESL----FRGRQIKV 72

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

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 46.4 bits (111), Expect = 9e-07
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +P  ATEE +  +  E G +    ++ D++TG+ KG  F ++   E A  A   L
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 69 QG 70
           G
Sbjct: 62 HG 63

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

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

 Score = 50.7 bits (121), Expect = 1e-06
 Identities = 29/97 (29%), Positives = 43/97 (44%), Gaps = 3/97 (3%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFV  +   A E  L E   +VG V   + + DR + + KG  + E+ D E+ + A  
Sbjct: 90  RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA 149

Query: 67  NLQGYEINGRQLRVDF--AENDKGADRNREQGRGGPG 101
            L G  + GR + V    AE ++ A     Q    P 
Sbjct: 150 -LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPN 185

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

>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + + NIP+   +EQL++I  ++G  + +      + G  +G  F  ++  E A +    L
Sbjct: 4  IVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEAL 63

Query: 69 QGYEINGRQLRVDF 82
           GYEI+GR+LRV++
Sbjct: 64 NGYEISGRRLRVEY 77

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

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

 Score = 50.3 bits (120), Expect = 1e-06
 Identities = 36/177 (20%), Positives = 60/177 (33%), Gaps = 8/177 (4%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V  +P   T+ +L  I    G +++ R++ D  TG  KG GF  +   + A  A + L
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 69  QGYEING--RQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
            G   +G    + V FA N   ++           + A+ +PQ      +    +    P
Sbjct: 152 NGTTPSGCTEPITVKFANNPSSSNSKGLL----SQLEAVQNPQTTRVPLSTILTAAGIGP 207

Query: 127 IGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRNQLNEI 183
             +H A        G   A     Q      Q   A    P              +I
Sbjct: 208 --MHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQI 262

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

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

 Score = 50.3 bits (120), Expect = 1e-06
 Identities = 26/78 (33%), Positives = 40/78 (51%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           C+FV N+  D  E  L ++    G V + +++ D  T + KGYGF    + + A  A  +
Sbjct: 271 CIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILS 330

Query: 68  LQGYEINGRQLRVDFAEN 85
           L GY +  R L+V F  N
Sbjct: 331 LNGYTLGNRVLQVSFKTN 348

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

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

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VG +    +  +L       G +      ID + G+   Y + EY+  E A +A+  L
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRR----IDYDPGRN--YAYIEYESIEAAQAAKEAL 54

Query: 69 QGYEIN--GRQLRVDFA 83
          +G+ +   GR+LRVDFA
Sbjct: 55 RGFPLGGPGRRLRVDFA 71

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 18/92 (19%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFR---LVIDRETGKPKGY------------- 50
          R VFVGN+P    ++ L ++ ++ GP+ S R   + +  +    K               
Sbjct: 1  RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 51 -GFCEYKDEETALSARRNLQGYEINGRQLRVD 81
            +  +K+EE+A  A   L G E  G  +RVD
Sbjct: 61 NAYVVFKEEESAEKA-LKLNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 20/75 (26%), Positives = 45/75 (60%), Gaps = 2/75 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+  D TE  ++++  ++GP  S ++++D     P  Y F E+ +   A ++   +
Sbjct: 2  LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP--YCFVEFFEHRHAAASLAAM 59

Query: 69 QGYEINGRQLRVDFA 83
           G +I G++++V++A
Sbjct: 60 NGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V  +P+  TE+ L +     G ++  ++  D +TG+ KG+GF  + D E  +      Q 
Sbjct: 4  VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS--QR 61

Query: 71 YEINGRQLRV 80
          + I+GR   V
Sbjct: 62 HMIDGRWCDV 71

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

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG + +D T++ L E   + G VV   + ID  TG+ +G+GF  +KD  + +    + 
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAAS-VEKVLDQ 59

Query: 69 QGYEINGR 76
          + ++++GR
Sbjct: 60 KEHKLDGR 67

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

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

 Score = 45.9 bits (108), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 41/75 (54%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+E+L  +   +G + S +LV D+ TG+  GYGF  Y D + A  A   L
Sbjct: 7  LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 69 QGYEINGRQLRVDFA 83
           G  +  + ++V +A
Sbjct: 67 NGLRLQTKTIKVSYA 81

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

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 15 PYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI 73
          PY   E  +      +G  V+S +++ ++ TG P GY F E+ DE TA      L G  I
Sbjct: 9  PY-MDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPI 67

Query: 74 NGRQLRVDFAEN 85
           G      F  N
Sbjct: 68 PGSNPPKRFKLN 79

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 49.6 bits (118), Expect = 2e-06
 Identities = 23/75 (30%), Positives = 43/75 (57%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V  +P D T+ +L  + R +GP+ + R++ D +TG   GY F ++  E  +  A +NL
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 69  QGYEINGRQLRVDFA 83
            G  +  ++L+V +A
Sbjct: 170 NGITVRNKRLKVSYA 184

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

>gnl|CDD|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 = 44.9 bits (107), Expect = 3e-06
 Identities = 23/75 (30%), Positives = 36/75 (48%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V N+P   TE +L E   + G  ++   ++  E GK +   F  YK EE A  A+   
Sbjct: 3  LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 69 QGYEINGRQLRVDFA 83
              IN  ++ V+FA
Sbjct: 63 NNTYINTSKISVEFA 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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGP-VVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +FVG++  +  E  L+ + +   P   S +++ D  TG  +GYGF  + DE     A   
Sbjct: 4  IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 68 LQGYEINGRQLRVDFA 83
          +QG    GR +R+  A
Sbjct: 64 MQGVYCGGRPMRISTA 79

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

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

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +FV NI  +  +E+L  +  + G + +          K +G+    Y D   A  A+R
Sbjct: 2  RTLFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRAARRAKR 56

Query: 67 NLQGYEINGRQLRVDFA 83
           LQG E+ GR+L + F+
Sbjct: 57 ALQGTELGGRKLDIHFS 73

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 23/79 (29%), Positives = 40/79 (50%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+      E L       GP+V   + +D  T +P+G+ + +++D   A  A  NL
Sbjct: 3  LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 69 QGYEINGRQLRVDFAENDK 87
              + GRQ+ + FA+ D+
Sbjct: 63 NRKWVCGRQIEIQFAQGDR 81

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRET--------GKPKGYGFCEYKDEET 60
          V++ N+ Y ++EE L E  ++  PV    ++I  +T         +P G  + E+   E 
Sbjct: 2  VYISNLSYSSSEEDLEEFLKDFEPV---SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQ 58

Query: 61 ALSARRNLQGYEINGRQLRV 80
          A    ++L G     R+L V
Sbjct: 59 AEKVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 9/82 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFR--------LVIDRETGKPKGYGFCEYKDEET 60
          +++  +P D TE+ L E+   +G +   +        +  D+ET +PKG     Y D   
Sbjct: 1  IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59

Query: 61 ALSARRNLQGYEINGRQLRVDF 82
          A +A     GYE  G +++V  
Sbjct: 60 AQAAIEWFNGYEFRGNKIKVSL 81

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 44.5 bits (105), Expect = 4e-06
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          CVFVGN+ ++  EE L  +  + G +   R+V D +T   KG+ + ++KDE     A
Sbjct: 1  CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 23/75 (30%), Positives = 40/75 (53%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+E+   +   +G + S +LV D+ TG+  GYGF  Y D + A  A   L
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 69 QGYEINGRQLRVDFA 83
           G  +  + ++V +A
Sbjct: 65 NGLRLQTKTIKVSYA 79

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 44.5 bits (105), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+    TE+ L +I +  GPV + +++ D+   K   YGF EY     A  A + L
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 69 QGYEINGRQLRVDFA 83
           G +I   ++RV++A
Sbjct: 60 NGRQIENNEIRVNWA 74

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

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V NIP+   +  L ++  + GP++   ++ + E G  KG+GF  + +   A  AR  L G
Sbjct: 5  VSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERGS-KGFGFVTFANSADADRAREKLHG 62

Query: 71 YEINGRQLRVDFA 83
            + GR++ V+ A
Sbjct: 63 TVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|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 = 44.3 bits (105), Expect = 6e-06
 Identities = 28/74 (37%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R + VG I    +E+ L E     G V   RL  DR+      + F E+ D E+ALSA  
Sbjct: 1  RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSA-L 57

Query: 67 NLQGYEINGRQLRV 80
          NL G  + G  LRV
Sbjct: 58 NLSGTLLGGHPLRV 71

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

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

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 23/75 (30%), Positives = 40/75 (53%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+E+   +   +G + S +LV D+ TG+  GYGF  Y D   A  A   L
Sbjct: 6  LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 69 QGYEINGRQLRVDFA 83
           G ++  + ++V +A
Sbjct: 66 NGLKLQTKTIKVSYA 80

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 20/75 (26%), Positives = 45/75 (60%), Gaps = 2/75 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+  D TE  ++++  ++GP  S +++ +  +  P  Y F E+ +   A +A   +
Sbjct: 2  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59

Query: 69 QGYEINGRQLRVDFA 83
           G +I G++++V++A
Sbjct: 60 NGRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 9/71 (12%)

Query: 9  VFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          VFVGN+  D  ++E L EI  + G ++   L         KGYGF ++ +EE A +A   
Sbjct: 3  VFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAG 54

Query: 68 LQGYEINGRQL 78
            G EI G++L
Sbjct: 55 ENGREIAGQKL 65

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 10/80 (12%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R VF GN  YDA + ++  +  + G V       DR   K  G+ F   +DE  A  A R
Sbjct: 1  RPVFCGNFEYDARQSEIERLFGKYGRV-------DRVDMK-SGFAFVYMEDERDAEDAIR 52

Query: 67 NLQGYEI--NGRQLRVDFAE 84
           L  +E     R+LRV++A+
Sbjct: 53 GLDNFEFGRQRRRLRVEWAK 72

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

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

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPK---GYGFCEYKDEETALS 63
          R ++V N+ +   E+ L  I  + G V S R+   ++  + +   G+ F  +KD  +A +
Sbjct: 1  REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 64 ARRNLQGYEINGRQLRV 80
          A   L G E+ GR++ V
Sbjct: 61 A-LQLNGTELGGRKISV 76

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

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

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 12/95 (12%)

Query: 7  RCVFVGNI--PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          R + + N+  P+  T  QL E+  E G  V     +D    K K + +  Y   E A++ 
Sbjct: 2  RALHIDNLVRPF--TLNQLKELLSETGTGVIEGFWMD----KIKSHCYVTYSTVEEAVAT 55

Query: 65 RRNLQGY---EINGRQLRVDFAENDKGADRNREQG 96
          R  L G      N ++L+VDF   ++  +   E+ 
Sbjct: 56 REALHGLQWPSSNPKRLKVDFVPQEE-LEEAIEEE 89

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 = 43.3 bits (102), Expect = 7e-06
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P +ATE+++  +  + G V+   ++        K YGF    D+  A  A RNL
Sbjct: 3  LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNL 54

Query: 69 QGYEINGRQLRVD 81
            Y+++G  + V+
Sbjct: 55 HHYKLHGVAINVE 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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 7/68 (10%)

Query: 17 DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE---ETALSARRNLQGYEI 73
          D     L E     G +    +  DRETG  KG+ + E+K     E AL     L G ++
Sbjct: 14 DDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKAL----ELDGSDL 69

Query: 74 NGRQLRVD 81
           G  L VD
Sbjct: 70 GGGNLVVD 77

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 14 IPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI 73
          IP   TEE L E  +E G +    +V D+ TG+ KG+G+ ++     A  A  N      
Sbjct: 8  IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCD---- 63

Query: 74 NGRQLRVDFAE 84
            +  +   AE
Sbjct: 64 --KSFKAVLAE 72

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FV N+      + L +   + G ++S ++  D E GK +GYGF  ++ EE+A +A + +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 69  QGYEINGRQLRV 80
            G  +N +++ V
Sbjct: 150 NGMLLNDKEVYV 161

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

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R ++VGN+    T +QL+E   + G V   R+  D    +P  Y F E+ ++ + ++A +
Sbjct: 5  RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINALK 62

Query: 67 NLQGYEINGRQLRVDFAEN 85
           L G    GR L+V+ + N
Sbjct: 63 -LNGAMFGGRPLKVNHSNN 80

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

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 21/60 (35%), Positives = 32/60 (53%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+V  +P +AT E L  +  + G VV   L   + TG  KG+ F E++  E A  A ++L
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V++G +PY A E  +    +  G     R+   RE     G+GF E++D   A  A   L
Sbjct: 2  VYIGRLPYRARERDVERFFKGYG-----RI---REINLKNGFGFVEFEDPRDADDAVYEL 53

Query: 69 QGYEINGRQLRVDFA 83
           G E+ G ++ V+ A
Sbjct: 54 NGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG I  D  E  L +   E G + +  ++ DR++GK +G+GF  + D +     +  L
Sbjct: 3  LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPV--DKIVL 60

Query: 69 QGYE-INGRQLRV 80
          Q Y  ING    V
Sbjct: 61 QKYHTINGHNAEV 73

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 13 NIPYDATE-EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY 71
          N+P+   +  +L +I    G V    +   R  GK  G+ F   K  + A  A  N  G 
Sbjct: 7  NLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALENTNGL 65

Query: 72 EINGRQLRVDFA 83
          EI+GR + VD+A
Sbjct: 66 EIDGRPVAVDWA 77

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRL--VIDRETGKPKGYGFCEYKDEETALSARR 66
          + V N+P++AT++ +  +    G + S R+    D+     +G+ F E+   + AL+A  
Sbjct: 3  ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAMN 59

Query: 67 NLQGYEINGRQLRVDFA 83
           L+   + GR+L + +A
Sbjct: 60 ALKDTHLLGRRLVLQYA 76

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

>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 42.8 bits (100), Expect = 2e-05
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 2/62 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFC--EYKDEETALSARR 66
          +FVG+IP   T+EQ++E   +V   ++  ++  +   K K  GFC  EY+D +TA  ARR
Sbjct: 5  LFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARR 64

Query: 67 NL 68
           L
Sbjct: 65 RL 66

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 85

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          ++GN+  D  E  L ++  E    VS  LV      K  GY F +  D+  A  A   L 
Sbjct: 2  YIGNLSSDVNESDLRQLFEEHKIPVSSVLV------KKGGYAFVDCPDQSWADKAIEKLN 55

Query: 70 GYEINGRQLRVDFA 83
          G  + G+ + V+ +
Sbjct: 56 GKILQGKVIEVEHS 69

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 18/72 (25%), Positives = 45/72 (62%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ ++P +  + +L+++    G V+S ++ +DR T + K +GF  + +  +A +A + +
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 69 QGYEINGRQLRV 80
           G++I  ++L+V
Sbjct: 67 NGFQIGMKRLKV 78

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

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 8  CVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           V +  +P+ ATEE + +    +  P     +V D + G+P G  + E+   E A  A R
Sbjct: 1  VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALR 59

Query: 67 NLQGYEINGRQLRV 80
                + GR + V
Sbjct: 60 KHNNK-MGGRYIEV 72

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVGN+P D TEE++ ++  + G      +       K KG+GF   +    A  A+  L
Sbjct: 4  LFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAKAEL 57

Query: 69 QGYEINGRQLRVDF 82
              + G+QLRV F
Sbjct: 58 DNMPLRGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 44.9 bits (106), Expect = 6e-05
 Identities = 23/73 (31%), Positives = 39/73 (53%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V  +P   T+E++  +   +G + S +LV D+ TG+  GYGF  Y   E A  A  +L G
Sbjct: 8  VNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNG 67

Query: 71 YEINGRQLRVDFA 83
            +  + ++V +A
Sbjct: 68 LRLQNKTIKVSYA 80

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

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

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +F+GN+    T   L E     G ++   + I ++ G P  Y F +Y D  + + A R
Sbjct: 3  RTLFIGNLEKTTTYSDLREAFERFGEIID--IDIKKQGGNPA-YAFIQYADIASVVKAMR 59

Query: 67 NLQGYEINGRQLRV 80
           + G  +   ++++
Sbjct: 60 KMDGEYLGNNRVKL 73

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

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          +F+G + +D T++ L +   + G VV   L +D  TG+ +G+GF  +K+ E+
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES 52

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 41.3 bits (97), Expect = 6e-05
 Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 12/85 (14%)

Query: 9  VFVGNIPYDATEEQLIEICREVG----------PVVSFRLVIDRETGKPKGYGFCEYKDE 58
          VFV N+P + TE+ L E    +G          P +   L  D++TG+PKG     Y D 
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKI--WLYKDKDTGEPKGEATVTYDDP 58

Query: 59 ETALSARRNLQGYEINGRQLRVDFA 83
            A +A       +  G  ++V  A
Sbjct: 59 HAASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG I  D  E  L +   + G +    ++ DR +GK +G+ F  + D ++    +  +
Sbjct: 3  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV--DKIVI 60

Query: 69 QGYE-INGRQLRV 80
          Q Y  +NG    V
Sbjct: 61 QKYHTVNGHNCEV 73

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  + TE+ + +   + G V    L+ D++T + +G+GF  ++ E+        +
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV-CEI 60

Query: 69 QGYEINGRQLRV 80
            +EIN + +  
Sbjct: 61 HFHEINNKMVEC 72

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 40.8 bits (96), Expect = 7e-05
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+ Y    ++L E+ +  G VV   +  D+E GK +G G  +++    A+ A    
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 69 QGYEINGRQLRV 80
           G  +  R +RV
Sbjct: 60 NGQMLFDRPMRV 71

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

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

 Score = 40.8 bits (96), Expect = 7e-05
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
          V N+P    E++L ++    G +   +L   ++ GK + +GF  YK EE A  A ++   
Sbjct: 5  VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKHFNN 63

Query: 71 YEINGRQLRVDFA 83
            I+  ++ V+  
Sbjct: 64 SFIDTSKITVEIC 76

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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+P D   + + ++  + G +    L   R  G P  + F E++D   A  A    
Sbjct: 2  IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRR--GPP--FAFVEFEDPRDAEDAVYGR 57

Query: 69 QGYEINGRQLRVDF 82
           GY+ +G +LRV+F
Sbjct: 58 DGYDYDGYRLRVEF 71

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 9/78 (11%)

Query: 7  RC-VFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          RC +FVGN+P D TE++  ++  + G P   F         K KG+GF + +    A  A
Sbjct: 1  RCRLFVGNLPADITEDEFKKLFAKYGEPGEVF-------INKGKGFGFIKLESRALAEIA 53

Query: 65 RRNLQGYEINGRQLRVDF 82
          +  L    + GRQLRV F
Sbjct: 54 KAELDDTPMRGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 20/72 (27%), Positives = 44/72 (61%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ ++P + T+  L +     G V+S ++ ID++T   K +GF  Y + ++A +A + +
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 69 QGYEINGRQLRV 80
           G++I  ++L+V
Sbjct: 67 NGFQIGTKRLKV 78

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

>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 41.2 bits (96), Expect = 8e-05
 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 4/80 (5%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFC--EYKDEETALSARR 66
          +FVG+IP + T+E ++E   +V   +   ++  +   K K  GFC  EY+D ++A  ARR
Sbjct: 5  LFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARR 64

Query: 67 NLQGYEIN--GRQLRVDFAE 84
           L   ++   G  + V++A+
Sbjct: 65 RLMSGKVKVWGNVVTVEWAD 84

This subgroup corresponds to the RRM2 of hnRNP R, a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. It contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif. hnRNP R binds RNA through its RRM domains. . Length = 85

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 15/52 (28%), Positives = 29/52 (55%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          +F+G + +D +++ L E     G V+   +  D  TG+ +G+GF  +KD  +
Sbjct: 2  MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAAS 53

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          FVG IP +  E+ L  +  + G +    ++ D+ TG  KG  F  Y   E+AL A+  L 
Sbjct: 9  FVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSALH 68

Query: 70 G 70
           
Sbjct: 69 E 69

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 7  RC-VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          RC +FVGN+P D TEE   ++  + G      + I+R+    +G+GF   +    A  A+
Sbjct: 1  RCRLFVGNLPTDITEEDFKKLFEKYGE--PSEVFINRD----RGFGFIRLESRTLAEIAK 54

Query: 66 RNLQGYEINGRQLRVDF 82
            L G  +  R LR+ F
Sbjct: 55 AELDGTILKNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 15/71 (21%)

Query: 13 NIPYDATEEQLIEICREV---------GPVVSFRLVIDRE------TGKPKGYGFCEYKD 57
          N+P    E++L E+  +            +   +++ D +       GK KGYGF E+ +
Sbjct: 7  NLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTN 66

Query: 58 EETALSARRNL 68
           E AL A R L
Sbjct: 67 HEHALKALRAL 77

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 40.6 bits (96), Expect = 1e-04
 Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 11/73 (15%)

Query: 8  CVFVGNIPYDATEEQ---LIEICR------EVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
           V V  +P    EE+   L ++ R       VG +V   + +D ETGK KGY F E+   
Sbjct: 3  VVVVDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATP 60

Query: 59 ETALSARRNLQGY 71
          E A  A + L GY
Sbjct: 61 EEAKEAVKALNGY 73

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 13/85 (15%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            +++G++    TEE L  +  E G + S  ++       P+G   C Y   ET   A R
Sbjct: 3  TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRG---CAYVCMETRQDAHR 53

Query: 67 NLQ---GYEINGRQLRVDFAENDKG 88
           LQ     ++ G++++V +A N KG
Sbjct: 54 ALQKLRNVKLAGKKIKVAWAPN-KG 77

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 12/84 (14%)

Query: 9  VFVGNIPYDATEEQLIEICREVG----------PVVSFRLVIDRETGKPKGYGFCEYKDE 58
          +FV  +  D T E + +  +++G          P+++  L  DRETGK KG     + D 
Sbjct: 5  IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMIN--LYTDRETGKLKGEATVSFDDP 62

Query: 59 ETALSARRNLQGYEINGRQLRVDF 82
           +A +A     G E +G  ++V F
Sbjct: 63 PSAKAAIDWFDGKEFSGNPIKVSF 86

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKG-YGFCEYKDEETALSAR 65
          R +FV  +P D  E +L  + R      + RLV   + G  K   GF ++   + A +A 
Sbjct: 1  RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 66 RNLQGY 71
            LQGY
Sbjct: 61 DALQGY 66

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 18/70 (25%)

Query: 10 FVGNIPYDATEEQLIEI------CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          F+ N+P + T+E L  +       +EV      RLV        +G  F E++ EE A  
Sbjct: 6  FLQNLPEETTKEMLEMLFNQFPGFKEV------RLV------PRRGIAFVEFETEEQATV 53

Query: 64 ARRNLQGYEI 73
          A + LQG++I
Sbjct: 54 ALQALQGFKI 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|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 8/82 (9%)

Query: 9  VFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          +F+G+IP +  +E+++E    +   V  V+ +    DR   K +G+ F EY+    A  A
Sbjct: 5  LFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRT--KNRGFAFVEYESHRAAAMA 62

Query: 65 RRNL--QGYEINGRQLRVDFAE 84
          RR L    +++ G  ++VD+A 
Sbjct: 63 RRKLIPGTFQLWGHTIQVDWAC 84

This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 14/49 (28%), Positives = 28/49 (57%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKD 57
          +F+G + ++ T++ L E   + G V    ++ D  TG+ +G+GF  +K 
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V  +P   T+++L ++  + G +++ R++ D+ TG  +G GF  +     A  A + L
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 69 QGYEING--RQLRVDFA 83
           G +  G    + V FA
Sbjct: 63 NGQKPEGASEPITVKFA 79

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 16/52 (30%), Positives = 29/52 (55%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          +FVG I  D  E  L +   + G + +  ++ DR++GK +G+ F  + D +T
Sbjct: 3  IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDT 54

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 10 FVGNIPYDATEEQLIEICREVGP----VVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          FVG IP   T+E+++E   +V      V+ +R   D+   K +G+ F EY+    A  AR
Sbjct: 5  FVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKN--KNRGFAFVEYESHRAAAMAR 62

Query: 66 RNL 68
          R L
Sbjct: 63 RKL 65

This subfamily corresponds to the RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

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

 Score = 40.1 bits (93), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+++L  +   +G V S +L+ D+  G   GYGF  Y + + A  A   L
Sbjct: 4  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 69 QGYEINGRQLRVDFA 83
           G  +  + ++V +A
Sbjct: 64 NGLRLQSKTIKVSYA 78

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

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.2 bits (93), Expect = 2e-04
 Identities = 18/71 (25%), Positives = 40/71 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++  +P + T++ L+++C+  G +VS + ++D+ T K KGYGF ++     A  A   L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 69 QGYEINGRQLR 79
          +   +  +  +
Sbjct: 70 KASGVQAQMAK 80

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 45/72 (62%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ ++P +  ++ L+++    G VVS ++ ID++T   K +GF  Y +  +A +A + +
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 69 QGYEINGRQLRV 80
           G++I  ++L+V
Sbjct: 70 NGFQIGMKRLKV 81

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

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 20/51 (39%), Positives = 29/51 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
          VFVG +  D TEEQ+ E     G + +  L +D +T + +G+ F  Y DEE
Sbjct: 2  VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 18/71 (25%), Positives = 40/71 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++  +P   T++ LI++C+  G +VS + ++D+ T + KGYGF ++     A  A  +L
Sbjct: 7  LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 69 QGYEINGRQLR 79
          +   +  +  +
Sbjct: 67 KANGVQAQMAK 77

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of calcineurin (RCANs) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 18/85 (21%), Positives = 23/85 (27%), Gaps = 22/85 (25%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVV------SFRLVIDRETGKPKGYGFCEYKDEE 59
             VF         +  L  +    G +       SFR                 +   E
Sbjct: 7  PSEVFT----NAELKAALESLFSSYGEIATFVYLPSFRRAR------------VVFSSPE 50

Query: 60 TALSARRNLQGYEINGRQLRVDFAE 84
           A  AR  L G    G  LRV F +
Sbjct: 51 EAALARIELHGTVFEGSVLRVYFGQ 75

This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic subunit. Overexpressed RCANs may bind and inhibit calcineurin. In contrast, low levels of phosphorylated RCANs may stimulate the calcineurin signaling. RCANs are characterized by harboring a central short, unique serine-proline motif containing FLIISPPxSPP box, which is strongly conserved from yeast to human but is absent in bacteria. They consist of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. . Length = 75

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          CV++  +    TE+ L       GPVV   +VIDR+    +G     +   E A +A   
Sbjct: 9  CVWLDGLDESVTEQYLTRHFSRYGPVV--HVVIDRQ----RGQALVFFDKVEAAQAAVNE 62

Query: 68 LQGYEINGRQLRVDF 82
          ++G ++ GR+L+VDF
Sbjct: 63 MKGRKLGGRKLQVDF 77

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          +FVG I +   E  L +   + G V   ++V DR  G  KGYGF  ++ +E A
Sbjct: 5  IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDA 56

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 21/88 (23%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYK-DEETALSAR 65
          + VFVG +P +ATEE + E+  + G +++ R+       K     FC  +  EE A+   
Sbjct: 7  KTVFVGGLPENATEEIIREVFEQCGEIIAIRM------SKKN---FCHIRFAEEFAVDKA 57

Query: 66 RNLQGYEI----------NGRQLRVDFA 83
            L GY +          +GR L VDFA
Sbjct: 58 IYLSGYRVRIGSSTDPKNSGR-LHVDFA 84

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          V+VGN  +  T++QLI++ R VG   VV  +   +R  G+ KGY       E +      
Sbjct: 4  VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63

Query: 67 NLQGYEINGRQLRVDFA 83
           L G  +NG ++ V  A
Sbjct: 64 LLPGKVLNGEKVDVRPA 80

This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 90

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

 Score = 39.0 bits (92), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 21 EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV 80
            L  +  + GPV+    ++  +T K +G  F  +KD E+A +A R LQG+    + +R+
Sbjct: 18 RSLYALFSQFGPVLD---IVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRI 74

Query: 81 DFA 83
           +A
Sbjct: 75 QYA 77

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

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

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 39/77 (50%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           V+VG+I ++  E+ +       GP+ S  +  D  TGK KG+ F EY+  E A  A   +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 69  QGYEINGRQLRVDFAEN 85
            G  + GR ++V    N
Sbjct: 170 NGQMLGGRNIKVGRPSN 186

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
           R V V  +P  A+ + L +  R+ G V    +  D+E     G G  E+  +E    A 
Sbjct: 1  FR-VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQE-----GEGVVEFTSQEDMERAL 54

Query: 66 RNLQGYEINGRQLRV 80
          R L G E  GR++RV
Sbjct: 55 RKLDGTEFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 19/61 (31%), Positives = 33/61 (54%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG++P   TE+++  +  E G V+   ++ D+ TG  +G  F +Y   + A  A R L
Sbjct: 2  LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 69 Q 69
           
Sbjct: 62 H 62

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 16/46 (34%), Positives = 29/46 (63%)

Query: 19 TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          T++ L+++C+  G +VS + ++D+ T K KGYGF ++     A  A
Sbjct: 14 TDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 59

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 22/84 (26%), Positives = 46/84 (54%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VG++  D TE +L ++ +  GPV+S R+  D  T +  GYG+  +++   A  A   +
Sbjct: 3  LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 69 QGYEINGRQLRVDFAENDKGADRN 92
              + G+ +R+ +++ D    R+
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSLRRS 86

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|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 12/82 (14%)

Query: 9  VFVGNIPYDATEEQLIEICREVG----------PVVSFRLVIDRETGKPKGYGFCEYKDE 58
          ++V  +  + T E+L +  +  G          P+V+  +  D+ETGKPKG     Y+D 
Sbjct: 3  IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVN--IYTDKETGKPKGDATVSYEDP 60

Query: 59 ETALSARRNLQGYEINGRQLRV 80
           +A +A     G +  G +L+V
Sbjct: 61 PSAKAAVEWFDGKDFQGSKLKV 82

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2)

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          + + + N+P++ TEE+LIE+C+  G +V+ +       G  +   F E+ D   A++
Sbjct: 3  KVLHLRNLPWECTEEELIELCKPFGKIVNTKC----NVGANRNQAFVEFADLNQAIA 55

This subfamily corresponds to the RRM1 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 81

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 14/87 (16%)

Query: 6  HRCVFVGNI--PYDATEEQLI-EI-------CREVGPVVSFRLVIDRETGKPKGYGFCEY 55
           RCV + N+  P + TE++   EI       C + GPV   +  +D+    P+G  + ++
Sbjct: 1  SRCVILKNMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIK--VDKN--SPEGVVYVKF 56

Query: 56 KDEETALSARRNLQGYEINGRQLRVDF 82
          K  E A    + L G   +GRQ+  ++
Sbjct: 57 KTVEAAQKCIQALNGRWFDGRQITAEY 83

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 14/79 (17%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + + N+P D TE  LI +    G V +  L+      + K     E    E   SA+  +
Sbjct: 2  LHLRNLPPDVTESDLIALVSPFGKVTNVLLL------RGKNQALVEMDSVE---SAKSMV 52

Query: 69 QGYE-----INGRQLRVDF 82
            Y      I GR++ + +
Sbjct: 53 DYYLTVPALIRGRRVYIQY 71

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 10/81 (12%)

Query: 10 FVGNIPYDATEEQLIEI-------CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          +V N+    TEE L+ I         E   +   RL+     G+ KG  F  +  EE A 
Sbjct: 5  YVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLM---TEGRMKGQAFVTFPSEEIAT 61

Query: 63 SARRNLQGYEINGRQLRVDFA 83
           A   + GY + G+ + + F 
Sbjct: 62 KALNLVNGYVLKGKPMVIQFG 82

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 20/135 (14%), Positives = 29/135 (21%), Gaps = 2/135 (1%)

Query: 214 QAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQEA 273
             Q       PQ       +     P  P        + Q        Q     P  Q  
Sbjct: 206 PPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQ--MPPPPPQPP 263

Query: 274 QIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQLAN 333
           Q Q       A  P  +     P   + Q            +P++       R       
Sbjct: 264 QQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQ 323

Query: 334 SSSLNQQVHPPSLEN 348
              L+QQ      + 
Sbjct: 324 LVQLSQQQREALSQE 338

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 35/171 (20%), Positives = 51/171 (29%), Gaps = 25/171 (14%)

Query: 193 QNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGHPAQPLFQDGQQQVA 252
           Q KEQ R  L             Q       P++ Q+P+     G   QP +  GQ    
Sbjct: 362 QRKEQRRAHL-------------QDQFMQLQPRMRQLPMGSPMGGAMGQPPYY-GQGPQQ 407

Query: 253 QLPGLPPLAQKMQLMPKVQEAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPG- 311
           Q  G P    +M +MP                        ++ P      A Q+  +   
Sbjct: 408 QFNGQPLGWPRMSMMPTPMGPGGP-----LRPNGLAPMNAVRAPSRNAQNAAQKPPMQPV 462

Query: 312 --QSGIPMLPSMHPSVRPQI---QLANSSSLNQQVHPPSLENQVQVSASNL 357
                   LP      +PQ    Q   +  L Q +   + + Q QV    L
Sbjct: 463 MYPPNYQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQVLGERL 513

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|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.5 bits (89), Expect = 7e-04
 Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 8/88 (9%)

Query: 9  VFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          +F+G IP     E+++E    +   V  V+ +    D+   K +G+ F EY+    A  A
Sbjct: 4  LFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKM--KNRGFAFVEYESHRAAAMA 61

Query: 65 RRNLQGYEIN--GRQLRVDFAENDKGAD 90
          RR L    I   G Q+ VD+AE +   D
Sbjct: 62 RRKLMPGRIQLWGHQIAVDWAEPEIDVD 89

This subgroup corresponds to the RRM2 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 89

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 14/84 (16%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKG-YGFCEYKDE---ET 60
            R VFV       +EEQL++     GPV++  +++D    K KG Y   E+  +   + 
Sbjct: 1  AERSVFVSGFKRGTSEEQLMDYFSAFGPVMN--VIMD----KDKGVYAIVEFDSKEGVDK 54

Query: 61 ALSARRNLQGYEINGRQLRVDFAE 84
           LS       + +NG +LRV   E
Sbjct: 55 VLSE----PQHTLNGHRLRVRPRE 74

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 19/51 (37%), Positives = 29/51 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
          +FVG +  D  EE++ E     G V S  L +D +T K +G+ F  +K+EE
Sbjct: 2  IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEE 52

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.3 bits (89), Expect = 8e-04
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP-----KGYGFCEYKDEETALS 63
          +FV N+ +  T + L +  + +   V  R+    +  +P      G+GF  +K +E A +
Sbjct: 3  LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 64 ARRNLQGYEINGRQLRVDFA 83
          A + + G+ ++G  L V F+
Sbjct: 63 ALKAMDGFVLDGHTLVVKFS 82

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 38.1 bits (89), Expect = 9e-04
 Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 17/94 (18%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKG--YGFCEYKDEETAL 62
          + R ++VG IP D T  +L +  +  G +    L       +  G  YGF  Y+    A 
Sbjct: 1  ERRVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-----RDDGDNYGFVTYRYACDAF 55

Query: 63 SA------RRNLQGYEI--NGR--QLRVDFAEND 86
           A            Y++   GR    +  +A+ D
Sbjct: 56 RAIEHGNDDPTEPKYDLCFGGRRQFCQSSYADLD 89

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 37.9 bits (89), Expect = 9e-04
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 15/81 (18%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP-----KGYGFC--EYKDEETA 61
          ++V N P    +  + ++  + G ++S R         P     K   FC  ++   E+A
Sbjct: 3  LWVTNFPPSFDQSDIRDLFEQYGEILSIRF--------PSLRFNKTRRFCYVQFTSPESA 54

Query: 62 LSARRNLQGYEINGRQLRVDF 82
           +A   L G    G +L V  
Sbjct: 55 AAAVALLNGKLGEGYKLVVKI 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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 38.0 bits (88), Expect = 9e-04
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG + +D +++ L +   + G V    + +D  TG+ +G+GF  +KD     S  + L
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDAS---SVEKVL 58

Query: 69 QGYE--INGRQL 78
          +  E  ++GR +
Sbjct: 59 EQKEHRLDGRLI 70

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 18/51 (35%), Positives = 32/51 (62%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
          +FVG +  +ATEE++ E   E G + +  L +D +T K +G+ F  +K+E+
Sbjct: 7  IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEED 57

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEIC-REVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          R VFVG +P   T  +L  I  R  G V    +  D     P G     + +E++ + A
Sbjct: 1  RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKA 59

This subfamily corresponds to the RRM2 of CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins has been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to the high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation. It directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 81

>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 = 0.001
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V   P D +E  + EI    G V   +++          + F E++  E+A+ A+ ++
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53

Query: 69 QGYEINGRQLRV 80
           G  +N   L V
Sbjct: 54 HGKVLNNNPLYV 65

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

>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 14/87 (16%)

Query: 9  VFVGNIPYDATEEQLIEICREVG----------PVVSFRLVIDRETGKPKGYGFCEYKDE 58
          V+V  +P D T E+ +E+  + G          P +  +L  D E G  KG   C Y  E
Sbjct: 4  VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKI--KLYRD-ENGNLKGDALCCYLKE 60

Query: 59 ETALSARRNLQGYEI-NGRQLRVDFAE 84
          E+   A + L G EI  G +++V+ A+
Sbjct: 61 ESVELAIQLLDGTEIGRGYKMKVERAK 87

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V N+    ++++L  +  + G V   R    R + K     F E+ D   A +A   L
Sbjct: 4  LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALDAL 58

Query: 69 QGYEINGRQLRVD 81
           G    G +L+V 
Sbjct: 59 NGRPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 11/84 (13%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V++G + Y A E  +    +  G ++   L          GYGF E+ D   A  A   L
Sbjct: 2  VYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYEL 53

Query: 69 QGYEINGRQLRVDFAENDKGADRN 92
           G ++ G ++ V   E+ +G  R+
Sbjct: 54 NGKDLCGERVIV---EHARGPRRD 74

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 16/74 (21%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFC----EYKDEETALSA 64
          V V N+P D TE ++ +  ++ G +        RE    +  G      E++ E+ AL+A
Sbjct: 3  VKVKNLPKDTTENKIRQFFKDCGEI--------REVKIVESEGGLVAVIEFETEDEALAA 54

Query: 65 R----RNLQGYEIN 74
               + L G EI+
Sbjct: 55 LTKDHKRLGGNEIS 68

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

>gnl|CDD|206472 pfam14304, CSTF_C, Transcription termination and cleavage factor C-terminal

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 17/35 (48%), Positives = 26/35 (74%)

Query: 511 SALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLR 545
           +AL+ QVL L+  Q+  LPPEQRQ +++L+Q + R
Sbjct: 8   AALIMQVLQLSEAQIAMLPPEQRQSILELRQQIQR 42

The C-terminal section of CSTF proteins is a discreet structure is crucial for mRNA 3'-end processing. This domain interacts with Pcf11 and possibly PC4, thus linking CstF2 to transcription, transcriptional termination, and cell growth. Length = 44

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+VGN+  +  + +L       GP+ S  +  +     P G+ F E++D   A  A R L
Sbjct: 7  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 61

Query: 69 QGYEINGRQLRVDFAENDK 87
           G  + G ++RV+ +  +K
Sbjct: 62 DGRTLCGCRVRVELSNGEK 80

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

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

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V N+P   TE++L E     G V   +++  R+ GK + +GF  +K EE A  A +  
Sbjct: 3  IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 69 QGYEINGRQLRVDFA 83
              I+  ++ V+ A
Sbjct: 62 NKTFIDTSKISVELA 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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
          +V N+     +E+L E     G + S +++ D E G+ KG+GF  +   E A  A   + 
Sbjct: 5  YVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 70 GYEINGRQLRVDFAE 84
          G  I G+ L V  A+
Sbjct: 64 GRIIGGKPLYVALAQ 78

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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  + T E + +   + G V    L+ D+ T + +G+GF  ++ E+  +     +
Sbjct: 2  IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI-VEKVCEI 60

Query: 69 QGYEINGRQL 78
            +EIN + +
Sbjct: 61 HFHEINNKMV 70

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 8  CVFVGNIPYDATEEQLIEI-CREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEETALSAR 65
           +FV N+  + TEE+L ++  R+ G    F RL +  + G P    F E++D   A  A 
Sbjct: 4  TLFVANLGPNTTEEELRQLFSRQPG----FRRLKMHNKGGGP--VCFVEFEDVSFATQAL 57

Query: 66 RNLQG 70
           +LQG
Sbjct: 58 NSLQG 62

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 17 DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGR 76
            TE+ L E     G +    +V D++T + KG  + ++    +A  A   + G  + G 
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 77 Q--LRV 80
             L+V
Sbjct: 73 TKPLKV 78

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 17/67 (25%), Positives = 38/67 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++V  +P   T+++L ++  + G +++ R+++D+ TG  +G GF  +     A  A + L
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 69 QGYEING 75
           G + +G
Sbjct: 65 NGQKPSG 71

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

>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 4/72 (5%)

Query: 13 NIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE 72
          NIP D ++  + ++ +E G  V  +   D +  +   + F   +D            G E
Sbjct: 7  NIPLDVSDYTIEDLIKEFGEPVYSKF-YDHKDSRTAVFEF---EDPSILEKVVEKYNGKE 62

Query: 73 INGRQLRVDFAE 84
          +NG ++ V+  E
Sbjct: 63 LNGAKIEVEIFE 74

This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 19/51 (37%), Positives = 26/51 (50%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
          +FVGN+P+D  E +L E     G VV  R+      GK   +GF  + D E
Sbjct: 8  LFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSE 58

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 4/72 (5%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+ G  P       +  +    GPV    ++          + F  +++ E A  A   L
Sbjct: 2  VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIETL 57

Query: 69 QGYEINGRQLRV 80
           G  ++G  ++V
Sbjct: 58 NGASVDGNCIKV 69

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

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS-ARRN 67
          +FVG +    TE  L E     G V    ++  ++ G  +G+ + + +  E  L   +  
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 68 LQGYEINGRQLRVDFA 83
          L G +  G  L+++ A
Sbjct: 62 LNGTKWKGSVLKIEEA 77

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|240965 cd12521, RRM3_MRN1, RNA recognition motif 3 of RNA-binding protein MRN1 and similar proteins

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 13/78 (16%)

Query: 7  RCVFVGNIPYDATEEQLIEICREV--GPVVSFRLVIDRETGKPKGYGFCEYKDEETALS- 63
          R V++GNI  D   E   EIC  V  G + S R + ++         F  + D   A   
Sbjct: 2  RTVYLGNIHPDTKIE---EICNAVRGGLLQSIRYIPEKHI------CFVTFIDPTAAAQF 52

Query: 64 -ARRNLQGYEINGRQLRV 80
           A  ++QG  ++ R+L+V
Sbjct: 53 YAMSSIQGLTLHNRRLKV 70

This subgroup corresponds to the RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	551
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.95
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.79
PF14327	84	CSTF2_hinge: Hinge domain of cleavage stimulation	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.66
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.63
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.59
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.59
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.57
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.51
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.49
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.49
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.49
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.48
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.47
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.46
KOG0122	270	consensus Translation initiation factor 3, subunit	99.46
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.44
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.44
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.43
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.43
smart00362	72	RRM_2 RNA recognition motif.	99.43
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.41
PLN03120	260	nucleic acid binding protein; Provisional	99.41
smart00360	71	RRM RNA recognition motif.	99.41
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.4
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.39
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.36
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.36
PLN03213	759	repressor of silencing 3; Provisional	99.35
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.35
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.35
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.33
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.33
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.32
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.32
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.3
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.3
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.28
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.28
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.27
PLN03121	243	nucleic acid binding protein; Provisional	99.27
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.25
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.24
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.22
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.22
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.2
smart00361	70	RRM_1 RNA recognition motif.	99.15
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.11
PF14304	46	CSTF_C: Transcription termination and cleavage fac	99.1
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.09
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.09
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.08
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.08
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.07
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.02
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.0
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.0
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.96
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.96
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.92
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.85
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.84
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.78
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.77
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.76
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.76
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.75
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.71
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.71
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.67
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.66
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.63
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.59
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.59
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.59
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.56
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.56
KOG0226	290	consensus RNA-binding proteins [General function p	98.52
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.45
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.41
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.38
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.23
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.22
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.2
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.18
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.16
KOG0151	877	consensus Predicted splicing regulator, contains R	98.09
KOG4210	285	consensus Nuclear localization sequence binding pr	98.07
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.94
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.8
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.52
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.51
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.49
KOG2314	698	consensus Translation initiation factor 3, subunit	97.38
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.35
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.23
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.22
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.11
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.01
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.0
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.94
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.86
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.82
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.76
KOG3152	278	consensus TBP-binding protein, activator of basal	96.56
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.52
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	96.51
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.48
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.4
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.2
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.17
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	95.98
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.96
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	95.79
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	95.75
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.62
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.54
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	94.94
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.74
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.47
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.38
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.27
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.04
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.46
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.21
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.16
KOG2591	684	consensus c-Mpl binding protein, contains La domai	93.04
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	92.56
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.38
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	91.89
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	91.64
KOG4210	285	consensus Nuclear localization sequence binding pr	91.63
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	91.27
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.44
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	90.1
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	87.91
KOG4660	549	consensus Protein Mei2, essential for commitment t	87.25
KOG2135	526	consensus Proteins containing the RNA recognition	86.33
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	85.39
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	82.78
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	82.02

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.95  E-value=1.2e-27  Score=255.81  Aligned_cols=181  Identities=39%  Similarity=0.549  Sum_probs=149.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ++||||||||+++||+|.++|+++|.|.++++++|++||++||||||+|.+.++|.+|++.|||.+++||+|+|+|+..+
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            89999999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCccchhhhHHhhhccCCcccCcCCCCCCcccccCCCCc
Q 008851           87 KGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPND  166 (551)
Q Consensus        87 ~~~~r~r~~grGG~G~~~~~~~~~~~Ggp~~~G~~~~~~P~gl~~~~~a~s~ma~~lgga~~~~~~~~~glp~~~~~a~D  166 (551)
                      +.+++....+.+.+..                     ..+++-+                         ..+   ..+.+
T Consensus        99 ~~~~~~~~~~~~~p~~---------------------~~~~~~~-------------------------~~~---~~a~~  129 (435)
T KOG0108|consen   99 KNAERSLASHNALPAE---------------------GAPYSSP-------------------------SYP---FDALK  129 (435)
T ss_pred             chhHHHHhhcccCccc---------------------cccCCCC-------------------------ccc---ccccc
Confidence            6554432221110000                     0000000                         000   11346


Q ss_pred             hhhHhhhcCChHHHHHHHHHHHHHH-hhCHHHHHHHHHhCCChHHH-HHHHHHHhCCCChhhhhcccccCCC
Q 008851          167 PLTLHLAKMSRNQLNEIMSEMKLMA-TQNKEQARQLLLAKPPLLKA-LFQAQIMLGMATPQVLQMPILRQGP  236 (551)
Q Consensus       167 ~IS~~Lakl~p~QL~eiLsqLK~l~-~~~P~~Ar~LL~~NPQLa~A-L~QA~llLgmid~~v~q~~~~~q~~  236 (551)
                      .+...++++++.++++++..++... ..++..++.+|..+|+++|+ ++|++..|++.|++++-..+....-
T Consensus       130 ~~~~~~~~~p~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~i~~s~~~~~~~~p~~~l~~~~~~~~  201 (435)
T KOG0108|consen  130 GNGSGVSNEPPSQLFELLSQGANNTNKSNPTPNPSGLTIPPAIVVKNIPQSLVKLTLAKPFTALYILRPYAF  201 (435)
T ss_pred             ccccccccCCccccccccchhhhhccccCCCcCccccccCchhhhccchhhhhhhhccChHhhhcccchhhh
Confidence            6778889999999999999999999 78899999999999999999 9999999999999988777765533

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

Probab=99.79  E-value=2.4e-18  Score=160.08  Aligned_cols=84  Identities=31%  Similarity=0.659  Sum_probs=80.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+++|||+||+++++|++|+++|++||.|++|++++|++|++++|||||+|.+.++|++|++.|++..|+|+.|+|+++.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      .+..
T Consensus       113 ~~~~  116 (144)
T PLN03134        113 DRPS  116 (144)
T ss_pred             cCCC
Confidence            6544

>PF14327 CSTF2_hinge: Hinge domain of cleavage stimulation factor subunit 2; PDB: 4EBA_G

Probab=99.72  E-value=1.6e-18  Score=147.78  Aligned_cols=70  Identities=46%  Similarity=0.641  Sum_probs=59.0

Q ss_pred             CCCchhhHhhhcCChHHHHHHHHHHHHHHhhCHHHHHHHHHhCCChHHHHHHHHHHhCCCChhhhhcccc
Q 008851          163 SPNDPLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPIL  232 (551)
Q Consensus       163 ~a~D~IS~~Lakl~p~QL~eiLsqLK~l~~~~P~~Ar~LL~~NPQLa~AL~QA~llLgmid~~v~q~~~~  232 (551)
                      .+.|.|+++|++|++.||+|+|++||.|+.++|++||+||.+||||+||||||+++|||||+++++.+++
T Consensus        14 ~~~~~Is~~l~~l~~~ql~ell~~mK~l~~~~p~~ar~lL~~nPqLa~Al~qa~l~lg~vd~~v~~~~l~   83 (84)
T PF14327_consen   14 SAPDAISQTLSSLPPEQLYELLSQMKQLAQQNPEQARQLLQQNPQLAYALFQALLLLGMVDPDVVQSILK   83 (84)
T ss_dssp             -HHHHHHTTSSTSHHHHHHHHHHHHHHHHC----HHHHHHHS-THHHHHHHHHHHHTSS-SSSCHHH---
T ss_pred             CcHHHHHHHHHhCCHHHHHHHHHHHHHHHHhCHHHHHHHHHHCcHHHHHHHHHHHHhCCCCHHHHHhhcc
Confidence            3679999999999999999999999999999999999999999999999999999999999999998875

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.66  E-value=6.1e-16  Score=159.81  Aligned_cols=82  Identities=32%  Similarity=0.532  Sum_probs=78.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +++|||+|||++++|++|+++|+.||.|.+|+|++|+.||++||||||+|.+.++|.+|+..|||..|+||.|+|+|+..
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            53

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.63  E-value=4.2e-15  Score=156.42  Aligned_cols=84  Identities=29%  Similarity=0.461  Sum_probs=78.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~~   82 (551)
                      ..++|||+|||+++||++|+++|++||.|++|+|+.|+.||++||||||+|.+.++|++|++.||+..+.|  +.|+|++
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            46789999999999999999999999999999999999999999999999999999999999999998865  7899999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      ++....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            987543

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=99.62  E-value=2.2e-15  Score=155.66  Aligned_cols=82  Identities=28%  Similarity=0.538  Sum_probs=78.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||+|.+|+|++|+.+|+++|||||+|.+.++|.+|++.|+|..|.|+.|+|+|++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      +.
T Consensus        82 ~~   83 (352)
T TIGR01661        82 PS   83 (352)
T ss_pred             cc
Confidence            53

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=2.5e-15  Score=158.07  Aligned_cols=82  Identities=28%  Similarity=0.575  Sum_probs=79.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++||++|+++|+.||.|++|+|++|+.|++++|||||+|.++++|++|++.|++..|.+++|+|+++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ++
T Consensus       185 ~p  186 (346)
T TIGR01659       185 RP  186 (346)
T ss_pred             cc
Confidence            64

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).

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

Probab=99.59  E-value=6.6e-15  Score=149.18  Aligned_cols=90  Identities=32%  Similarity=0.554  Sum_probs=82.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+-+||||+.|+++++|..|+..|+.||+|+.|+||.|+.||+++|||||||+++.+...|++..+|..|+|+.|.|++-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCCCCCC
Q 008851           84 ENDKGADRNR   93 (551)
Q Consensus        84 ~~~~~~~r~r   93 (551)
                      ....-+.+..
T Consensus       179 RgRTvkgW~P  188 (335)
T KOG0113|consen  179 RGRTVKGWLP  188 (335)
T ss_pred             cccccccccc
Confidence            7654444433

>PF00076 RRM_1: RNA recognition motif

Probab=99.59  E-value=8.2e-15  Score=116.07  Aligned_cols=70  Identities=41%  Similarity=0.766  Sum_probs=67.6

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      |||+|||+++++++|+++|+.||.|..+.+..+ .+++.+|||||+|.+.++|++|++.|++..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999988 6899999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.57  E-value=2.7e-15  Score=147.97  Aligned_cols=79  Identities=29%  Similarity=0.577  Sum_probs=74.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      -++||||+|+|++..|+|+++|++||+|++..++.|+.|||+||||||+|+|.+.|.+||+.-+ -.|+||+..|++|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhhh
Confidence            3689999999999999999999999999999999999999999999999999999999997644 578999999999875

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

Probab=99.51  E-value=2.8e-14  Score=129.87  Aligned_cols=82  Identities=29%  Similarity=0.549  Sum_probs=78.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++||||||.+.++||+|.++|+++|.|+.|.+-.|+.+..+.|||||||...++|+.|++.+++..++.|.|+|+|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ..
T Consensus       114 ~G  115 (153)
T KOG0121|consen  114 AG  115 (153)
T ss_pred             cc
Confidence            54

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.49  E-value=1.4e-13  Score=153.44  Aligned_cols=82  Identities=22%  Similarity=0.411  Sum_probs=78.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+||++++++++|+++|+.||.|++|+|.+|+.+|++||||||+|.+.++|.+|++.||++.|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            54

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=99.49  E-value=1.7e-13  Score=110.17  Aligned_cols=70  Identities=40%  Similarity=0.743  Sum_probs=65.6

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      |||+|||+++++++|+++|+.||.|..+++..+++ |+.+|+|||+|.+.++|.+|++.+++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999987 99999999999999999999999999999999985

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 ....

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.49  E-value=4.5e-15  Score=141.75  Aligned_cols=81  Identities=35%  Similarity=0.714  Sum_probs=77.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++..|||||||++.||.+|..+|++||.|++|.+++|+.||+++||||..|+|.....-|+.+|||+.|.||.|+|+...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            57789999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            4

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.48  E-value=1.1e-13  Score=154.35  Aligned_cols=80  Identities=30%  Similarity=0.522  Sum_probs=76.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++||||||+++++|++|+++|+.||.|++|++++|+.||++||||||+|.+.++|++|++.|||..|+||.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999998543

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.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.47  E-value=1.9e-13  Score=131.11  Aligned_cols=84  Identities=27%  Similarity=0.538  Sum_probs=76.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         1 ma~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      |....+++|||||||.++.|.+|+++|.+||.|++|.|...   -....||||||+|..+|+.||..-+|+.++|.+|+|
T Consensus         1 ~~gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRV   77 (241)
T KOG0105|consen    1 MSGRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRV   77 (241)
T ss_pred             CCCcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEE
Confidence            56677899999999999999999999999999999998643   345689999999999999999999999999999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      +|+....
T Consensus        78 Efprggr   84 (241)
T KOG0105|consen   78 EFPRGGR   84 (241)
T ss_pred             EeccCCC
Confidence            9998765

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

Probab=99.46  E-value=2.8e-13  Score=149.72  Aligned_cols=79  Identities=27%  Similarity=0.572  Sum_probs=76.3

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      +|||||||+++||++|+++|++||.|++|+|++|+.|++++|||||+|.+.++|++|++.+++..|+|+.|+|.|+..+
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~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999998643

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.46  E-value=2.3e-13  Score=135.09  Aligned_cols=82  Identities=32%  Similarity=0.553  Sum_probs=79.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|-|.||+.+++|++|+++|..||.|..+.|.+|++||.+||||||.|.+.++|.+||+.|||+-++.-.|+|+|++
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            56789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.44  E-value=5e-13  Score=127.04  Aligned_cols=80  Identities=50%  Similarity=0.842  Sum_probs=77.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+||++++++++|+++|..||.|..+++..|+.+|+++|||||+|.+.++|..|++.+++..|.|+.|+|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999763

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.44  E-value=3.9e-13  Score=127.94  Aligned_cols=79  Identities=30%  Similarity=0.528  Sum_probs=73.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      -.++||||||+.++++.||+.+|..||+|..|.|-..     +.|||||||+|..+|+.|++.|+|..|.|..|+|++++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            4789999999999999999999999999999988754     48999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ....
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            7554

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.43  E-value=3.1e-13  Score=138.64  Aligned_cols=82  Identities=24%  Similarity=0.482  Sum_probs=76.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +..++|+|.||||...|-||+.+|++||+|.+|+|+++.  ..+||||||+|++.+||++|-.+|||..|.||+|+|..|
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            356899999999999999999999999999999999975  567999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +.+-
T Consensus       172 TarV  175 (376)
T KOG0125|consen  172 TARV  175 (376)
T ss_pred             chhh
Confidence            8753

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.43  E-value=8.3e-13  Score=143.43  Aligned_cols=82  Identities=33%  Similarity=0.556  Sum_probs=78.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.|+.||+++|||||+|.+.++|..|+..|+|..|+|+.|+|.++.
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            35789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
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.

>smart00362 RRM_2 RNA recognition motif

Probab=99.43  E-value=1e-12  Score=101.97  Aligned_cols=72  Identities=44%  Similarity=0.773  Sum_probs=67.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      +|||+|||.++++++|+++|+.||.|.++++..++  ++++|+|||+|.+.++|..|++.+++..++|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998876  7889999999999999999999999999999999874

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.41  E-value=8.5e-13  Score=141.67  Aligned_cols=80  Identities=34%  Similarity=0.679  Sum_probs=77.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||++++|++|+++|+.||.|..|.++.|+.+|+++|||||+|.+.++|.+|++.|+|..|.|+.|+|.|+..
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            58999999999999999999999999999999999999999999999999999999999999999999999999999874

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.41  E-value=8.3e-13  Score=133.40  Aligned_cols=76  Identities=25%  Similarity=0.311  Sum_probs=71.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+||+++++|++|+++|+.||.|++|+|+.|++   .+|||||+|.+.++|+.|+ .|+|..|.||.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998864   4799999999999999999 5999999999999999864

>smart00360 RRM RNA recognition motif

Probab=99.41  E-value=1e-12  Score=101.40  Aligned_cols=71  Identities=48%  Similarity=0.784  Sum_probs=67.7

Q ss_pred             EecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851           11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus        11 VGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      |+|||+++++++|+++|+.||.|.++.+..++.+++++|||||+|.+.++|.+|++.+++..++|+.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999998889999999999999999999999999999999999874

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

Probab=99.40  E-value=1.1e-12  Score=145.03  Aligned_cols=81  Identities=30%  Similarity=0.534  Sum_probs=77.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+||++++|+++|+++|+.||.|++|+++.| .+|+++|||||+|.+.++|.+|++.||+..|+|++|+|.+|.
T Consensus       284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            4678999999999999999999999999999999999 689999999999999999999999999999999999999997


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      .+
T Consensus       363 ~k  364 (562)
T TIGR01628       363 RK  364 (562)
T ss_pred             Cc
Confidence            54

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=99.39  E-value=1.7e-12  Score=139.29  Aligned_cols=80  Identities=30%  Similarity=0.477  Sum_probs=76.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||+|||+++++++|+++|+.||.|.+|+++.|+.||+++|||||+|.+.++|.+|+. |+|..|.|+.|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            57899999999999999999999999999999999999999999999999999999999995 89999999999999875


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus       167 ~  167 (457)
T TIGR01622       167 A  167 (457)
T ss_pred             h
Confidence            4

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.

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.36  E-value=1.2e-12  Score=120.35  Aligned_cols=83  Identities=30%  Similarity=0.471  Sum_probs=79.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..+.|||.++..+++|++|.+.|+.||+|+.+.+..|+.||-.||||+|||++.+.|++|+..+||..|.|..|.|+||.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus       151 v~g  153 (170)
T KOG0130|consen  151 VKG  153 (170)
T ss_pred             ecC
Confidence            543

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.36  E-value=1.3e-12  Score=131.21  Aligned_cols=83  Identities=33%  Similarity=0.556  Sum_probs=79.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ....||||.|..+++-|+|++.|..||+|.++++++|..|+|+||||||.|.+.++|++||..+||..|++|.||..||.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus       141 RKp  143 (321)
T KOG0148|consen  141 RKP  143 (321)
T ss_pred             cCc
Confidence            654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.35  E-value=2.1e-12  Score=137.78  Aligned_cols=77  Identities=18%  Similarity=0.376  Sum_probs=72.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCceeCCEEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE--ETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~--e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...+||||||.|++++++|+.+|+.||.|.+|.|+  ++||  ||||||+|.+.  .++.+||..|||.+++||.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            35789999999999999999999999999999999  6678  99999999977  789999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            986

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.35  E-value=2.4e-12  Score=143.17  Aligned_cols=79  Identities=37%  Similarity=0.644  Sum_probs=73.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-GRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-GR~LrV~~A   83 (551)
                      ..++|||+|||++++|++|+++|++||.|.+|+|++| .+|+++|||||+|.+.++|++|++.||+++|. |+.|.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            3689999999999999999999999999999999999 78999999999999999999999999999985 788888776


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      .
T Consensus       136 ~  136 (578)
T TIGR01648       136 V  136 (578)
T ss_pred             c
Confidence            4

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.

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.35  E-value=2.8e-12  Score=124.92  Aligned_cols=83  Identities=25%  Similarity=0.457  Sum_probs=79.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      -.+|-|-||.+.++.++|+.+|++||.|.+|.|.+|+.|+.++|||||.|.+..+|+.|++.|+|..|+|+.|+|.+|+-
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCC
Q 008851           86 DKG   88 (551)
Q Consensus        86 ~~~   88 (551)
                      +..
T Consensus        93 gr~   95 (256)
T KOG4207|consen   93 GRP   95 (256)
T ss_pred             CCC
Confidence            654

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.33  E-value=3.2e-12  Score=135.34  Aligned_cols=82  Identities=33%  Similarity=0.596  Sum_probs=77.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI-NGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I-~GR~LrV~~   82 (551)
                      +..|.||||.||.|+.|++|..+|++.|+|-++||+.|+.+|.+||||||.|.+.++|++|++.||+++| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            3578999999999999999999999999999999999999999999999999999999999999999999 589998888


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +..
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            764

>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=99.33  E-value=1.3e-11  Score=96.29  Aligned_cols=74  Identities=50%  Similarity=0.814  Sum_probs=69.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +|||+|||+++++++|+++|+.||.|..+.+..++.+ +.+|+|||+|.+.++|..|++.+++..++|+++.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999988765 7799999999999999999999999999999999874

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).

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.32  E-value=5.6e-12  Score=133.12  Aligned_cols=86  Identities=36%  Similarity=0.621  Sum_probs=77.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHH-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICR-EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs-~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+.+||.||||++.|.+|+++|+ +.|+|.+|.+.+|. .||+||||.|||+++|.+++|+++||.++++||.|.|+..
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            467799999999999999999995 69999999999996 6999999999999999999999999999999999999987


Q ss_pred             cCCCCCCC
Q 008851           84 ENDKGADR   91 (551)
Q Consensus        84 ~~~~~~~r   91 (551)
                      ....+..+
T Consensus       122 ~d~q~~~~  129 (608)
T KOG4212|consen  122 HDEQRDQY  129 (608)
T ss_pred             Cchhhhhh
Confidence            76544333

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.32  E-value=1e-11  Score=138.25  Aligned_cols=75  Identities=27%  Similarity=0.465  Sum_probs=69.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREV--GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~--G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .++|||+||+++++||+|+++|+.|  |.|++|+++        ++||||+|.+.++|++|++.||+.+|+|+.|+|+|+
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            5789999999999999999999999  999999876        469999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      ++...
T Consensus       305 kp~~~  309 (578)
T TIGR01648       305 KPVDK  309 (578)
T ss_pred             cCCCc
Confidence            87543

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.30  E-value=1.1e-11  Score=124.65  Aligned_cols=80  Identities=28%  Similarity=0.527  Sum_probs=75.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +++.++||||||+..++|++|++.|+.||.|.+||+.+|      +||+||.|++.|.|..||..+|+.+|+|..+||.|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            567899999999999999999999999999999999987      79999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      -++...
T Consensus       235 GKe~~~  240 (321)
T KOG0148|consen  235 GKEGDD  240 (321)
T ss_pred             cccCCC
Confidence            887544

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.30  E-value=2.6e-12  Score=123.04  Aligned_cols=81  Identities=38%  Similarity=0.596  Sum_probs=78.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ....+||||||+..++|+.|+++|-+.|+|+++++.+|+.|.+.+|||||||.++|+|+-||+.||..++.||+|+|..+
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            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            8

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.28  E-value=2.1e-12  Score=126.74  Aligned_cols=86  Identities=30%  Similarity=0.548  Sum_probs=82.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++||||+|..+++|.-|...|-.||.|++|.+..|.+++|+||||||||...|+|.+|+.++|+.++.||.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 008851           85 NDKGAD   90 (551)
Q Consensus        85 ~~~~~~   90 (551)
                      +.+-+.
T Consensus        89 P~kike   94 (298)
T KOG0111|consen   89 PEKIKE   94 (298)
T ss_pred             CccccC
Confidence            865443

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=4.7e-12  Score=133.66  Aligned_cols=85  Identities=28%  Similarity=0.480  Sum_probs=76.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-e--CCEEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE-I--NGRQLRVD   81 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~-I--~GR~LrV~   81 (551)
                      +.-++|||-||..|+|+||+++|++||.|.+|.|++||.||.++|||||.|.+.++|.+|+..||+.+ |  ....|.|+
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            35679999999999999999999999999999999999999999999999999999999999998854 4  34679999


Q ss_pred             eecCCCCC
Q 008851           82 FAENDKGA   89 (551)
Q Consensus        82 ~A~~~~~~   89 (551)
                      +|+..+.+
T Consensus       113 ~Ad~E~er  120 (510)
T KOG0144|consen  113 YADGERER  120 (510)
T ss_pred             ccchhhhc
Confidence            99876543

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.27  E-value=1.6e-11  Score=108.49  Aligned_cols=79  Identities=25%  Similarity=0.505  Sum_probs=73.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..+.+||.|||+++|.|+..++|.+||.|+.++|-.+++   .+|-|||.|+|..+|++||+.|.|+.+.++.|.|-+..
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            468899999999999999999999999999999986654   48999999999999999999999999999999999977


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        94 ~~   95 (124)
T KOG0114|consen   94 PE   95 (124)
T ss_pred             HH
Confidence            54

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.27  E-value=2.1e-11  Score=121.90  Aligned_cols=77  Identities=16%  Similarity=0.169  Sum_probs=70.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...+|||+||++.+||++|+++|+.||.|.+|+|++|.   +.+|||||+|++.+.++.|+ .|+|..|.++.|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            56899999999999999999999999999999999884   44689999999999999999 799999999999998876


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            3

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.25  E-value=2.5e-11  Score=132.66  Aligned_cols=76  Identities=25%  Similarity=0.355  Sum_probs=69.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCEEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL--QGYEINGRQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L--ng~~I~GR~LrV~~   82 (551)
                      ++++|||+|||++++|++|+++|+.||.|.+|+++.+      ||||||+|++.++|++|++.+  ++..|+|+.|+|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            5799999999999999999999999999999999854      689999999999999999864  77899999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +..+
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            9754

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).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=2.3e-11  Score=121.91  Aligned_cols=82  Identities=27%  Similarity=0.529  Sum_probs=78.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .+.+.|.-||..+|+||++.+|...|+|++|++++|+-||.+.|||||.|-+++||++|+..|||..+..+.|+|.||++
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            45688889999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      ..
T Consensus       121 Ss  122 (360)
T KOG0145|consen  121 SS  122 (360)
T ss_pred             Ch
Confidence            54

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.22  E-value=4.5e-11  Score=130.62  Aligned_cols=78  Identities=19%  Similarity=0.272  Sum_probs=72.6

Q ss_pred             CCcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ++++|||+||++ .+++++|+++|+.||.|.+|++++++     +|||||+|.+.++|..|++.||+..|.|+.|+|.++
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            678999999998 69999999999999999999999874     799999999999999999999999999999999998


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +...
T Consensus       349 ~~~~  352 (481)
T TIGR01649       349 KQQN  352 (481)
T ss_pred             cccc
Confidence            7543

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).

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=2.6e-11  Score=130.95  Aligned_cols=83  Identities=35%  Similarity=0.554  Sum_probs=77.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-----CC-ceeCCEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL-----QG-YEINGRQL   78 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L-----ng-~~I~GR~L   78 (551)
                      ..++|||+||||++|||+|+..|++||.|.++.|+.|+.||+++|+|||.|.+..+|.+||...     .| +.|+||.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~L  370 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLL  370 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEE
Confidence            3589999999999999999999999999999999999999999999999999999999999876     23 67899999


Q ss_pred             EEEeecCCC
Q 008851           79 RVDFAENDK   87 (551)
Q Consensus        79 rV~~A~~~~   87 (551)
                      +|..|..+.
T Consensus       371 kv~~Av~Rk  379 (678)
T KOG0127|consen  371 KVTLAVTRK  379 (678)
T ss_pred             eeeeccchH
Confidence            999998654

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=1.3e-11  Score=130.47  Aligned_cols=87  Identities=29%  Similarity=0.531  Sum_probs=77.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCC--EEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY-EING--RQLRVD   81 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~-~I~G--R~LrV~   81 (551)
                      +++++|||-|+..++|+|++++|++||.|++|+|.+|.+ |.+||||||.|.+.|.|..|++.||+. ++.|  .+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            367899999999999999999999999999999999975 999999999999999999999999985 4555  579999


Q ss_pred             eecCCCCCCCC
Q 008851           82 FAENDKGADRN   92 (551)
Q Consensus        82 ~A~~~~~~~r~   92 (551)
                      ||+..+.+..+
T Consensus       202 FADtqkdk~~~  212 (510)
T KOG0144|consen  202 FADTQKDKDGK  212 (510)
T ss_pred             ecccCCCchHH
Confidence            99987665443

>smart00361 RRM_1 RNA recognition motif

Probab=99.15  E-value=1.6e-10  Score=94.34  Aligned_cols=61  Identities=21%  Similarity=0.339  Sum_probs=56.7

Q ss_pred             HHHHHHHHH----cCCCeeEEE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851           20 EEQLIEICR----EVGPVVSFR-LVIDRET--GKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus        20 EEeLre~Fs----~~G~V~~vr-Lv~Dr~T--GksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      +++|+++|+    .||.|.++. ++.|+.+  ++++|||||+|.+.++|.+|++.|||..++||.|++
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            678888888    999999995 8888877  999999999999999999999999999999999986

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.11  E-value=2.8e-10  Score=114.18  Aligned_cols=82  Identities=33%  Similarity=0.537  Sum_probs=78.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||-||..|++|.-|..+|+.||.|..|++++|..|.++||||||...+.++|..|+..|||+.+++|.|.|.|..
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            46899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      .+
T Consensus       357 nk  358 (360)
T KOG0145|consen  357 NK  358 (360)
T ss_pred             CC
Confidence            53

>PF14304 CSTF_C: Transcription termination and cleavage factor C-terminal; PDB: 2J8P_A

Probab=99.10  E-value=8.5e-11  Score=89.35  Aligned_cols=41  Identities=61%  Similarity=0.950  Sum_probs=33.6

Q ss_pred             hHHHHHHHHHHhcCHHHHhcCChHHHHHHHHHHHHHHhhhc
Q 008851          508 DVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQM  548 (551)
Q Consensus       508 ~~~~~~~~qv~~l~~~q~~~lp~~q~~~v~~~~~~~~~~~~  548 (551)
                      ..|.+||+|||+||+|||+.||||+|.+|..||+++.++.|
T Consensus         5 ~~q~aLl~QVL~Lt~eQI~~LPp~qR~~I~~Lr~ql~~~~~   45 (46)
T PF14304_consen    5 PEQAALLMQVLQLTPEQINALPPDQRQQILQLRQQLMRGEM   45 (46)
T ss_dssp             HTHHHHHHHHHTS-HHHHHTS-HHHHTHHHHHHHHHH----
T ss_pred             HHHHHHHHHHHcCCHHHHHhCCHHHHHHHHHHHHHHHhcCC
Confidence            46889999999999999999999999999999999998755

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=5.7e-11  Score=123.39  Aligned_cols=77  Identities=31%  Similarity=0.556  Sum_probs=74.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      |+||||.|.|+..|+.|+..|..||+|+++.+.+|+.|+++||||||||+-.|.|.-|++.+||..++||.|+|.+-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999853

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.09  E-value=1.4e-10  Score=120.34  Aligned_cols=83  Identities=28%  Similarity=0.476  Sum_probs=80.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .++.++|||..|..-+++|+|.-+|+.||.|++|.+++|+.||.+..||||||++.++|+.|+-.|++..|+.|+|.|+|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +.+
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            875

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.08  E-value=1.6e-10  Score=117.49  Aligned_cols=72  Identities=35%  Similarity=0.659  Sum_probs=68.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      .++||||||.++++.+|+.+|++||+|.+|.|+        |.||||..+|...++.||++||+++|+|..|+|+-++++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--------KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV--------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee--------cccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            469999999999999999999999999999999        569999999999999999999999999999999999876

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.08  E-value=3.9e-10  Score=119.78  Aligned_cols=79  Identities=25%  Similarity=0.447  Sum_probs=71.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      -+.|||+||+.++|||.|++.|..||.|.+|+.++|        ||||.|.++++|.+|++.+|+++|+|..|.|.+|++
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            478999999999999999999999999999987744        999999999999999999999999999999999998


Q ss_pred             CCCCCCC
Q 008851           86 DKGADRN   92 (551)
Q Consensus        86 ~~~~~r~   92 (551)
                      ...++..
T Consensus       331 ~~k~k~~  337 (506)
T KOG0117|consen  331 VDKKKKE  337 (506)
T ss_pred             hhhhccc
Confidence            6544333

>PF13893 RRM_5: RNA recognition motif

Probab=99.07  E-value=6.5e-10  Score=86.40  Aligned_cols=56  Identities=30%  Similarity=0.612  Sum_probs=50.9

Q ss_pred             HHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851           23 LIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus        23 Lre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      |+++|++||.|.++.+..+.     +++|||+|.+.++|.+|++.||+..++|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999987543     699999999999999999999999999999999986

(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 ....

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.02  E-value=8.4e-10  Score=119.54  Aligned_cols=82  Identities=24%  Similarity=0.509  Sum_probs=75.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +..+|.|+||||.+.+.+|+.+|+.||.|++|.|.+.++ |+..|||||.|.+..+|..|++.+|+.+|+||+|-|+||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            467899999999999999999999999999999998776 5555999999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
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=99.00  E-value=3.3e-10  Score=117.81  Aligned_cols=87  Identities=23%  Similarity=0.433  Sum_probs=78.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         1 ma~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      ++..+.+++|||+|+|+++||.|++.|++||+|.+|.+++|+.|++++||+||+|.+.+.+.+++. ...+.|+||.|.+
T Consensus         1 ~~~~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~   79 (311)
T KOG4205|consen    1 SESGESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEP   79 (311)
T ss_pred             CCccCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccc
Confidence            355688999999999999999999999999999999999999999999999999999888887774 4557899999999


Q ss_pred             EeecCCCC
Q 008851           81 DFAENDKG   88 (551)
Q Consensus        81 ~~A~~~~~   88 (551)
                      +.|.++..
T Consensus        80 k~av~r~~   87 (311)
T KOG4205|consen   80 KRAVSRED   87 (311)
T ss_pred             eeccCccc
Confidence            99987653

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.00  E-value=2.2e-09  Score=115.51  Aligned_cols=83  Identities=28%  Similarity=0.446  Sum_probs=70.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      ...|||+|||.++++++|+++|..||.|+..+|......++..+||||+|.+.+.++.||.. +-..|++++|.|+..+.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            34599999999999999999999999999987765433456569999999999999999975 47789999999999877


Q ss_pred             CCCC
Q 008851           86 DKGA   89 (551)
Q Consensus        86 ~~~~   89 (551)
                      ..+.
T Consensus       367 ~~~g  370 (419)
T KOG0116|consen  367 GFRG  370 (419)
T ss_pred             cccc
Confidence            5443

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.96  E-value=6.1e-10  Score=112.13  Aligned_cols=86  Identities=22%  Similarity=0.498  Sum_probs=81.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      +.++.|.|||-.||.+..+.||..+|-.||.|++.++..||.|..+|+||||.|++...++.||..+||+.|+-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      +.+++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            977654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.96  E-value=7.4e-10  Score=120.15  Aligned_cols=78  Identities=33%  Similarity=0.659  Sum_probs=75.1

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      +|||||.++++|++|+.+|+.||.|..|.+..|.+||.+||||||+|.+.++|.+|++.|||++|-||.|+|..-...
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            899999999999999999999999999999999999999999999999999999999999999999999999887654

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.92  E-value=1.4e-09  Score=104.41  Aligned_cols=82  Identities=28%  Similarity=0.502  Sum_probs=76.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~v-rLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +..+|||||.++++|..|.++|+.||.+... ++++|.+||.++|||||.|.+.+.+.+|+..++|..++.|+++|+++.
T Consensus        96 ganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~  175 (203)
T KOG0131|consen   96 GANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAF  175 (203)
T ss_pred             cccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEE
Confidence            4679999999999999999999999998764 889999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus       176 k~~  178 (203)
T KOG0131|consen  176 KKD  178 (203)
T ss_pred             ecC
Confidence            643

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.88  E-value=4.6e-09  Score=102.59  Aligned_cols=81  Identities=30%  Similarity=0.532  Sum_probs=76.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcC-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREV-GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~-G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...+||+.+|....|.++..+|++| |.|..+++-+.+.||.+||||||||++.+.|+-|-+.||++-+.|+.|.|.+..
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            4568999999999999999999998 788889998999999999999999999999999999999999999999999988


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ++
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            76

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.85  E-value=1.1e-08  Score=111.43  Aligned_cols=83  Identities=22%  Similarity=0.295  Sum_probs=70.8

Q ss_pred             CCCcEEEEecCCCCC----------CHHHHHHHHHcCCCeeEEEEeec---CCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 008851            4 SQHRCVFVGNIPYDA----------TEEQLIEICREVGPVVSFRLVID---RETGKPKGYGFCEYKDEETALSARRNLQG   70 (551)
Q Consensus         4 ~~srtVFVGNLP~d~----------TEEeLre~Fs~~G~V~~vrLv~D---r~TGksKGyAFVEF~d~e~A~sAi~~Lng   70 (551)
                      .+.++|+|.|+.+..          ..++|+++|++||.|+.|.|.++   ..++..+||+||+|.+.++|.+|+..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            357889999996421          13678999999999999999865   34567789999999999999999999999


Q ss_pred             ceeCCEEEEEEeecCC
Q 008851           71 YEINGRQLRVDFAEND   86 (551)
Q Consensus        71 ~~I~GR~LrV~~A~~~   86 (551)
                      ..|+|+.|.|.|....
T Consensus       487 r~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       487 RKFNDRVVVAAFYGED  502 (509)
T ss_pred             CEECCeEEEEEEeCHH
Confidence            9999999999998754

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.84  E-value=5.6e-09  Score=108.80  Aligned_cols=82  Identities=22%  Similarity=0.403  Sum_probs=77.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      -++|||..+..|.+|++|+.+|+.||+|++|.+-+++.++.+|||||+||.+......|+..+|-+.++|..|||..+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      ..
T Consensus       290 PP  291 (544)
T KOG0124|consen  290 PP  291 (544)
T ss_pred             CC
Confidence            43

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.78  E-value=1.8e-08  Score=99.63  Aligned_cols=83  Identities=23%  Similarity=0.507  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHH----HHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ   77 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLre----~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~   77 (551)
                      +..+..+|||.||+..+..++|++    +|++||.|.+|...   .|.+.+|-|||.|.+.+.|-.|++.|+|+.+.|+.
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~   81 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKP   81 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCch
Confidence            344566999999999999998887    99999999999876   47899999999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q 008851           78 LRVDFAENDK   87 (551)
Q Consensus        78 LrV~~A~~~~   87 (551)
                      ++|.||+.+.
T Consensus        82 mriqyA~s~s   91 (221)
T KOG4206|consen   82 MRIQYAKSDS   91 (221)
T ss_pred             hheecccCcc
Confidence            9999998754

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=4.2e-09  Score=106.19  Aligned_cols=83  Identities=24%  Similarity=0.446  Sum_probs=74.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-C--CEEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI-N--GRQLRVD   81 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I-~--GR~LrV~   81 (551)
                      +++++|||-|...-.|||++++|..||.|.+|.+.+..+ |.+|||+||.|.+..+|+.||..|||... -  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            578999999999999999999999999999999998875 99999999999999999999999998643 3  3569999


Q ss_pred             eecCCCC
Q 008851           82 FAENDKG   88 (551)
Q Consensus        82 ~A~~~~~   88 (551)
                      |++.++.
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9987654

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.76  E-value=8e-09  Score=105.25  Aligned_cols=76  Identities=28%  Similarity=0.488  Sum_probs=71.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+.+++||||.+.++..||+..|++||+|++|.|+        |+|+||.|.-.++|..|++.|++.+|.|++++|.++.
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeee--------cceeEEEEeeccchHHHHhcccccccccceeeeeeec
Confidence            57899999999999999999999999999999998        5699999999999999999999999999999999998


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ++-+
T Consensus       149 srlr  152 (346)
T KOG0109|consen  149 SRLR  152 (346)
T ss_pred             cccc
Confidence            7543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.76  E-value=1.3e-08  Score=108.05  Aligned_cols=76  Identities=28%  Similarity=0.486  Sum_probs=70.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....|+|||+|||+++||..|++-|..||.|.+..|+   +.|+++|  .|.|.+.++|++||+.+++..++||.|+|.|
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            3467899999999999999999999999999999985   4689988  7899999999999999999999999999987


Q ss_pred             e
Q 008851           83 A   83 (551)
Q Consensus        83 A   83 (551)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            4

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.75  E-value=2.3e-08  Score=106.62  Aligned_cols=78  Identities=29%  Similarity=0.564  Sum_probs=72.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ..|||.||+.++|.++|+++|+.||.|++|++..|.+ | +||| ||+|+++++|.+|++.+||..+.|++|.|.....+
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            4499999999999999999999999999999999974 5 9999 99999999999999999999999999999888764


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus       154 ~  154 (369)
T KOG0123|consen  154 E  154 (369)
T ss_pred             h
Confidence            4

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

Probab=98.71  E-value=3.6e-08  Score=107.36  Aligned_cols=82  Identities=22%  Similarity=0.390  Sum_probs=77.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      ++.+||.+|...+...+|+.+|++||.|+..+++.+-.+-..++||||++.+.++|.+||..||..+|.||.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            57899999999999999999999999999999999888888899999999999999999999999999999999999986


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      ..
T Consensus       485 Ep  486 (940)
T KOG4661|consen  485 EP  486 (940)
T ss_pred             Cc
Confidence            43

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.71  E-value=2.2e-08  Score=104.30  Aligned_cols=82  Identities=26%  Similarity=0.511  Sum_probs=76.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++||||+|+.+++|+++++.|.+||.|.++.+++|+++.+++||+||.|.+++.+++++. ..-+.|+|+.+.|+.|.+
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccc
Confidence            5689999999999999999999999999999999999999999999999999999998884 567899999999999998


Q ss_pred             CCC
Q 008851           86 DKG   88 (551)
Q Consensus        86 ~~~   88 (551)
                      +..
T Consensus       176 k~~  178 (311)
T KOG4205|consen  176 KEV  178 (311)
T ss_pred             hhh
Confidence            654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.67  E-value=4.2e-08  Score=110.03  Aligned_cols=76  Identities=24%  Similarity=0.456  Sum_probs=71.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      ++|||||.|+..++|.+|..+|+.||+|.+|.++-.      +|||||......+|++|+.+|+++.+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            689999999999999999999999999999998743      79999999999999999999999999999999999986


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      ..
T Consensus       495 ~G  496 (894)
T KOG0132|consen  495 KG  496 (894)
T ss_pred             CC
Confidence            43

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.66  E-value=1.7e-08  Score=112.32  Aligned_cols=82  Identities=27%  Similarity=0.499  Sum_probs=76.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|+|.|||+.++-.+++.+|..||.|++|+|......+.++|||||+|-+.++|.+|++.|....+.||+|.++||..
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            46899999999999999999999999999999987766778899999999999999999999999999999999999987


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      +.
T Consensus       693 d~  694 (725)
T KOG0110|consen  693 DN  694 (725)
T ss_pred             ch
Confidence            54

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.63  E-value=7.3e-08  Score=102.78  Aligned_cols=75  Identities=27%  Similarity=0.496  Sum_probs=70.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ..+|||   .++||..|+++|+.+|+|+++++.+|- |  +-|||||.|.+.++|++|++.+|...|.|+.|+|-|+..+
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   999999999999999999999999998 6  9999999999999999999999999999999999998765


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            4

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.59  E-value=5.2e-08  Score=96.64  Aligned_cols=73  Identities=29%  Similarity=0.580  Sum_probs=67.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ..||||+|++.+.+++|+++|.+||.+.++.++        .||+||+|.|..+|..|+..|++..|.|.++.|++++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            469999999999999999999999999999886        689999999999999999999999999998999998864


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus        74 ~   74 (216)
T KOG0106|consen   74 R   74 (216)
T ss_pred             c
Confidence            3

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.59  E-value=1.1e-07  Score=106.08  Aligned_cols=78  Identities=29%  Similarity=0.562  Sum_probs=70.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETG---KPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TG---ksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +++||.||+|+++.++|..+|+.+|.|.++.|...++..   .+.|||||+|.+.++|.+|++.|+|..|+|+.|.|+++
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            349999999999999999999999999999887655321   24499999999999999999999999999999999999


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.59  E-value=1.6e-07  Score=97.72  Aligned_cols=74  Identities=20%  Similarity=0.429  Sum_probs=66.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH-hCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN-LQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~-Lng~~I~GR~LrV~~A~   84 (551)
                      .++||||+|-..++|.+|+++|.+||+|+++++...      +|||||+|.+.+.|+.|.+. ++...|+|++|+|.|..
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            578999999999999999999999999999998754      57999999999999988875 46678899999999988


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            7

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.56  E-value=2.3e-07  Score=93.75  Aligned_cols=83  Identities=22%  Similarity=0.429  Sum_probs=76.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...+|+|.||++.+++++|+++|..||.++.+.+.+|+ .|++.|+|-|.|...++|..|++.++++.++|+.+++....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34789999999999999999999999999999999997 69999999999999999999999999999999999999887


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ....
T Consensus       161 ~~~~  164 (243)
T KOG0533|consen  161 SPSQ  164 (243)
T ss_pred             Cccc
Confidence            6543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.56  E-value=1.2e-07  Score=95.33  Aligned_cols=82  Identities=24%  Similarity=0.422  Sum_probs=77.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      -+.+.+||||+.+.+|.+++..+|+.||.|..+.+..|+.+|.+|||+||+|.+.+.++.+++ |++..|.|+.+.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            357889999999999999999999999999999999999999999999999999999999998 9999999999999988


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      +-.
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            754

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.52  E-value=6e-08  Score=97.44  Aligned_cols=82  Identities=22%  Similarity=0.476  Sum_probs=76.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+.+||+|.|--+++++.|.+.|.+|-.....++++|+.||+++||+||.|.|..++..|++.++|..++.|.|+...+.
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999998877665


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      .+
T Consensus       269 wk  270 (290)
T KOG0226|consen  269 WK  270 (290)
T ss_pred             HH
Confidence            43

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.45  E-value=5.9e-07  Score=93.55  Aligned_cols=84  Identities=29%  Similarity=0.482  Sum_probs=75.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~--------vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      ...++.|||.|||.++|.+++.++|++||-|..        |+|.+|.. |+.||=|.|.|...+.+.-|+..|++..|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccccc
Confidence            445678999999999999999999999998753        77877765 999999999999999999999999999999


Q ss_pred             CEEEEEEeecCCC
Q 008851           75 GRQLRVDFAENDK   87 (551)
Q Consensus        75 GR~LrV~~A~~~~   87 (551)
                      |+.|+|+.|.-..
T Consensus       210 g~~~rVerAkfq~  222 (382)
T KOG1548|consen  210 GKKLRVERAKFQM  222 (382)
T ss_pred             CcEEEEehhhhhh
Confidence            9999999998543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.41  E-value=1.2e-06  Score=86.81  Aligned_cols=88  Identities=20%  Similarity=0.354  Sum_probs=72.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---CEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVID-RETGKPKGYGFCEYKDEETALSARRNLQGYEIN---GRQLRV   80 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~D-r~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~---GR~LrV   80 (551)
                      .-+++||.+||.|+...||+.+|+.|-..+.+.|.+. +.....+-+||+.|.+..+|.+|+..|||+.|+   +..|++
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            3689999999999999999999999977777777643 222233579999999999999999999999995   788999


Q ss_pred             EeecCCCCCCCC
Q 008851           81 DFAENDKGADRN   92 (551)
Q Consensus        81 ~~A~~~~~~~r~   92 (551)
                      ++|+...+..|+
T Consensus       113 ElAKSNtK~kr~  124 (284)
T KOG1457|consen  113 ELAKSNTKRKRR  124 (284)
T ss_pred             eehhcCcccccC
Confidence            999976554433

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.38  E-value=8.4e-06  Score=85.20  Aligned_cols=77  Identities=21%  Similarity=0.416  Sum_probs=66.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G--~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..++|||||-|++|+++|.+.+...|  .+.++++..++.+|.+||||+|...+....+..++.|...+|+|..-.|--
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            45799999999999999999988766  567778888899999999999999999999999999999999887544433

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.23  E-value=8.5e-06  Score=71.78  Aligned_cols=79  Identities=27%  Similarity=0.394  Sum_probs=69.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHc--CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC----CEEEEE
Q 008851            7 RCVFVGNIPYDATEEQLIEICRE--VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN----GRQLRV   80 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~--~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~----GR~LrV   80 (551)
                      ++|-|+|||-..|.++|.+++..  .|....+-+..|..++.+.|||||.|.+.+.|.+-.+.++|..+.    .+.+.|
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            68999999999999999998865  467778889999999999999999999999999999999998774    566888


Q ss_pred             EeecC
Q 008851           81 DFAEN   85 (551)
Q Consensus        81 ~~A~~   85 (551)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88864

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.22  E-value=7.7e-07  Score=97.57  Aligned_cols=83  Identities=36%  Similarity=0.606  Sum_probs=78.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...++||++||...++.++++++..||.+..++++.|..+|.+|||||+||.|......|+..|||..++++.|.|..|.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus       368 ~g~  370 (500)
T KOG0120|consen  368 VGA  370 (500)
T ss_pred             ccc
Confidence            654

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.20  E-value=5.6e-07  Score=89.02  Aligned_cols=80  Identities=18%  Similarity=0.286  Sum_probs=73.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++|||+|+-..++||.|.++|-+.|+|+.+.|..+++ ++.| ||||+|.++....-|+..+||..+.++.+.|.+.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            4578999999999999999999999999999999998875 7777 9999999999999999999999999999998886


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ..
T Consensus        85 ~G   86 (267)
T KOG4454|consen   85 CG   86 (267)
T ss_pred             cC
Confidence            54

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.18  E-value=4.1e-06  Score=90.65  Aligned_cols=79  Identities=22%  Similarity=0.401  Sum_probs=67.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ....|-+++|||++|++||.+||+.|+ |.++.+  .+++||..|-|||||.+++++++|++ .+...+..|.|.|--+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~--~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEI--PRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEE--eccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            456788899999999999999999997 777554  45689999999999999999999997 46678889999998886


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus        85 ~~e   87 (510)
T KOG4211|consen   85 GAE   87 (510)
T ss_pred             Ccc
Confidence            543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.16  E-value=1.1e-06  Score=96.07  Aligned_cols=70  Identities=26%  Similarity=0.420  Sum_probs=64.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      ..++|+|-|||..+++++|+++|+.||+|++++.     |-..+|.+||+|.|..+|+.|++.|++.+|.|+.|+
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4688999999999999999999999999999764     455589999999999999999999999999999887

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.09  E-value=5.1e-06  Score=92.97  Aligned_cols=81  Identities=22%  Similarity=0.450  Sum_probs=73.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR---ETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr---~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      +..+.+||+||+..++|+.|-..|..||+|..++|++.+   +..+.+-||||.|.+..+|++|++.|+|..+.++.+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            346789999999999999999999999999999998754   45566789999999999999999999999999999999


Q ss_pred             Eeec
Q 008851           81 DFAE   84 (551)
Q Consensus        81 ~~A~   84 (551)
                      -|++
T Consensus       252 gWgk  255 (877)
T KOG0151|consen  252 GWGK  255 (877)
T ss_pred             cccc
Confidence            9985

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.07  E-value=3.3e-06  Score=87.38  Aligned_cols=84  Identities=27%  Similarity=0.485  Sum_probs=75.8

Q ss_pred             CCcEEE-EecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVF-VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVF-VGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++| |+++++++++++|+.+|..+|.|..+++..++.+|.++|||||+|.+...+..++.. ....+.++.+++++.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            345566 999999999999999999999999999999999999999999999999999999977 788999999999998


Q ss_pred             cCCCCC
Q 008851           84 ENDKGA   89 (551)
Q Consensus        84 ~~~~~~   89 (551)
                      ......
T Consensus       262 ~~~~~~  267 (285)
T KOG4210|consen  262 EPRPKS  267 (285)
T ss_pred             CCCccc
Confidence            875443

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.94  E-value=2.1e-05  Score=82.58  Aligned_cols=84  Identities=26%  Similarity=0.436  Sum_probs=77.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING   75 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~--------vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G   75 (551)
                      ...-+|||-+|+..+++..|.++|.++|.|..        |.|-+|++|+++||-|.|.|.|...|+.|+..+++..+.|
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            35678999999999999999999999998853        6788899999999999999999999999999999999999


Q ss_pred             EEEEEEeecCCC
Q 008851           76 RQLRVDFAENDK   87 (551)
Q Consensus        76 R~LrV~~A~~~~   87 (551)
                      ..|+|.+|....
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999999998654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.80  E-value=5.7e-06  Score=90.52  Aligned_cols=83  Identities=28%  Similarity=0.430  Sum_probs=75.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++||+--|.-.+++.+|++||+.+|.|.+|+++.|+.++++||.|||||.|.+....|+ .|.|..+.|-+|.|....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccH
Confidence            4577888888899999999999999999999999999999999999999999999999999 799999999999999876


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ..++
T Consensus       257 aekn  260 (549)
T KOG0147|consen  257 AEKN  260 (549)
T ss_pred             HHHH
Confidence            5443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.52  E-value=0.00028  Score=70.32  Aligned_cols=76  Identities=26%  Similarity=0.528  Sum_probs=68.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-GRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-GR~LrV~~   82 (551)
                      ++...+|+.|||.+++.+.+..+|++|...++++++..+     ++.|||||.+...+..|...+.+..|. ...++|.+
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            467899999999999999999999999999999998654     789999999999999999999998886 77788887


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      ++
T Consensus       219 a~  220 (221)
T KOG4206|consen  219 AK  220 (221)
T ss_pred             cC
Confidence            65

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.51  E-value=0.00075  Score=72.25  Aligned_cols=76  Identities=21%  Similarity=0.385  Sum_probs=68.4

Q ss_pred             CcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+.|.|.||.. .+|++.|.-+|+-||.|.+|+|.+.+     +--|.|.|.|...|+-|++.|+|+.+.|++|||.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            47788888865 58899999999999999999999875     4678999999999999999999999999999999998


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            54

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.49  E-value=0.0002  Score=77.86  Aligned_cols=78  Identities=24%  Similarity=0.396  Sum_probs=65.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVS-FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~-vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...+|-+++|||.|||++|.+||+..--|.. +.++.|+ .+++.|-|||.|++.+.|+.|+.. |...|+.|-|.|..+
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            4567999999999999999999998755544 5567776 488999999999999999999964 556788888998887


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            5

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.38  E-value=0.00057  Score=75.50  Aligned_cols=78  Identities=27%  Similarity=0.429  Sum_probs=64.7

Q ss_pred             CCCcEEEEecCCCCCCH------HHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CE
Q 008851            4 SQHRCVFVGNIPYDATE------EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-GR   76 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TE------EeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-GR   76 (551)
                      .-+.+|+|-|+|.--..      .-|.++|+++|+|+.+.+..|.++| .+||.|+||.+..+|+.|++.|||+.|+ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            34678999999975432      2477889999999999999998755 8999999999999999999999999885 45


Q ss_pred             EEEEEe
Q 008851           77 QLRVDF   82 (551)
Q Consensus        77 ~LrV~~   82 (551)
                      ++.|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            566654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.35  E-value=0.00052  Score=77.26  Aligned_cols=76  Identities=25%  Similarity=0.470  Sum_probs=66.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVS-FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~-vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .++|-+.|+|++++-+||.+||..|-.+-. |++.+. +.|+..|-|.|.|++.++|.+|...|++..|..|++++.+
T Consensus       867 p~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            347889999999999999999999987644 444444 5699999999999999999999999999999999998875

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.23  E-value=0.00024  Score=70.92  Aligned_cols=72  Identities=25%  Similarity=0.431  Sum_probs=63.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..+.++|.++..++.+.+|.++|+.+|.+....+        ..+++||+|...+++.+|+..|++..+.|+.|++...-
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecccC
Confidence            4678999999999999999999999999855443        26799999999999999999999999999999995543

>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=97.22  E-value=0.0011  Score=57.25  Aligned_cols=70  Identities=20%  Similarity=0.470  Sum_probs=48.0

Q ss_pred             cEEEEecCCCCCCHHHH----HHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            7 RCVFVGNIPYDATEEQL----IEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeL----re~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ..|||.|||.+.+...|    +.++..|| .|.++.          .+.|+|.|.+.+.|.+|.+.|+|..+-|++|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            46899999999997664    55556776 565552          4789999999999999999999999999999999


Q ss_pred             eecCC
Q 008851           82 FAEND   86 (551)
Q Consensus        82 ~A~~~   86 (551)
                      |....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            98543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.11  E-value=0.0005  Score=68.71  Aligned_cols=65  Identities=18%  Similarity=0.287  Sum_probs=53.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      -+.++||.||..+++|++|+.+|+.|-....++|..    ...-.+||++|++.+.|..|+..|.|..|
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            356899999999999999999999998777666642    12245899999999999999988887655

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.01  E-value=0.0017  Score=71.27  Aligned_cols=64  Identities=28%  Similarity=0.416  Sum_probs=60.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHH-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICR-EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN   67 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs-~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~   67 (551)
                      ++.+|||||+||.-++.++|..+|. -||.|+.+-|-.|++-+-+||-|-|.|.+.....+||..
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3689999999999999999999998 599999999999988899999999999999999999974

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.00  E-value=0.00074  Score=72.60  Aligned_cols=67  Identities=33%  Similarity=0.468  Sum_probs=57.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeec---CC--CCCc--------ceEEEEEeCCHHHHHHHHHHhCC
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVID---RE--TGKP--------KGYGFCEYKDEETALSARRNLQG   70 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~D---r~--TGks--------KGyAFVEF~d~e~A~sAi~~Lng   70 (551)
                      -++++|.+-|||.+-.-|-|.++|+.||.|+.|+|+..   ++  .|..        +-||||||...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            47899999999999999999999999999999999865   22  2222        45899999999999999998864

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=96.94  E-value=0.0013  Score=58.59  Aligned_cols=70  Identities=17%  Similarity=0.299  Sum_probs=43.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-----ceeCCEEEEEE
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG-----YEINGRQLRVD   81 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng-----~~I~GR~LrV~   81 (551)
                      +.|+|.++..+++.++|+++|+.||.|..|.+...      -..|||.|.+.+.|+.|+..+..     ..|.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57899999999999999999999999999887642      23689999999999999987643     35566555555


Q ss_pred             e
Q 008851           82 F   82 (551)
Q Consensus        82 ~   82 (551)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=96.86  E-value=0.0021  Score=71.14  Aligned_cols=68  Identities=24%  Similarity=0.331  Sum_probs=55.7

Q ss_pred             HHHHHHHHcCCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCCCC
Q 008851           21 EQLIEICREVGPVVSFRLVIDRE---TGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDKG   88 (551)
Q Consensus        21 EeLre~Fs~~G~V~~vrLv~Dr~---TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~~~   88 (551)
                      |+++.-+++||.|..|.+..+..   -.-..|..||||.+.++|++|.+.|+|.+++||.+...|..+++.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY  494 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKY  494 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHh
Confidence            34556677899999999987722   223357789999999999999999999999999999999877654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.82  E-value=0.0027  Score=66.65  Aligned_cols=79  Identities=19%  Similarity=0.320  Sum_probs=61.4

Q ss_pred             CcEEEEecCCCCCCHHH----H--HHHHHcCCCeeEEEEeecCCC-CCcce--EEEEEeCCHHHHHHHHHHhCCceeCCE
Q 008851            6 HRCVFVGNIPYDATEEQ----L--IEICREVGPVVSFRLVIDRET-GKPKG--YGFCEYKDEETALSARRNLQGYEINGR   76 (551)
Q Consensus         6 srtVFVGNLP~d~TEEe----L--re~Fs~~G~V~~vrLv~Dr~T-GksKG--yAFVEF~d~e~A~sAi~~Lng~~I~GR   76 (551)
                      ..-|||-+|+..+..|+    |  .++|.+||.|..|.+-+.-.. ....+  -.||.|...|+|.+||...+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            45689999998877666    2  678999999999877543200 11112  239999999999999999999999999


Q ss_pred             EEEEEeec
Q 008851           77 QLRVDFAE   84 (551)
Q Consensus        77 ~LrV~~A~   84 (551)
                      .|+..|..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99999865

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.76  E-value=0.0035  Score=68.87  Aligned_cols=64  Identities=31%  Similarity=0.433  Sum_probs=48.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEee-cC--CCCCcce---EEEEEeCCHHHHHHHHHHhC
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVI-DR--ETGKPKG---YGFCEYKDEETALSARRNLQ   69 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~-Dr--~TGksKG---yAFVEF~d~e~A~sAi~~Ln   69 (551)
                      -+++||||+||++++|++|...|..||.+.- .+.. ..  .---++|   |+|..|+++..+.+-+..+.
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVKV-DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceEe-ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            3789999999999999999999999997642 2221 11  1123467   99999999998887766553

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.56  E-value=0.0019  Score=65.63  Aligned_cols=71  Identities=24%  Similarity=0.321  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCC--------CCcce----EEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRET--------GKPKG----YGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~T--------GksKG----yAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      -+||+++||..++-.-|+++|+.||.|-.|.+-....+        |+.++    -|+|||.+...|.++...||+..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            57999999999999999999999999998887655444        33333    3679999999999999999999998


Q ss_pred             CEE
Q 008851           75 GRQ   77 (551)
Q Consensus        75 GR~   77 (551)
                      |++
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            865

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=96.52  E-value=0.017  Score=56.61  Aligned_cols=61  Identities=28%  Similarity=0.336  Sum_probs=55.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      ..+|.|.+||...+|.+|+++..+-|.|+...+.+|       |++.|+|...|+.+-|+++|+...+
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccc
Confidence            467999999999999999999999999999988776       5899999999999999999987665

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=96.51  E-value=0.0054  Score=65.88  Aligned_cols=78  Identities=23%  Similarity=0.318  Sum_probs=65.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCE-EEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGR-QLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR-~LrV~~   82 (551)
                      +++.++.+.|||.+++||+|+..|..-|..++....+    ++.+-++++.+.+.|+|..|+-.+|++.+++. .|||.|
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            4677899999999999999999999887665543332    44567999999999999999999999998755 899999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            875

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.48  E-value=0.0028  Score=67.48  Aligned_cols=79  Identities=22%  Similarity=0.401  Sum_probs=67.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCe-eE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPV-VS--FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V-~~--vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+|-+++|||+++.|+|-+||..|-.- +.  |.++.+. -|++.|-|||+|.+.|+|..|....+++...+|.|+|--
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            5679999999999999999999998753 33  5666664 599999999999999999999998888777789898887


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +..
T Consensus       359 ~S~  361 (508)
T KOG1365|consen  359 CSV  361 (508)
T ss_pred             ccH
Confidence            654

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.40  E-value=0.011  Score=62.30  Aligned_cols=78  Identities=24%  Similarity=0.452  Sum_probs=62.8

Q ss_pred             CCcEEEEecC----CCCCC-------HHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            5 QHRCVFVGNI----PYDAT-------EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         5 ~srtVFVGNL----P~d~T-------EEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      ..++|.|.|+    -++.+       +++|++-+.+||.|.+|.|. |   ..+.|.+-|.|.+.++|..||+.|+|..|
T Consensus       264 ~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d---~hPdGvvtV~f~n~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  264 ADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-D---RHPDGVVTVSFRNNEEADQCIQTMDGRWF  339 (382)
T ss_pred             CCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-c---cCCCceeEEEeCChHHHHHHHHHhcCeee
Confidence            3567888886    22333       35677789999999998764 4   35689999999999999999999999999


Q ss_pred             CCEEEEEEeecCC
Q 008851           74 NGRQLRVDFAEND   86 (551)
Q Consensus        74 ~GR~LrV~~A~~~   86 (551)
                      +||.|........
T Consensus       340 dgRql~A~i~DG~  352 (382)
T KOG1548|consen  340 DGRQLTASIWDGK  352 (382)
T ss_pred             cceEEEEEEeCCc
Confidence            9999988877643

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.20  E-value=0.012  Score=46.26  Aligned_cols=53  Identities=21%  Similarity=0.352  Sum_probs=42.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR   65 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi   65 (551)
                      ++.|-|.+.+.+..+ .+.++|..||+|+++.+-      ..+-+.||.|.+..+|++|+
T Consensus         1 ~~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            357888898877654 455689999999998875      22458899999999999985

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.17  E-value=0.0034  Score=72.33  Aligned_cols=79  Identities=27%  Similarity=0.377  Sum_probs=68.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      ...|||.|.|+..|.++++.+|.++|.+.+.+++..+ .|+++|.+||+|.++.++.+++...+...++-+.+.|..+.+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            4569999999999999999999999999999988886 599999999999999999999877776666666677777665

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=95.98  E-value=0.078  Score=56.78  Aligned_cols=71  Identities=27%  Similarity=0.455  Sum_probs=59.7

Q ss_pred             ecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-C-EEEEEEeecCCC
Q 008851           12 GNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-G-RQLRVDFAENDK   87 (551)
Q Consensus        12 GNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-G-R~LrV~~A~~~~   87 (551)
                      -|-=|-+|-+-|+.++...|+|.+|.|.+.  +|.   -|.|||++.+.|++|...|||..|. | ..|+|+||++.+
T Consensus       128 lNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  128 LNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             ecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            366678999999999999999999988743  333   5899999999999999999999884 3 579999998754

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.96  E-value=0.0069  Score=67.59  Aligned_cols=77  Identities=26%  Similarity=0.345  Sum_probs=65.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHH-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICR-EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI---NGRQLR   79 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs-~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I---~GR~Lr   79 (551)
                      ..++.|||.||-.-.|.-+|+.++. .+|.|+++  +.|+    -|..|||.|.+.++|.+....|||..+   +++.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            3578999999999999999999998 46667777  3443    377899999999999999999999876   778899


Q ss_pred             EEeecCC
Q 008851           80 VDFAEND   86 (551)
Q Consensus        80 V~~A~~~   86 (551)
                      ++|....
T Consensus       516 adf~~~d  522 (718)
T KOG2416|consen  516 ADFVRAD  522 (718)
T ss_pred             eeecchh
Confidence            9998753

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=95.79  E-value=0.042  Score=58.74  Aligned_cols=78  Identities=15%  Similarity=0.204  Sum_probs=68.7

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+++.+.|-+|... +.-+.|-.+|..||.|.+|++++.+     .|-|.||..|....++|+..||+..+-|.+|.|.+
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            36788899999876 4557799999999999999999776     58899999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      ++-.
T Consensus       360 SkQ~  363 (494)
T KOG1456|consen  360 SKQN  363 (494)
T ss_pred             cccc
Confidence            8743

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=95.75  E-value=0.023  Score=60.82  Aligned_cols=75  Identities=27%  Similarity=0.361  Sum_probs=56.8

Q ss_pred             EEEEecCCCCCCHHHHHHHHHc---C-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICRE---V-GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~---~-G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .|-.++|||++++.++.+||..   . |..+.+.+++.. .|+..|-|||.|..+++|+.|+++ |...|+-|.|++-.+
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRS  240 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHH
Confidence            4667899999999999999963   2 345566666554 599999999999999999999976 334555565655544


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      +
T Consensus       241 T  241 (508)
T KOG1365|consen  241 T  241 (508)
T ss_pred             h
Confidence            3

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.62  E-value=0.062  Score=50.86  Aligned_cols=56  Identities=32%  Similarity=0.570  Sum_probs=45.2

Q ss_pred             HHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851           22 QLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus        22 eLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      +|-+.|..||.++-+|++.+        .-+|+|.+.+.|.+|+ .++|.+|+|+.|+|+...++
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCCcc
Confidence            67778899999999998843        3589999999999999 58999999999999997753

; PDB: 1UFW_A 2DNR_A.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.54  E-value=0.035  Score=57.67  Aligned_cols=67  Identities=22%  Similarity=0.280  Sum_probs=54.0

Q ss_pred             HHHHHHHHHcCCCeeEEEEeecCCCCCcc-eEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851           20 EEQLIEICREVGPVVSFRLVIDRETGKPK-GYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus        20 EEeLre~Fs~~G~V~~vrLv~Dr~TGksK-GyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      |+++++.+++||.|..|.|..++.--... ---||+|...+.|.+|+-.|||..|+||.++..|-...
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~e  367 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLE  367 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHH
Confidence            45788899999999999887765322222 23599999999999999999999999999988876543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=94.94  E-value=0.015  Score=65.90  Aligned_cols=79  Identities=15%  Similarity=0.127  Sum_probs=66.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVS-FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~-vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..+|||-.||..+++.++.++|...-.|++ |.|.+-+ |++.++.|||+|..++++.+|...-+.+.++.|.|+|+-..
T Consensus       434 g~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  434 GGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             cceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            578999999999999999999999888887 5555544 78899999999999888888887667777888999998765


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      +
T Consensus       513 ~  513 (944)
T KOG4307|consen  513 D  513 (944)
T ss_pred             h
Confidence            3

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=94.74  E-value=0.15  Score=45.47  Aligned_cols=80  Identities=15%  Similarity=0.147  Sum_probs=52.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEe-ecC------CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLV-IDR------ETGKPKGYGFCEYKDEETALSARRNLQGYEINGR   76 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv-~Dr------~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR   76 (551)
                      ..++.|.|-+.|.. ....|.+.|++||.|++..-. ++.      ..-....+-.|.|.+..+|.+|++ .||..|+|.
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            34567888899988 456778889999999877511 100      001124577899999999999995 699999875


Q ss_pred             -EEEEEeecC
Q 008851           77 -QLRVDFAEN   85 (551)
Q Consensus        77 -~LrV~~A~~   85 (551)
                       .+-|.++++
T Consensus        82 ~mvGV~~~~~   91 (100)
T PF05172_consen   82 LMVGVKPCDP   91 (100)
T ss_dssp             EEEEEEE-HH
T ss_pred             EEEEEEEcHH
Confidence             566888753

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.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.47  E-value=0.0026  Score=73.25  Aligned_cols=68  Identities=22%  Similarity=0.274  Sum_probs=59.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      .+++||.||+..+.+++|...|..+|.+..+++.....+++.+|+||++|.+.+++.+|+...++..+
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            46789999999999999999999999998888877778899999999999999999999976554433

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.38  E-value=0.02  Score=58.40  Aligned_cols=62  Identities=16%  Similarity=0.284  Sum_probs=50.5

Q ss_pred             HHHHHHH-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851           22 QLIEICR-EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus        22 eLre~Fs-~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++...|+ +||+|+++.+.... .-..+|=+||.|..+++|++|+..||+..++|++|..++..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3444444 89999998665432 34567889999999999999999999999999999999865

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.27  E-value=0.045  Score=63.80  Aligned_cols=76  Identities=21%  Similarity=0.351  Sum_probs=66.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~~   82 (551)
                      ..+.+|||+|..++....|...|..||.|..|.+-      +..-|++|.|++...++.|++.+.+..|+|  ++++|+|
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            46789999999999999999999999999987653      224599999999999999999999999975  6799999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +...
T Consensus       528 a~~~  531 (975)
T KOG0112|consen  528 ASPP  531 (975)
T ss_pred             ccCC
Confidence            9864

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.04  E-value=0.035  Score=60.13  Aligned_cols=74  Identities=23%  Similarity=0.390  Sum_probs=60.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCEEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREV--GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY-EINGRQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~--G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~-~I~GR~LrV~~A   83 (551)
                      .++|+|||...++..+|+.+|...  |.-..|.+.        .||+||++.|..-|.+|++.+++. ++.|+++.|+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k--------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK--------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee--------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            468999999999999999999754  222222221        689999999999999999999984 789999999998


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      -..+.
T Consensus        74 v~kkq   78 (584)
T KOG2193|consen   74 VPKKQ   78 (584)
T ss_pred             hhHHH
Confidence            76543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=93.46  E-value=0.32  Score=40.27  Aligned_cols=55  Identities=20%  Similarity=0.237  Sum_probs=43.8

Q ss_pred             CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851           17 DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus        17 d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      .++-++++..+..|+- .  +|..|+     .|| ||.|.|.++|++|.+..++..+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4677899999999972 3  334454     577 99999999999999999998887776654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

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

Probab=93.21  E-value=0.045  Score=62.02  Aligned_cols=70  Identities=31%  Similarity=0.470  Sum_probs=61.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ++..+|||||+-+.+..+-++.++..||-|..+....         ||||+|.+......|++.|+...++|..+.+..
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            3567899999999999999999999999998876542         999999999999999999998889888775554

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.16  E-value=0.46  Score=38.90  Aligned_cols=56  Identities=20%  Similarity=0.207  Sum_probs=44.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcC---CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREV---GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL   68 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~---G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L   68 (551)
                      .-.+|+|.++. +.+.++|+.+|..|   .....+.++-|.       -|-|.|.+.+.|.+|+..|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            34679999985 47788999999998   235688888774       4688999999999999764

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=93.04  E-value=0.11  Score=58.12  Aligned_cols=68  Identities=15%  Similarity=0.302  Sum_probs=54.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHc--CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICRE--VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG--YEINGRQLR   79 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~--~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng--~~I~GR~Lr   79 (551)
                      ..|.|.++.||..+-+|+++.+|+.  |-++.+|.+-.+      .++ ||+|++..||+.|++.|..  .+|.|+.|.
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N------~nW-yITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN------DNW-YITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec------Cce-EEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            3577888999999999999999975  778888887543      233 8999999999999998854  366777653

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=92.56  E-value=0.14  Score=52.44  Aligned_cols=77  Identities=26%  Similarity=0.366  Sum_probs=63.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC----ceeCCEEEEEEe
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG----YEINGRQLRVDF   82 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng----~~I~GR~LrV~~   82 (551)
                      ..|||.||..-++-|.+.+.|+.||+|....++.|- .++..|-++|+|...-.+.+|.+.+..    ..+.++.+-|+-
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  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            679999999999999999999999999877666663 589999999999999999999988742    244566666665


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      ..
T Consensus       111 ~e  112 (275)
T KOG0115|consen  111 ME  112 (275)
T ss_pred             hh
Confidence            54

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.38  E-value=0.043  Score=57.85  Aligned_cols=80  Identities=21%  Similarity=0.353  Sum_probs=60.5

Q ss_pred             cEEEEecCCCCCCHHH-H--HHHHHcCCCeeEEEEeecCC--CCCc-ceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            7 RCVFVGNIPYDATEEQ-L--IEICREVGPVVSFRLVIDRE--TGKP-KGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         7 rtVFVGNLP~d~TEEe-L--re~Fs~~G~V~~vrLv~Dr~--TGks-KGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      .-+||-+|+.....+. |  .+.|.+||.|..+..-.+..  .+.. ..-++|+|...++|..||..++|+.++|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            4578888887765544 4  45689999999998877652  1111 123789999999999999999999999999888


Q ss_pred             EeecCC
Q 008851           81 DFAEND   86 (551)
Q Consensus        81 ~~A~~~   86 (551)
                      .+....
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            776643

>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=91.89  E-value=0.32  Score=47.23  Aligned_cols=83  Identities=20%  Similarity=0.259  Sum_probs=52.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHc-CCCe---eEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCceeC---
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICRE-VGPV---VSFRLVIDRETGK--PKGYGFCEYKDEETALSARRNLQGYEIN---   74 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~-~G~V---~~vrLv~Dr~TGk--sKGyAFVEF~d~e~A~sAi~~Lng~~I~---   74 (551)
                      ....+|.|++||...||+++.+.++. ++.-   ..+.-..+...-+  ...-|||.|.+.+++..-++.++|+.+.   
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            35678999999999999999887665 5555   3443222221111  2356899999999999999999998772   


Q ss_pred             C--EEEEEEeecCC
Q 008851           75 G--RQLRVDFAEND   86 (551)
Q Consensus        75 G--R~LrV~~A~~~   86 (551)
                      |  ....|++|.-.
T Consensus        85 g~~~~~~VE~Apyq   98 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQ   98 (176)
T ss_dssp             S-EEEEEEEE-SS-
T ss_pred             CCCcceeEEEcchh
Confidence            2  34678888753

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.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=91.64  E-value=0.055  Score=63.07  Aligned_cols=79  Identities=20%  Similarity=0.306  Sum_probs=66.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++||+||++..+++.+|+..|..+|.|.+|.|..-+ -+.-..|+||.|.+.+.+.+|+..+.+..|....+++.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            36789999999999999999999999999999987653 24445689999999999999999888887766666666654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=91.63  E-value=0.12  Score=54.00  Aligned_cols=81  Identities=16%  Similarity=0.156  Sum_probs=69.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .+++|+|++.+.+.+++...++..+|.+..+...........+||+++.|...+.+..|+.....+.+.++.+...+...
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~  167 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTR  167 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccccc
Confidence            57899999999999999999999999999998888788899999999999999999999976655677777776666554


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      .
T Consensus       168 ~  168 (285)
T KOG4210|consen  168 R  168 (285)
T ss_pred             c
Confidence            3

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=91.27  E-value=0.28  Score=52.89  Aligned_cols=78  Identities=19%  Similarity=0.219  Sum_probs=60.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRE---TGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~---TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...|.|.||...++.++++.+|.-.|.|.+++|.-..+   .......|||.|.|...+..|-. |-++.|-++.|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            35899999999999999999999999999998864321   22335689999999999988875 555566566655554


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      .-
T Consensus        86 ~~   87 (479)
T KOG4676|consen   86 YG   87 (479)
T ss_pred             cC
Confidence            43

>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=90.44  E-value=0.69  Score=45.41  Aligned_cols=61  Identities=28%  Similarity=0.353  Sum_probs=45.2

Q ss_pred             CHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCEEEEEEeecC
Q 008851           19 TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ--GYEINGRQLRVDFAEN   85 (551)
Q Consensus        19 TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln--g~~I~GR~LrV~~A~~   85 (551)
                      ..+.|+++|..|+.+..+.....      -+-..|.|.+.++|.+|...|+  +..+.|..|+|-|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34789999999999998887743      2345889999999999999999  8999999999999854

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=90.10  E-value=1.1  Score=39.12  Aligned_cols=55  Identities=11%  Similarity=0.248  Sum_probs=41.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ   69 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln   69 (551)
                      +...||+ +|.+|...||.++|+.||.|. |.++.|       .-|||...+.+.|..++..+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            4456665 999999999999999999764 555544       368999999999999998876

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=87.91  E-value=3.9  Score=37.06  Aligned_cols=68  Identities=15%  Similarity=0.213  Sum_probs=49.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING   75 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G   75 (551)
                      ...+.+...|+.++-++|..+.+.+- .|..++|++|.  ..++-.+.+.|++.+.|..-.+.+||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34445566677777777876666653 56778888763  2355668889999999999999999987753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=87.25  E-value=0.84  Score=51.18  Aligned_cols=78  Identities=21%  Similarity=0.312  Sum_probs=54.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHH-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce---eCC-EEEEEEe
Q 008851            8 CVFVGNIPYDATEEQLIEICR-EVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE---ING-RQLRVDF   82 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs-~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~---I~G-R~LrV~~   82 (551)
                      ++-|.|++...|...|.+.-+ ..|.-..+.+..|..+....|||||.|.+.+.+..+.+.+||..   |++ +.+.+.|
T Consensus       390 t~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itY  469 (549)
T KOG4660|consen  390 TLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITY  469 (549)
T ss_pred             hhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeeh
Confidence            344445554444443333322 25666667788888888999999999999999999999999874   344 4467888


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      |+-
T Consensus       470 ArI  472 (549)
T KOG4660|consen  470 ARI  472 (549)
T ss_pred             hhh
Confidence            764

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=86.33  E-value=0.45  Score=52.49  Aligned_cols=73  Identities=12%  Similarity=0.151  Sum_probs=57.0

Q ss_pred             cEEEEecCCCCCC-HHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            7 RCVFVGNIPYDAT-EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         7 rtVFVGNLP~d~T-EEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +.+-+.-+++... -++|...|.+||.|..|.+-+.      .-.|.|+|.+..+|-.|. ..++..|++|.|+|.|-..
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchh-ccccceecCceeEEEEecC
Confidence            3344444555544 5789999999999999988654      236789999999997777 4688999999999999876


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      .
T Consensus       446 s  446 (526)
T KOG2135|consen  446 S  446 (526)
T ss_pred             C
Confidence            3

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=85.39  E-value=3.4  Score=39.45  Aligned_cols=73  Identities=19%  Similarity=0.275  Sum_probs=54.1

Q ss_pred             CCCcEEEEecCCCCCCH-HHHHH---HHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            4 SQHRCVFVGNIPYDATE-EQLIE---ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TE-EeLre---~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      ++=.+|.|+-|..++.. |++++   .++.||+|.+|.+.     |  +--|.|.|+|...|=+|+..++. ..-|..+.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~q  155 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQ  155 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceEE
Confidence            34557778777666543 44544   46789999999875     3  34689999999999999998876 55677888


Q ss_pred             EEeec
Q 008851           80 VDFAE   84 (551)
Q Consensus        80 V~~A~   84 (551)
                      +.|-.
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            88854

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=82.78  E-value=0.17  Score=55.00  Aligned_cols=78  Identities=22%  Similarity=0.316  Sum_probs=65.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLV-IDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv-~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .++++.|.|||....+|.|..++..||.|..|..+ .|.+    ....-|.|...+.+..|+..|++..+....++|.|.
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e----tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE----TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH----HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            36778999999999999999999999999999754 3333    334457899999999999999999999999999997


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ...
T Consensus       155 Pde  157 (584)
T KOG2193|consen  155 PDE  157 (584)
T ss_pred             chh
Confidence            643

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=82.02  E-value=6.7  Score=41.50  Aligned_cols=73  Identities=18%  Similarity=0.201  Sum_probs=54.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE-EEEEeec
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ-LRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~-LrV~~A~   84 (551)
                      +..|-|-+++.... .-|-.+|++||.|++...      +..-.+-+|.|.+.-+|++|+ ..+|..|+|.. |-|+.+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~------~~ngNwMhirYssr~~A~KAL-skng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVT------PSNGNWMHIRYSSRTHAQKAL-SKNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeec------CCCCceEEEEecchhHHHHhh-hhcCeeeccceEEeeeecC
Confidence            45566667777644 456678999999987653      333458899999999999999 46888898765 5677766


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      .+
T Consensus       269 Dk  270 (350)
T KOG4285|consen  269 DK  270 (350)
T ss_pred             CH
Confidence            43

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	551
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-30
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		7e-19
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		7e-19
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		5e-18
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-10
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-09
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		2e-09
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		4e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-08
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-08
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		5e-08
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		5e-08
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		8e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-07
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-07
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		4e-07
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		5e-07
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		6e-07
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		7e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		1e-06
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		2e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-06
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-06
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		5e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-06
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		7e-06
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		8e-06
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		9e-06
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		9e-06
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-05
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		2e-05
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		2e-05
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		2e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		2e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		3e-05
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		3e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		4e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-05
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		5e-05
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		5e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		5e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		6e-05
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		7e-05
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		8e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		8e-05
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		9e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-04
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		1e-04
2khc_A	118	Bruno Rrm3+ Length = 118		1e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		1e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-04
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		2e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		5e-04
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		5e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		6e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		6e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		6e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		7e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		7e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		8e-04
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		9e-04

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score =  130 bits (327), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 65/94 (69%), Positives = 74/94 (78%)
Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           NL G E +GR LRVD A ++K  +  +  G G P
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 92.0 bits (227), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 36/79 (45%), Positives = 59/79 (74%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R V++G+IPYD TEEQ++++C  VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 67 NLQGYEINGRQLRVDFAEN 85
          NL GY++  R L+  ++ N
Sbjct: 63 NLNGYQLGSRFLKCGYSSN 81

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 92.0 bits (227), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 36/79 (45%), Positives = 59/79 (74%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R V++G+IPYD TEEQ++++C  VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 5  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 67 NLQGYEINGRQLRVDFAEN 85
          NL GY++  R L+  ++ N
Sbjct: 65 NLNGYQLGSRFLKCGYSSN 83

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 89.4 bits (220), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 36/79 (45%), Positives = 59/79 (74%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R V++G+IPYD TEEQ++++C  VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 4  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 67 NLQGYEINGRQLRVDFAEN 85
          NL GY++  R L+  ++ N
Sbjct: 64 NLNGYQLGSRFLKCGYSSN 82

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/81 (41%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R ++VGN+ Y AT EQ+ E+  + G V + +L+ DRET KPKG+GF E + EE+   A  
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 67 NLQGYEINGRQLRVDFAENDK 87
           L   +  GR +RV  A   K
Sbjct: 61 KLDNTDFMGRTIRVTEANPKK 81

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           + +FV  + YD TE +L       GP+    +V  + +GKP+GY F EY+ E    SA +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 67  NLQGYEINGRQLRVD 81
           +  G +I+GR++ VD
Sbjct: 163 HADGKKIDGRRVLVD 177

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           + +FV  + YD TE +L       GP+    +V  + +GKP+GY F EY+ E    SA +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 67  NLQGYEINGRQLRVD 81
           +  G +I+GR++ VD
Sbjct: 163 HADGKKIDGRRVLVD 177

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++VG++ ++ TE+ L  I    G + S +L++D ETG+ KGYGF  + D E A  A   L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 69  QGYEINGRQLRV 80
            G+E+ GR ++V
Sbjct: 89  NGFELAGRPMKV 100

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/99 (34%), Positives = 50/99 (50%), Gaps = 7/99 (7%)
Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            SS    ++VG++ ++ TE+ L  I    G + +  L+ D +TG+ KGYGF  + D E A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             A   L G+E+ GR +RV       G    R  G  GP
Sbjct: 61  RRALEQLNGFELAGRPMRV-------GHVTERLDGGSGP 92

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
            S H+ +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D     
Sbjct: 112 DSAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 63  SARRNLQGYEINGRQLRV 80
            A   L G ++  ++L V
Sbjct: 171 QAIAGLNGMQLGDKKLLV 188

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D      A   L
Sbjct: 99  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 69  QGYEINGRQLRV 80
            G ++  ++L V
Sbjct: 159 NGMQLGDKKLLV 170

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D      A   L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 69  QGYEINGRQLRV 80
            G ++  ++L V
Sbjct: 157 NGMQLGDKKLLV 168

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 55.5 bits (132), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 45/81 (55%)
Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          +S H  VFVG++  + T E +       G +   R+V D  TGK KGYGF  + ++  A 
Sbjct: 12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71
Query: 63 SARRNLQGYEINGRQLRVDFA 83
          +A + + G  + GRQ+R ++A
Sbjct: 72 NAIQQMGGQWLGGRQIRTNWA 92

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 50/83 (60%), Gaps = 1/83 (1%)
Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          MAS + + +FVG + +D  E+ L ++  + G +    +V DRET + +G+GF  +++ + 
Sbjct: 8  MASDEGK-LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 66
Query: 61 ALSARRNLQGYEINGRQLRVDFA 83
          A  A   + G  ++GRQ+RVD A
Sbjct: 67 AKDAMMAMNGKSVDGRQIRVDQA 89

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 43/77 (55%)
Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R + V  IP    E QL ++    GP+ S ++V DRET + +GYGF +++   +A  A  
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 67  NLQGYEINGRQLRVDFA 83
            L G+ I  ++L+V  A
Sbjct: 103 GLNGFNILNKRLKVALA 119

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 40/75 (53%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D      A   L
Sbjct: 4  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 69 QGYEINGRQLRVDFA 83
           G ++  ++L V  A
Sbjct: 64 NGMQLGDKKLLVQRA 78

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          S   + +FV  +  D TEE L E        V  R+V DRETG  KG+GF ++  EE A 
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 63 SARRNLQGYEINGRQLRVDFAE 84
          +A+  ++  EI+G ++ +D+A+
Sbjct: 69 AAKEAMEDGEIDGNKVTLDWAK 90

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/91 (32%), Positives = 52/91 (57%), Gaps = 2/91 (2%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FV +I  +A E+++ E   + G + +  L +DR TG  KGY   EY+  + AL+A+  L
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 69  QGYEINGRQLRVD--FAENDKGADRNREQGR 97
            G EI G+ ++VD  F +  K   ++ ++ R
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+  +P+  T+E+L EIC+  G V   RLV +R  GKPKG  + EY++E  A  A   +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 69 QGYEINGRQLRV 80
           G  I    ++V
Sbjct: 79 DGMTIKENIIKV 90

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FV +I  +A E+++ E   + G + +  L +DR TG  KGY   EY+  + AL+A+  L
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 69  QGYEINGRQLRVDF 82
            G EI G+ ++VD+
Sbjct: 89  NGAEIMGQTIQVDW 102

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 46/80 (57%)
Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          +Q   V+VG +    +E  L E+  + GPVV+  +  DR TG+ +GYGF E+  EE A  
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 64 ARRNLQGYEINGRQLRVDFA 83
          A + +   ++ G+ +RV+ A
Sbjct: 73 AIKIMDMIKLYGKPIRVNKA 92

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 3/93 (3%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++VGN+ +  TEEQ+ E+  + G +    + +D+      G+ F EY     A +A R +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            G  ++ R +R D+   D G    R+ GRG  G
Sbjct: 102 NGTRLDDRIIRTDW---DAGFKEGRQYGRGRSG 131

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 44/76 (57%)
Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+  
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 68 LQGYEINGRQLRVDFA 83
            G E++GR++RVDF+
Sbjct: 74 ANGMELDGRRIRVDFS 89

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 44/76 (57%)
Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+  
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 68 LQGYEINGRQLRVDFA 83
            G E++GR++RVDF+
Sbjct: 77 ANGMELDGRRIRVDFS 92

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 46/75 (61%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG++  +  +E L    ++    +S  ++ D +TG  +GYGF  +  ++ A +A  ++
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 69 QGYEINGRQLRVDFA 83
          QG ++NGR LR+++A
Sbjct: 64 QGQDLNGRPLRINWA 78

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG IP++  E +L E  ++ G V    ++ D E  +P+G+GF  ++DE++   A  N+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNM 71
Query: 69 QGYEINGRQLRVDFAE 84
            ++I G+++ V  AE
Sbjct: 72 HFHDIMGKKVEVKRAE 87

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 46/75 (61%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FVG++  +  +E L    ++    +S  ++ D +TG  +GYGF  +  ++ A +A  ++
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 69  QGYEINGRQLRVDFA 83
           QG ++NGR LR+++A
Sbjct: 150 QGQDLNGRPLRINWA 164

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 44/76 (57%)
Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+  
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 68  LQGYEINGRQLRVDFA 83
             G E++GR++RVDF+
Sbjct: 108 ANGMELDGRRIRVDFS 123

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 42/75 (56%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P D T+ +L  + R +GP+ + R++ D +TG   GY F ++  E  +  A + L
Sbjct: 6  LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 QGYEINGRQLRVDFA 83
           G  +  ++L+V +A
Sbjct: 66 NGITVRNKRLKVSYA 80

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P D T+ +L  + R +GP+ + R+  D +TG   GY F ++  E  +  A + L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 69 QGYEINGRQLRVDFA 83
           G  +  ++L+V +A
Sbjct: 77 NGITVRNKRLKVSYA 91

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 36/72 (50%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+ Y ++EE L ++    GP+      ID  T KPKG+ F  +   E A+ A   +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 69 QGYEINGRQLRV 80
           G    GR L V
Sbjct: 71 DGQVFQGRMLHV 82

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V N+P   T++Q  E+ R  G +    LV    TG+ KGYGF EY  +++A  A+ +L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 69  QGYEINGRQLRVDFAE 84
            G  +  R L V + +
Sbjct: 158 LGKPLGPRTLYVHWTD 173

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V N+P   T++Q  E+ R  G +    LV    TG+ KGYGF EY  +++A  A+ +L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 69  QGYEINGRQLRVDFAE 84
            G  +  R L V + +
Sbjct: 158 LGKPLGPRTLYVHWTD 173

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V N+P   T++Q  E+ R  G +    LV    TG+ KGYGF EY  +++A  A+ +L
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 69  QGYEINGRQLRVDFAE 84
            G  +  R L V + +
Sbjct: 156 LGKPLGPRTLYVHWTD 171

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/74 (39%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R VFVGN+     EE L E+  + GP+    +  DRE GKPK +GF  +K  E+   A  
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 67 NLQGYEINGRQLRV 80
           L G  + GR + V
Sbjct: 76 LLNGIRLYGRPINV 89

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 45/81 (55%)
Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          +S H  VFVG++  + T E +       G +   R+V D  TGK KGYGF  + ++  A 
Sbjct: 12 TSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAE 71
Query: 63 SARRNLQGYEINGRQLRVDFA 83
          +A  ++ G  + GRQ+R ++A
Sbjct: 72 NAIVHMGGQWLGGRQIRTNWA 92

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 42/75 (56%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P D T+ +L  + R +GP+ + R++ D +TG   GY F ++  E  +  A + L
Sbjct: 6  LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 QGYEINGRQLRVDFA 83
           G  +  ++L+V +A
Sbjct: 66 NGITVRNKRLKVSYA 80

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V ++  D +++ +  +    G + S  L  D  TGK KGYGF EY+  +++  A  ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 69  QGYEINGRQLRV 80
             +++ G+ LRV
Sbjct: 188 NLFDLGGQYLRV 199

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 46/72 (63%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ ++P +  ++ L+++    G VVS ++ ID++T   K +GF  Y +  +A +A +++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 69 QGYEINGRQLRV 80
           G++I  ++L+V
Sbjct: 88 NGFQIGMKRLKV 99

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 9/91 (9%)
Query: 10  FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
           +VGN+P++  +  +  I +++  + S RLV D++T K KG+ + E+ DE  +L       
Sbjct: 19  YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYD 76
Query: 70  GYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           G  +  R LRVD AE        R+Q + GP
Sbjct: 77  GALLGDRSLRVDIAE-------GRKQDKSGP 100

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 QGYEINGRQLRVDF 82
           G ++ G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALS 63
          R ++VGN+ Y AT E+L       G V    ++ D+ +G PKG+ + E+ D+E   T+L+
Sbjct: 6  RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 64 ARRNLQGYEINGRQLRV 80
             +L      GRQ++V
Sbjct: 66 LDESL----FRGRQIKV 78

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALS 63
          R ++VGN+ Y AT E+L       G V    ++ D+ +G PKG+ + E+ D+E   T+L+
Sbjct: 7  RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 64 ARRNLQGYEINGRQLRV 80
             +L      GRQ++V
Sbjct: 67 LDESL----FRGRQIKV 79

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 QGYEINGRQLRVDF 82
           G ++ G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 15/92 (16%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+GN+P +ATE+++  +  + G V+   ++        K YGF   +D+  A  A RNL
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             Y+++G  + V+       A +N+ +   GP
Sbjct: 63  HHYKLHGVNINVE-------ASKNKSKASSGP 87

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 69 QGYEINGRQLRVDF 82
           G ++ G+ + VD+
Sbjct: 85 NGQDLMGQPISVDW 98

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V ++  D +++ +  +    G + S  L  D  TGK KGYGF EY+  +++  A  ++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 69  QGYEINGRQLRV 80
             +++ G+ LRV
Sbjct: 173 NLFDLGGQYLRV 184

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+++   +   +G + S +LV D+ TG+  GYGF  Y D   A  A   L
Sbjct: 7  LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 69 QGYEINGRQLRVDFA 83
           G ++  + ++V +A
Sbjct: 67 NGLKLQTKTIKVSYA 81

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 QGYEINGRQLRVDF 82
           G ++ G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 69 QGYEINGRQLRVDF 82
           G ++ G+ + VD+
Sbjct: 72 NGQDLMGQPISVDW 85

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V+V N+P+  T   L  I  + G VV   ++ D++T K KG  F  + D+++A +  R +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 69 QGYEINGRQLRVDFA 83
             ++ GR ++   A
Sbjct: 79 NNKQLFGRVIKASIA 93

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 2/87 (2%)
Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS    +FV N+P+D T + L +   E G V+     I  E GK KG G  +++  E A
Sbjct: 1  GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVA 58
Query: 62 LSARRNLQGYEINGRQLRVDFAENDKG 88
            A R + G +++GR++ V    N  G
Sbjct: 59 ERACRMMNGMKLSGREIDVRIDRNASG 85

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 69 QGYEINGRQLRVDF 82
           G ++ G+ + VD+
Sbjct: 86 NGQDLMGQPISVDW 99

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/86 (31%), Positives = 50/86 (58%), Gaps = 6/86 (6%)
Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          ++ + VF+ N+ +D+ EE L E+ ++ G +   R+V+  +T   KG  F ++  +E A  
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 64 --ARRNLQ----GYEINGRQLRVDFA 83
            A  +L+    G +++GRQL+VD A
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLA 98

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 43/84 (51%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+E+   +   +G + S +LV D+ TG+  GYGF  Y D + A  A   L
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 69 QGYEINGRQLRVDFAENDKGADRN 92
           G  +  + ++V +A     + R+
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRD 88

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R +   N+PY  T+++L E+  +   +   RLV   + GK KG  + E+K E  A     
Sbjct: 94  RTLLAKNLPYKVTQDELKEVFEDAAEI---RLV--SKDGKSKGIAYIEFKTEADAEKTFE 148
Query: 67  NLQGYEINGRQLRVDFAENDKG 88
             QG EI+GR + + +    KG
Sbjct: 149 EKQGTEIDGRSISLYYTGEPKG 170

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 41/73 (56%)
Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+  
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 68 LQGYEINGRQLRV 80
            G E++GR++RV
Sbjct: 77 ANGMELDGRRIRV 89

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 42/83 (50%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+++   +   +G + S +LV D+ TG+  GYGF  Y D   A  A   L
Sbjct: 7  LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 69 QGYEINGRQLRVDFAENDKGADR 91
           G ++  + ++V +A     + R
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIR 89

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +PY  T+  L +     G +    ++ DR+TGK +GYGF    D   A  A ++ 
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 69 QGYEINGRQLRVDFA 83
              I+GR+  V+ A
Sbjct: 80 NPI-IDGRKANVNLA 93

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FV N+P+D T + L +   E G V+     I  E GK KG G  +++  E A  A R +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 69 QGYEINGRQLRVDFAENDKG 88
           G +++GR++ V    N  G
Sbjct: 69 NGMKLSGREIDVRIDRNASG 88

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 42/72 (58%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+ ++P + T+  L       G V+S ++ ID++T   K +GF  + + ++A  A + +
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 69  QGYEINGRQLRV 80
            G+++  ++L+V
Sbjct: 103 NGFQVGTKRLKV 114

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V ++  D +++ +  +    G + S  L  D  TGK KGYGF EY+  +++  A  + 
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 69  QGYEINGRQLRV 80
             +++ G+ LRV
Sbjct: 172 NLFDLGGQYLRV 183

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 44/83 (53%)
Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           S+  R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E A
Sbjct: 1  GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 62 LSARRNLQGYEINGRQLRVDFAE 84
           +A  N+   E+ GR +RV+ A+
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAK 83

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          + + + + N+ Y ATEE L    +EV    +F  V   + GK KGY F E+   E A  A
Sbjct: 14 ESKTLVLSNLSYSATEETL----QEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 65 RRNLQGYEINGRQLRVD 81
            +    EI GR +R++
Sbjct: 70 LNSCNKREIEGRAIRLE 86

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP-----KGYGFCEYK 56
           SS    +F+ N+ +  TEE L  +  +VG + S    I ++  K       G+GF EYK
Sbjct: 1  GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKS--CTISKKKNKAGVLLSMGFGFVEYK 58
Query: 57 DEETALSARRNLQGYEINGRQLRVDFAE 84
            E A  A + LQG+ ++G +L V  +E
Sbjct: 59 KPEQAQKALKQLQGHTVDGHKLEVRISE 86

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          MA+++ R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E 
Sbjct: 3  MATTK-RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 61 ALSARRNLQGYEINGRQLRVDFAE 84
          A +A  N+   E+ GR +RV+ A+
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLAK 85

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 43/81 (53%)
Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           ++  R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E A 
Sbjct: 60  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 63  SARRNLQGYEINGRQLRVDFA 83
           +A  N+   E+ GR +RV+ A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 6   HRCVFVGNIPYDATEEQLIEICREV----GPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           ++ +++ N+    TE  L+ +        GP + FR++    TG+ +G  F  + ++E A
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIA 80
Query: 62  LSARRNLQGYEINGRQLRVDFAENDK 87
             A   + GY++ G+ L ++F +N K
Sbjct: 81  WQALHLVNGYKLYGKILVIEFGKNKK 106

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/73 (24%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G +  +  E+ L  +  + GP+    L+ DR T K +G+ F  +++   A +A +++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 69 QGYEINGRQLRVD 81
           G  ++G+ ++V+
Sbjct: 69 NGKSLHGKAIKVE 81

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          H  VFVG++  + T   +       G +   R+V D  TGK KGYGF  + ++  A +A 
Sbjct: 6  HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65
Query: 66 RNLQGYEINGRQLRVDFA 83
          + + G  + GRQ+R ++A
Sbjct: 66 QQMGGQWLGGRQIRTNWA 83

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+++L  +   +G V S +L+ D+  G   GYGF  Y   + A  A   L
Sbjct: 7  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 69 QGYEINGRQLRVDFAE 84
           G  +  + ++V +A 
Sbjct: 67 NGLRLQSKTIKVSYAR 82

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 41/77 (53%)
Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E A +A  
Sbjct: 3  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 67 NLQGYEINGRQLRVDFA 83
          N+   E+ GR +RV+ A
Sbjct: 63 NMNESELFGRTIRVNLA 79

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          +Q   +FVGN+P D TEE++ ++  + G      +       K KG+GF   +    A  
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEI 73
Query: 64 ARRNLQGYEINGRQLRVDFA 83
          A+  L    + G+QLRV FA
Sbjct: 74 AKVELDNMPLRGKQLRVRFA 93

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          MA+++ R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E 
Sbjct: 8  MATTK-RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 66
Query: 61 ALSARRNLQGYEINGRQLRVDFAE 84
          A +A  N+   E+ GR +RV+ A+
Sbjct: 67 AAAAIDNMNESELFGRTIRVNLAK 90

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 22/79 (27%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          Q R ++VGN+  D TE  ++++  ++GP  S +++ +  +  P  Y F E+ +   A +A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAA 71
Query: 65 RRNLQGYEINGRQLRVDFA 83
             + G +I G++++V++A
Sbjct: 72 LAAMNGRKILGKEVKVNWA 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	551
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-43
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-41
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-34
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-34
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-34
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-33
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-33
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-33
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-32
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-32
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-32
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	9e-32
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-31
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-31
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-31
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	8e-31
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-30
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-30
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-30
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-30
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-30
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	9e-30
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-29
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-29
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-29
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-29
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-29
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	7e-28
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-28
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-27
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-27
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-27
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-27
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-27
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-27
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-27
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-27
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-27
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-26
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-26
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-26
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-19
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-26
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-26
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-25
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-25
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-25
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-24
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-24
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-24
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-24
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-24
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	8e-24
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-24
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-24
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-17
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-23
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-22
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-23
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-23
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-21
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-22
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-22
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-22
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-22
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-22
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-22
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-22
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-22
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-21
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-21
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-21
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-21
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-21
2div_A	99	TRNA selenocysteine associated protein; structural	9e-21
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	9e-21
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-20
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-20
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-20
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-20
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-20
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-20
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-20
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-20
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-20
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-16
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-20
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	7e-20
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-19
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-17
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-19
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-19
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-19
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-19
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-18
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-18
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-18
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-18
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-18
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-18
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-17
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-17
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-17
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-17
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-17
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-17
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-16
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-16
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-16
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-16
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	8e-16
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-15
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-15
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-15
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-15
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-15
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-14
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-14
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-10
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-14
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-14
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-14
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-14
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-13
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-13
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	8e-13
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-12
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-12
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-10
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-09
4eba_G	174	RNA15, KLLA0F09383P; HAT domain, heat repeat, monk	4e-09
4eba_G	174	RNA15, KLLA0F09383P; HAT domain, heat repeat, monk	1e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	9e-09
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	7e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-06
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	5e-06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-04
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-04
2j8p_A	49	Cleavage stimulation factor 64 kDa subunit; cleava	6e-04

>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 =  149 bits (378), Expect = 1e-43
 Identities = 65/94 (69%), Positives = 74/94 (78%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           NL G E +GR LRVD A ++K  +  +  G G P
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 =  143 bits (362), Expect = 3e-41
 Identities = 37/90 (41%), Positives = 62/90 (68%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R V++G+IPYD TEEQ++++C  VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 67 NLQGYEINGRQLRVDFAENDKGADRNREQG 96
          NL GY++  R L+  ++ N   +  + E  
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>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 =  127 bits (321), Expect = 1e-34
 Identities = 29/95 (30%), Positives = 50/95 (52%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S +   +FV +I  +A E+++ E   + G + +  L +DR TG  KGY   EY+  + AL
Sbjct: 69  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
           +A+  L G EI G+ ++VD+          + + R
Sbjct: 129 AAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score =  123 bits (312), Expect = 4e-34
 Identities = 28/84 (33%), Positives = 47/84 (55%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
             S +   +FV +I  +A E+++ E   + G + +  L +DR TG  KGY   EY+  + 
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80

Query: 61  ALSARRNLQGYEINGRQLRVDFAE 84
           AL+A+  L G EI G+ ++VD+  
Sbjct: 81  ALAAKEALNGAEIMGQTIQVDWCF 104

>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 =  122 bits (308), Expect = 8e-34
 Identities = 22/77 (28%), Positives = 40/77 (51%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            V+V N+P+  T   L  I  + G VV   ++ D++T K KG  F  + D+++A +  R
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 67 NLQGYEINGRQLRVDFA 83
           +   ++ GR ++   A
Sbjct: 77 AINNKQLFGRVIKASIA 93

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  122 bits (308), Expect = 1e-33
 Identities = 26/84 (30%), Positives = 43/84 (51%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
             S +   +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + 
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77

Query: 61  ALSARRNLQGYEINGRQLRVDFAE 84
           A +A   L G ++ G+ + VD+  
Sbjct: 78  AQAAMEGLNGQDLMGQPISVDWCF 101

>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 =  120 bits (303), Expect = 5e-33
 Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 11/98 (11%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S + + + + N+ Y ATEE L E+  +   +     V   + GK KGY F E+   E A 
Sbjct: 12  SGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAK 67

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
            A  +    EI GR +R++           R     GP
Sbjct: 68  EALNSCNKREIEGRAIRLELQ-------GPRGSPNSGP 98

>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 =  119 bits (301), Expect = 7e-33
 Identities = 33/89 (37%), Positives = 49/89 (55%), Gaps = 1/89 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R ++VGN+ Y AT EQ+ E+  + G V + +L+ DRET KPKG+GF E ++E     A  
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIA 60

Query: 67 NLQGYEINGRQLRVDFAENDKGADRNREQ 95
           L   +  GR +RV  A   K  + +   
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 =  119 bits (301), Expect = 1e-32
 Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 3/98 (3%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
             +Q   V+VG +    +E  L E+  + GPVV+  +  DR TG+ +GYGF E+  EE A
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
             A + +   ++ G+ +RV+ A       +N      G
Sbjct: 71  DYAIKIMDMIKLYGKPIRVNKASAHN---KNLSGPSSG 105

>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 =  118 bits (299), Expect = 2e-32
 Identities = 28/104 (26%), Positives = 51/104 (49%), Gaps = 13/104 (12%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
            ++ + VF+ N+ +D+ EE L E+ ++ G +   R+V+  +T   KG  F ++  +E A 
Sbjct: 12  VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 71

Query: 63  SARRNLQ------GYEINGRQLRVDFAENDKGADRNREQGRGGP 100
                        G +++GRQL+VD A         R++   GP
Sbjct: 72  KCLAAASLEAEGGGLKLDGRQLKVDLA-------VTRDEAASGP 108

>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 =  118 bits (297), Expect = 9e-32
 Identities = 28/91 (30%), Positives = 44/91 (48%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FV  +  +ATEE + +   E G + +  L +DR TG  KGY   EY+  + A +A   L
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGG 99
            G ++ G+ + VD+          R  GR  
Sbjct: 85  NGQDLMGQPISVDWCFVRGPPKGKRRGGRRR 115

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score =  116 bits (294), Expect = 9e-32
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           S +   +F+  +P+  T+E+L EIC+  G V   RLV +R  GKPKG  + EY++E  A
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQA 71

Query: 62 LSARRNLQGYEINGRQLRVDFAE 84
            A   + G  I    ++V  + 
Sbjct: 72 SQAVMKMDGMTIKENIIKVAISN 94

>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 =  118 bits (298), Expect = 1e-31
 Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 3/100 (3%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
              +   ++VGN+ +  TEEQ+ E+  + G +    + +D+      G+ F EY     A
Sbjct: 35  LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 94

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            +A R + G  ++ R +R D+   D G    R+ GRG  G
Sbjct: 95  ENAMRYINGTRLDDRIIRTDW---DAGFKEGRQYGRGRSG 131

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score =  116 bits (292), Expect = 2e-31
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
            +VGN+P++  +  +  I +++  + S RLV D++T K KG+ + E+ + ++   A    
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-LTY 75

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQG 96
            G  +  R LRVD AE  K        G
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>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 =  115 bits (289), Expect = 6e-31
 Identities = 33/98 (33%), Positives = 52/98 (53%), Gaps = 10/98 (10%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S   + +FV  +  D TEE L E        V  R+V DRETG  KG+GF ++  EE A 
Sbjct: 12  SQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           +A+  ++  EI+G ++ +D+A       + + +G  GP
Sbjct: 69  AAKEAMEDGEIDGNKVTLDWA-------KPKGEGGSGP 99

>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 =  115 bits (289), Expect = 8e-31
 Identities = 21/97 (21%), Positives = 48/97 (49%), Gaps = 3/97 (3%)

Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          +    +R +++ N+PY  T E++ +I  + GP+   R+     T + +G  +  Y+D   
Sbjct: 3  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFD 59

Query: 61 ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
          A +A  +L G+ ++ R L V +   ++   +   + +
Sbjct: 60 AKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKK 96

>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 =  113 bits (286), Expect = 1e-30
 Identities = 33/100 (33%), Positives = 49/100 (49%), Gaps = 7/100 (7%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            SS    ++VG++ ++ TE+ L  I    G + +  L+ D +TG+ KGYGF  + D E A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
             A   L G+E+ GR +RV            R  G  GP 
Sbjct: 61  RRALEQLNGFELAGRPMRVGHV-------TERLDGGSGPS 93

>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 =  113 bits (286), Expect = 1e-30
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCE 54
           S +  +FV  +  + T E + +  +++G + +          L  DRETGK KG     
Sbjct: 10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 69

Query: 55 YKDEETALSARRNLQGYEINGRQLRVDFA 83
          + D  +A +A     G E +G  ++V FA
Sbjct: 70 FDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 =  112 bits (282), Expect = 4e-30
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +   N+ ++ TE++L E+  +   +      +  + GK KG  + E+K E  A     
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 67 NLQGYEINGRQLRVDFAENDKGADR 91
            QG EI+GR + + +   +KG  R
Sbjct: 72 EKQGAEIDGRSVSLYYT-GEKGGTR 95

>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 =  111 bits (281), Expect = 7e-30
 Identities = 28/89 (31%), Positives = 49/89 (55%), Gaps = 3/89 (3%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVID-RETGKPKGYGFCEYKDEETALSARRN 67
            F+GN+PYD TEE + E  R +  + + RL  +     + KG+G+ E++D ++ LSA  +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LS 75

Query: 68  LQGYEINGRQLRVDFAENDKGADRNREQG 96
           L    +  +++RVD A+  +  D     G
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 =  111 bits (280), Expect = 8e-30
 Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
             R VFVGN+     EE L E+  + GP+    +  DRE GKPK +GF  +K  E+   
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72

Query: 64 ARRNLQGYEINGRQLRVDFAEN 85
          A   L G  + GR + V    +
Sbjct: 73 AIALLNGIRLYGRPINVSGPSS 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score =  112 bits (281), Expect = 9e-30
 Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 8/105 (7%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPV--------VSFRLVIDRETGKPKGYGFCE 54
           +S +  +FV  +  + T E + +  +++G +            L  DRETGK KG     
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 55  YKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
           + D  +A +A     G E +G  ++V FA      +R    GRGG
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGG 108

>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 =  109 bits (275), Expect = 5e-29
 Identities = 20/77 (25%), Positives = 41/77 (53%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+ 
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 67 NLQGYEINGRQLRVDFA 83
             G E++GR++RV   
Sbjct: 76 RANGMELDGRRIRVSGP 92

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score =  109 bits (275), Expect = 5e-29
 Identities = 29/98 (29%), Positives = 44/98 (44%), Gaps = 2/98 (2%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS    +FV N+ Y ++EE L ++    GP+      ID  T KPKG+ F  +   E A
Sbjct: 4  GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
          + A   + G    GR L V  +   K  + ++     G
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIKK--EASQSGPSSG 99

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  109 bits (275), Expect = 5e-29
 Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 7/94 (7%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
            + V N+ Y  + + L  +  + G V    +  +  T  P+G+ F  + D   A  A   
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 68  LQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           + G E++GR+LRV  A       R   +   GP 
Sbjct: 75  MDGAELDGRELRVQVA-------RYGRRDLSGPS 101

>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 =  108 bits (273), Expect = 7e-29
 Identities = 27/82 (32%), Positives = 47/82 (57%), Gaps = 3/82 (3%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRET-GKPKGYGFCEYKDEETALSAR 65
             F+GN+PYD TEE + E  R +  + + RL  +     + KG+G+ E++D ++ LSA 
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA- 77

Query: 66 RNLQGYEINGRQLRVDFAENDK 87
           +L    +  R++RVD A+  +
Sbjct: 78 LSLNEESLGNRRIRVDVADQAQ 99

>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 =  108 bits (272), Expect = 8e-29
 Identities = 22/82 (26%), Positives = 44/82 (53%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          ++  R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E A 
Sbjct: 4  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 63 SARRNLQGYEINGRQLRVDFAE 84
          +A  N+   E+ GR +RV+ A+
Sbjct: 64 AAIDNMNESELFGRTIRVNLAK 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score =  106 bits (266), Expect = 7e-28
 Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 13/96 (13%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R ++VGN+ Y AT E+L       G V    ++ D+ +G PKG+ + E+ D+E+  ++  
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM 102
            L      GRQ++V     ++            PG+
Sbjct: 67  -LDESLFRGRQIKVIPKRTNR------------PGI 89

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  105 bits (265), Expect = 9e-28
 Identities = 31/98 (31%), Positives = 46/98 (46%), Gaps = 9/98 (9%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS    +FV N+P+D T + L +   E G V+     I  E GK KG G  +++  E A
Sbjct: 4  GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVA 61

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
            A R + G +++GR++ V         DRN      G
Sbjct: 62 ERACRMMNGMKLSGREIDVRI-------DRNASGPSSG 92

>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 =  105 bits (265), Expect = 1e-27
 Identities = 22/85 (25%), Positives = 47/85 (55%), Gaps = 2/85 (2%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
            Q R ++VGN+  D TE  ++++  ++GP  S +++ +  +  P  Y F E+ +   A 
Sbjct: 12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAA 69

Query: 63 SARRNLQGYEINGRQLRVDFAENDK 87
          +A   + G +I G++++V++A    
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPS 94

>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 =  105 bits (263), Expect = 2e-27
 Identities = 29/100 (29%), Positives = 50/100 (50%), Gaps = 7/100 (7%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            +S    +FVG + +D  E+ L ++  + G +    +V DRET + +G+GF  +++ + A
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
             A   + G  ++GRQ+RVD A             R GP 
Sbjct: 68  KDAMMAMNGKSVDGRQIRVDQA-------GKSSDNRSGPS 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score =  105 bits (263), Expect = 3e-27
 Identities = 28/76 (36%), Positives = 45/76 (59%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++VG++ ++ TE+ L  I    G + S +L++D ETG+ KGYGF  + D E A  A   L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

Query: 69  QGYEINGRQLRVDFAE 84
            G+E+ GR ++V    
Sbjct: 89  NGFELAGRPMKVGHVT 104

>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 =  104 bits (261), Expect = 4e-27
 Identities = 23/100 (23%), Positives = 47/100 (47%), Gaps = 5/100 (5%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            ++  R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E A
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            +A  N+   E+ GR +RV+ A+         ++     G
Sbjct: 68  AAAIDNMNESELFGRTIRVNLAK-----PMRIKESGPSSG 102

>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 =  105 bits (263), Expect = 5e-27
 Identities = 22/81 (27%), Positives = 45/81 (55%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+ 
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 67  NLQGYEINGRQLRVDFAENDK 87
              G E++GR++RVDF+   +
Sbjct: 107 RANGMELDGRRIRVDFSITKR 127

>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 =  104 bits (261), Expect = 5e-27
 Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 15/107 (14%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPV--------VSFRLVIDRETGKPKGYGFCE 54
            S +  ++V  +    T + L +  ++ G V            + +D+ETGKPKG     
Sbjct: 12  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71

Query: 55  YKDEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           Y+D  TA +A     G +  G +L+V  A       R +     GP 
Sbjct: 72  YEDPPTAKAAVEWFDGKDFQGSKLKVSLA-------RKKPPMNSGPS 111

>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 =  103 bits (258), Expect = 7e-27
 Identities = 27/101 (26%), Positives = 50/101 (49%), Gaps = 15/101 (14%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
             SS    +F+GN+P +ATE+++  +  + G V+   ++        K YGF   +D+  
Sbjct: 3   SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           A  A RNL  Y+++G  + V+ +       +N+ +   GP 
Sbjct: 55  AEDAIRNLHHYKLHGVNINVEAS-------KNKSKASSGPS 88

>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 =  103 bits (260), Expect = 7e-27
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
                R VF   +        L +    VG V   R++ DR + + KG  + E+ + ++ 
Sbjct: 21  EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQG 96
             A   L G  + G  + V  ++    A++NR  G
Sbjct: 81  PLA-IGLTGQRLLGVPIIVQASQ----AEKNRLSG 110

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  106 bits (267), Expect = 8e-27
 Identities = 27/82 (32%), Positives = 40/82 (48%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
                 +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D     
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170

Query: 63  SARRNLQGYEINGRQLRVDFAE 84
            A   L G ++  ++L V  A 
Sbjct: 171 QAIAGLNGMQLGDKKLLVQRAS 192

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 82.0 bits (203), Expect = 4e-18
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRL-----VIDRETGKPKGYGFCEYKDE 58
          +  R ++VGNIP+  TEE +++       +          V+  +  + K + F E++  
Sbjct: 2  AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 59 ETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
          +    A     G    G+ L++    + +      E   
Sbjct: 62 DETTQA-MAFDGIIFQGQSLKIRRPHDYQPLPGMSENPS 99

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  104 bits (261), Expect = 1e-26
 Identities = 22/82 (26%), Positives = 44/82 (53%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           +++  R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E A
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118

Query: 62  LSARRNLQGYEINGRQLRVDFA 83
            +A  N+   E+ GR +RV+ A
Sbjct: 119 AAAIDNMNESELFGRTIRVNLA 140

>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 =  103 bits (258), Expect = 1e-26
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 7/99 (7%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           +  +  + V N+  D  E  L E+ R  G +    L  D+ TG+ KG+ F  +   E A 
Sbjct: 12  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            A   + G+  +   L V++A       +         G
Sbjct: 72  RAIAGVSGFGYDHLILNVEWA-------KPSTNSGPSSG 103

>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 =  104 bits (262), Expect = 2e-26
 Identities = 27/81 (33%), Positives = 40/81 (49%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
                 +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D     
Sbjct: 91  LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 150

Query: 63  SARRNLQGYEINGRQLRVDFA 83
            A   L G ++  ++L V  A
Sbjct: 151 QAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 83.0 bits (206), Expect = 7e-19
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 6/93 (6%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRL-----VIDRETGKPKGYGFCEYKDE 58
             R ++VGNIP+  TEE +++       +          V+  +  + K + F E++  
Sbjct: 2  GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 59 ETALSARRNLQGYEINGRQLRVDFAENDKGADR 91
          +    A     G    G+ L++    + +    
Sbjct: 62 DETTQA-MAFDGIIFQGQSLKIRRPHDYQPLPG 93

>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 =  103 bits (259), Expect = 3e-26
 Identities = 22/86 (25%), Positives = 40/86 (46%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
            + V N+ Y  + + L  +  + G V    +  DR T + +G+ F  + D+  A  A   
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131

Query: 68  LQGYEINGRQLRVDFAENDKGADRNR 93
           + G  ++GR+LRV  A   +  D + 
Sbjct: 132 MDGAVLDGRELRVQMARYGRPPDSHH 157

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  102 bits (256), Expect = 4e-26
 Identities = 22/86 (25%), Positives = 40/86 (46%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
            + V N+ Y  + + L  +  + G V    +  DR T + +G+ F  + D+  A  A   
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108

Query: 68  LQGYEINGRQLRVDFAENDKGADRNR 93
           + G  ++GR+LRV  A   +  D + 
Sbjct: 109 MDGAVLDGRELRVQMARYGRPPDSHH 134

>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 = 99.7 bits (249), Expect = 2e-25
 Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRE-TGKPKGYGFCEYKDEETA 61
                 + V NIP+ A + ++ E+    G + + RL      TG  +G+GF ++  ++ A
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71

Query: 62  LSARRNL-QGYEINGRQLRVDFAENDKGAD 90
             A   L     + GR+L +++A+++    
Sbjct: 72  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 =  100 bits (250), Expect = 2e-25
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 2/88 (2%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R V+VGN+ Y +T + L       G +    ++ D+ +G PKGY + E+ +  +  +A  
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-V 95

Query: 67  NLQGYEINGRQLRVDFA-ENDKGADRNR 93
            +      GR ++V     N  G     
Sbjct: 96  AMDETVFRGRTIKVLPKRTNMPGISSTD 123

>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 = 98.4 bits (246), Expect = 3e-25
 Identities = 19/79 (24%), Positives = 40/79 (50%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS    +++  +    T++ L+++C+  G +VS + ++D+ T K KGYGF ++     A
Sbjct: 1  GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 62 LSARRNLQGYEINGRQLRV 80
            A   L+   +  +  + 
Sbjct: 61 QKAVTALKASGVQAQMAKQ 79

>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 =  100 bits (252), Expect = 4e-25
 Identities = 22/80 (27%), Positives = 44/80 (55%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          + +  + V  +P D T+ +L  + R +GP+ + R++ D +TG   GY F ++  E  +  
Sbjct: 1  ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 64 ARRNLQGYEINGRQLRVDFA 83
          A + L G  +  ++L+V +A
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 81.1 bits (201), Expect = 4e-18
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V N+P   T++QL  I  + G +V   ++ D+ TG+P+G  F  Y   E A  A   L
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 69  QGYEING--RQLRVDFA 83
                 G  + L V  A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168

>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 = 97.7 bits (244), Expect = 6e-25
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGP--VVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          +++GN+ +  T+E L E    +G   ++  +   +R  G+ KG+       E ++     
Sbjct: 4  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 67 NLQGYEINGRQLRVDFAE 84
           L   E++G+   V  + 
Sbjct: 64 LLPKRELHGQNPVVTPSN 81

>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 =  103 bits (260), Expect = 6e-25
 Identities = 26/77 (33%), Positives = 41/77 (53%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V N+P   T++Q  E+ R  G +    LV    TG+ KGYGF EY  +++A  A+ +L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 69  QGYEINGRQLRVDFAEN 85
            G  +  R L V + + 
Sbjct: 158 LGKPLGPRTLYVHWTDA 174

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 84.6 bits (210), Expect = 2e-18
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
             R + +  +P D T +++ ++  +         +      K KG  F    + E A +
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEA 72

Query: 64 ARRNLQGYEINGRQLRVDFAEND 86
          A        +  R+L V     D
Sbjct: 73 AINAFHQSRLRERELSVQLQPTD 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 = 83.1 bits (206), Expect = 8e-18
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 2   ASSQHRCVFVGNIPYDATE-EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           A    RC+ V  +P    + + L      V      +L    + G+ KG+   EY+  E 
Sbjct: 180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEM 238

Query: 61  ALSARRNLQGYEINGRQLRVDFAE 84
           A  A++   G  + G  LRV F  
Sbjct: 239 AEEAQQQADGLSLGGSHLRVSFCA 262

>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 = 98.5 bits (246), Expect = 6e-25
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 3/95 (3%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           A +    ++VGN+P D   + + ++  + G +    L   R       + F E++D   A
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDA 74

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQG 96
             A     GY+ +G +LRV+F  + +G       G
Sbjct: 75  EDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 97.1 bits (242), Expect = 2e-24
 Identities = 18/98 (18%), Positives = 32/98 (32%), Gaps = 2/98 (2%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           + V    +  +  E  L ++CR+ G V    +++   T K  G     +     A    +
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAA 104
           NL    + G  +        KG  R +       G   
Sbjct: 67  NLHLTSVMGNIIHAQLD--IKGQQRMKYYELIVNGSYT 102

>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 = 98.3 bits (245), Expect = 2e-24
 Identities = 31/93 (33%), Positives = 47/93 (50%), Gaps = 2/93 (2%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V  IP    E QL ++    GP+ S ++V DRET + +GYGF +++   +A  A   L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            G+ I  ++L+V  A    G  R    G  G G
Sbjct: 105 NGFNILNKRLKVALAA--SGHQRPGIAGAVGDG 135

>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 = 96.0 bits (240), Expect = 2e-24
 Identities = 23/76 (30%), Positives = 46/76 (60%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG++  +  +E L    ++    +S  ++ D +TG  +GYGF  +  ++ A +A  ++
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 69 QGYEINGRQLRVDFAE 84
          QG ++NGR LR+++A 
Sbjct: 64 QGQDLNGRPLRINWAA 79

>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 = 96.4 bits (240), Expect = 3e-24
 Identities = 30/104 (28%), Positives = 49/104 (47%), Gaps = 5/104 (4%)

Query: 2   ASSQHRC-VFVGNIPYDATEEQLIEICREVGPVVSFRLVI--DRETGKPKGYGFCEYKDE 58
           + S   C +F+G IP     E+++E   +V   V   +V     +  K +G+ F EY+  
Sbjct: 3   SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62

Query: 59  ETALSARRNLQ--GYEINGRQLRVDFAENDKGADRNREQGRGGP 100
             A  ARR L     ++ G Q+ VD+AE +   D +  +   GP
Sbjct: 63  RAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  101 bits (254), Expect = 3e-24
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +++ N P   T+  + ++ +++  V     +        + + + +   +E A      L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 69  QGYEINGRQLRVDFA---ENDKGADRNREQGR 97
            G +I G  L    +   E  K  D    +GR
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR 211

>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 = 86.6 bits (215), Expect = 5e-19
 Identities = 12/84 (14%), Positives = 29/84 (34%), Gaps = 3/84 (3%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
            +   V V N+P    + ++ +  +  GP++   +       K   +   E+   + AL+
Sbjct: 39  RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALA 96

Query: 64  ARRNLQGYEINGRQLRVDFAENDK 87
           A        +   ++ V       
Sbjct: 97  AITKTHKV-VGQNEIIVSHLTECT 119

>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 = 79.6 bits (197), Expect = 1e-16
 Identities = 14/86 (16%), Positives = 36/86 (41%), Gaps = 3/86 (3%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLI-EICREVGPVVSFRLVIDR-ETGKPKGYGFCEYKDE 58
            A+ + R + + N+  +  +E L+ E     G +    +   + E        F  ++++
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264

Query: 59  ETALSARRNLQGYEINGRQLRVDFAE 84
           ++A  A   +    +  R++ V  A+
Sbjct: 265 DSAERA-LQMNRSLLGNREISVSLAD 289

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 98.5 bits (246), Expect = 8e-24
 Identities = 22/90 (24%), Positives = 42/90 (46%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S     ++VG++  D TE  L E     GP++S R+  D  T +  GY +  ++    A 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRN 92
            A   +    I G+ +R+ +++ D    ++
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRDPSLRKS 101

>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 = 75.8 bits (187), Expect = 6e-16
 Identities = 24/107 (22%), Positives = 42/107 (39%), Gaps = 6/107 (5%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+ N+      + L +     G ++S ++V D      KGYGF  ++ +E A  A   +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGP 115
            G  +N R++ V   ++ K     RE   G               G 
Sbjct: 164 NGMLLNDRKVFVGRFKSRK----EREAELGARAKEFYPYDVPDYAGS 206

>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 = 94.6 bits (236), Expect = 8e-24
 Identities = 22/99 (22%), Positives = 44/99 (44%), Gaps = 14/99 (14%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           SS    +++GN+    T + L ++  +        L +  +     GY F +Y D+  A+
Sbjct: 5   SSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAI 58

Query: 63  SARRNLQG-YEINGRQLRVDFAENDKGADRNREQGRGGP 100
            A   L G  E++G+ + VD++        +++    GP
Sbjct: 59  RAIETLSGKVELHGKIMEVDYS-------VSKKLRSSGP 90

>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 = 95.4 bits (238), Expect = 9e-24
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           + +++ N+    TE  L+ +           +     TG+ +G  F  + ++E A  A  
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRG 98
            + GY++ G+ L ++F +N K   R+     G
Sbjct: 86  LVNGYKLYGKILVIEFGKNKK--QRSSGPSSG 115

>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 = 95.1 bits (237), Expect = 9e-24
 Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 10/95 (10%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +F+G IP +  E+ L  +  E G +    ++ DR TG  KG  F  Y + E+AL A+  L
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 69  QGYEI---NGRQLRVDFAENDKGADRNREQGRGGP 100
              +      R ++V  A+       +  +G  GP
Sbjct: 76  HEQKTLPGMNRPIQVKPAD-------SESRGGSGP 103

>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 = 94.1 bits (235), Expect = 1e-23
 Identities = 16/77 (20%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR-ETGKPKGYGFCEYKDEETALSARRN 67
          V +G +  + T++ ++EI    G +    + ++R      KGY + E+++ + A  A ++
Sbjct: 7  VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 68 LQGYEINGRQLRVDFAE 84
          + G +I+G+++      
Sbjct: 67 MDGGQIDGQEITATAVL 83

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 96.1 bits (240), Expect = 2e-23
 Identities = 24/85 (28%), Positives = 43/85 (50%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+E+   +   +G + S +LV D+ TG+  GYGF  Y D + A  A   L
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 69 QGYEINGRQLRVDFAENDKGADRNR 93
           G  +  + ++V +A     + R+ 
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDA 89

>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 = 79.2 bits (196), Expect = 2e-17
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           ++V  +P   T+++L ++  + G +++ R+++D+ TG  +G GF  +     A  A + L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 69  QGYEING--RQLRVDFA 83
            G + +G    + V FA
Sbjct: 151 NGQKPSGATEPITVKFA 167

>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 = 93.5 bits (233), Expect = 2e-23
 Identities = 18/94 (19%), Positives = 43/94 (45%), Gaps = 7/94 (7%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S+    +F+GN+  + +  +L     E+        V+D  TG  + +G+ +++  E   
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQG 96
            A   L G ++ G +++++  +      R+  +G
Sbjct: 73  KA-LELTGLKVFGNEIKLEKPK-----GRDGTRG 100

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 97.4 bits (243), Expect = 2e-23
 Identities = 27/96 (28%), Positives = 43/96 (44%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           A +    V+VG+I Y+  E+ + +     GP+ S  +  D  T K KG+ F EY+  E A
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
             A   +    + GR ++V    N   A    +Q  
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 92.0 bits (229), Expect = 2e-21
 Identities = 22/82 (26%), Positives = 43/82 (52%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           +     ++V ++  D +++ +  +    G + S  L  D  TGK KGYGF EY+  +++ 
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ 181

Query: 63  SARRNLQGYEINGRQLRVDFAE 84
            A  ++  +++ G+ LRV  A 
Sbjct: 182 DAVSSMNLFDLGGQYLRVGKAV 203

>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 = 95.7 bits (239), Expect = 3e-23
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 6/88 (6%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
                 R +   N+ ++ TE++L E+  +   +         + GK KG  + E+K E  
Sbjct: 94  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEAD 148

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKG 88
           A       QG EI+GR + + +   +KG
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYT-GEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 92.7 bits (231), Expect = 4e-22
 Identities = 17/95 (17%), Positives = 41/95 (43%), Gaps = 4/95 (4%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S+    +F+GN+  + +  +L     E+        V+D  TG  + +G+ +++  E   
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLE 68

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
            A   L G ++ G +++++  +      +     R
Sbjct: 69  KA-LELTGLKVFGNEIKLEKPKGRD--SKKVRAAR 100

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 93.9 bits (234), Expect = 3e-23
 Identities = 22/102 (21%), Positives = 48/102 (47%), Gaps = 5/102 (4%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           + +     +F+G +  +  E+ L  +  + GP+    L+ DR T K +G+ F  +++   
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60

Query: 61  ALSARRNLQGYEINGRQLRVDFA----ENDKGADRNREQGRG 98
           A +A +++ G  ++G+ ++V+ A        G  R     R 
Sbjct: 61  AKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRN 102

>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 = 92.8 bits (231), Expect = 6e-23
 Identities = 29/99 (29%), Positives = 49/99 (49%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           +S H  VFVG++  + T E +       G +   R+V D  TGK KGYGF  + ++  A 
Sbjct: 12  TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           +A + + G  + GRQ+R ++A     A ++  +      
Sbjct: 72  NAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110

>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 = 91.9 bits (229), Expect = 8e-23
 Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 5/100 (5%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP---KGYGFCEYKDE 58
           SS    +F+ N+ +  TEE L  +  +VG + S  +   +         G+GF EYK  
Sbjct: 1  GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 59 ETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRG 98
          E A  A + LQG+ ++G +L V  +E  +          G
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISE--RATKPASGPSSG 98

>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 = 94.1 bits (235), Expect = 9e-23
 Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R ++VGN+    TE+ L +  +  GP+ + +++ID+   K   Y F EY     A  A +
Sbjct: 1  RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 67 NLQGYEINGRQLRVDFAENDKGADR 91
           L G +I    +++++A   + +  
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSS 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 = 89.1 bits (222), Expect = 5e-21
 Identities = 23/76 (30%), Positives = 46/76 (60%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FVG++  +  +E L    ++    +S  ++ D +TG  +GYGF  +  ++ A +A  ++
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 69  QGYEINGRQLRVDFAE 84
           QG ++NGR LR+++A 
Sbjct: 150 QGQDLNGRPLRINWAA 165

>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 = 91.1 bits (227), Expect = 1e-22
 Identities = 26/84 (30%), Positives = 42/84 (50%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
             H  VFVG++  + T   +       G +   R+V D  TGK KGYGF  + ++  A 
Sbjct: 3  LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 63 SARRNLQGYEINGRQLRVDFAEND 86
          +A + + G  + GRQ+R ++A   
Sbjct: 63 NAIQQMGGQWLGGRQIRTNWATRK 86

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 93.1 bits (231), Expect = 2e-22
 Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGP--VVSFRLVIDRETGKPKGYGFCEYKDEE 59
             ++   V+VG+  +  T++QLI++ R +G   VV  +   +R  G+ KGY       E 
Sbjct: 51  LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110

Query: 60  TALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           +       L G  +NG ++ V  A   +   +   Q R   
Sbjct: 111 SVHKLLELLPGKVLNGEKVDVRPA-TRQNLSQFEAQARKRE 150

>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 = 90.8 bits (226), Expect = 2e-22
 Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 9/98 (9%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            S  + ++V N+    +EE + +    + P    R+       K + Y F  + + E A
Sbjct: 11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDA 64

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
          + A + L G  ++G  + V  A   K  D++      G
Sbjct: 65 VEAMKALNGKVLDGSPIEVTLA---KPVDKDSSGPSSG 99

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 90.5 bits (225), Expect = 2e-22
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEET 60
                + + NI      + ++          V + RL+ D++T + +G+ F +      
Sbjct: 6  HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 61 ALSARRNLQGYE----INGRQLRVDFA 83
          A    + LQ       I+G+ + VDFA
Sbjct: 66 ASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 90.0 bits (224), Expect = 5e-22
 Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 9/100 (9%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           + S  + + V NIP+   +  L ++  + G ++   ++ +      KG+GF  +++   A
Sbjct: 11  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 68

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
             AR  L G  + GR++ V+ A         R     GP 
Sbjct: 69  DRAREKLHGTVVEGRKIEVNNA-------TARVMTNSGPS 101

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 89.4 bits (222), Expect = 7e-22
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 8/89 (8%)

Query: 7  RCVFVGNIPY------DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          + + V   P          ++ L  +  + G VV+    ID  TGK KG+ F E      
Sbjct: 7  QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66

Query: 61 ALSARRNLQGYEINGR-QLRVD-FAENDK 87
          A    ++  G  ++ + +L +    + ++
Sbjct: 67 AKKIIKSFHGKRLDLKHRLFLYTMKDVER 95

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 89.3 bits (222), Expect = 8e-22
 Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           V+VGN+   A + +L       GP+ +  +  +     P G+ F E++D   A  A R L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            G  I G ++RV+ +    G  R     R    
Sbjct: 58  DGKVICGSRVRVELS---TGMPRRSRFDRPPAR 87

>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 = 89.3 bits (222), Expect = 9e-22
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V N+ +  ++  + E+  E G +    +  DR +G+  G     ++ +  AL A +  
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 90

Query: 69  QGYEINGRQLRVDFAEN 85
            G  ++GR + +    +
Sbjct: 91  NGVPLDGRPMNIQLVTS 107

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 88.6 bits (220), Expect = 1e-21
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 10/95 (10%)

Query: 1   MASSQHRCVFVGNIP------YDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCE 54
            A      + V N+P       +  +  + +I  + G + +       E GK KGY F E
Sbjct: 10  EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLE 67

Query: 55  YKDEETALSARRNLQGYEINGR-QLRVD-FAENDK 87
           Y     A+ A +N  GY+++ +   RV+ F + DK
Sbjct: 68  YASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102

>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 = 88.1 bits (219), Expect = 2e-21
 Identities = 12/76 (15%), Positives = 32/76 (42%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           + V N+P+  + +++++       +     +   E G P G     ++  + A +A  +
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 68 LQGYEINGRQLRVDFA 83
          L    I  R++++   
Sbjct: 77 LNDRPIGSRKVKLSGP 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 87.2 bits (216), Expect = 4e-21
 Identities = 27/87 (31%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
            +     V+VGN+P DA    L    RE+G  V  RL        P+   F  Y D   
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQG----PRRRAFLHYPDSAA 68

Query: 61 ALSARRNLQGYEINGRQLRVDFAENDK 87
          A  A   LQG  +    LRV  A   +
Sbjct: 69 AQQAVSCLQGLRLGTDTLRVALARQQR 95

>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 = 87.4 bits (217), Expect = 4e-21
 Identities = 12/76 (15%), Positives = 32/76 (42%)

Query: 8  CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           + V N+P+  + +++++       +     +   E G P G     ++  + A +A  +
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 68 LQGYEINGRQLRVDFA 83
          L    I  R++++   
Sbjct: 77 LNDRPIGSRKVKLVLG 92

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 88.4 bits (219), Expect = 7e-21
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
            +      V+VGN+  +  + +L       GP+ S  +  +     P G+ F E++D   
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRD 122

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDK 87
           A  A R L G  + G ++RV+ +  +K
Sbjct: 123 AADAVRELDGRTLCGCRVRVELSNGEK 149

>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 = 86.2 bits (214), Expect = 9e-21
 Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 5/93 (5%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          +S     +++G++     E  +      +G  V+S +++ +R TG P GY F E+ D  T
Sbjct: 5  SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64

Query: 61 ALSARRNLQGYEING----RQLRVDFAENDKGA 89
          A      + G  + G    ++ ++++A     +
Sbjct: 65 AEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 86.7 bits (215), Expect = 9e-21
 Identities = 18/84 (21%), Positives = 45/84 (53%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           +   +   +F+ ++P + T+  L       G V+S ++ ID++T   K +GF  + + ++
Sbjct: 35  IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94

Query: 61  ALSARRNLQGYEINGRQLRVDFAE 84
           A  A + + G+++  ++L+V   +
Sbjct: 95  AQVAIKAMNGFQVGTKRLKVQLKK 118

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 87.0 bits (216), Expect = 1e-20
 Identities = 15/87 (17%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + V N+ +  ++  + E+  E G +    +  DR +G+  G     ++    AL A +  
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQY 96

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQ 95
           +G  ++GR + +    +    + +   
Sbjct: 97  KGVPLDGRPMDIQLVASQIDLEHHHHH 123

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 28/98 (28%), Positives = 43/98 (43%), Gaps = 13/98 (13%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
            +Q   +FVGN+P D TEE++ ++  + G      +       K KG+GF   +    A 
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAE 65

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
            A+  L    + G+QLRV FA        +      GP
Sbjct: 66  IAKVELDNMPLRGKQLRVRFA-------CHSASLTSGP 96

>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 = 85.4 bits (212), Expect = 2e-20
 Identities = 25/93 (26%), Positives = 38/93 (40%), Gaps = 15/93 (16%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           + VGNI    T ++L     E GPV+   +V        K Y F   +  E A+ A R L
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGL 64

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
              E  G+++ V  +        +R +   GP 
Sbjct: 65  DNTEFQGKRMHVQLS-------TSRLRTASGPS 90

>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 = 85.2 bits (211), Expect = 2e-20
 Identities = 18/100 (18%), Positives = 34/100 (34%), Gaps = 14/100 (14%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           SS    + V N+P D+  +++ ++ ++      +         + K   F    + E A 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCY-------VDRNKRTAFVTLLNGEQAQ 54

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM 102
           +A +    Y   G+ L V     D            GP  
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPTDA-------LLCSGPSS 87

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 85.4 bits (212), Expect = 2e-20
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
             SQ + + V NIP+   +  L ++  + G ++   ++ +      KG+GF  +++   A
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 82

Query: 62  LSARRNLQGYEINGRQLRVDFAE 84
             AR  L G  + GR++ V+ A 
Sbjct: 83  DRAREKLHGTVVEGRKIEVNNAT 105

>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 = 85.4 bits (212), Expect = 3e-20
 Identities = 23/98 (23%), Positives = 53/98 (54%), Gaps = 7/98 (7%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
             +   +F+ ++P +  ++ L+++    G VVS ++ ID++T   K +GF  Y +  +A 
Sbjct: 22  GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQ 81

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           +A +++ G++I  ++L+V          R++   + GP
Sbjct: 82  AAIQSMNGFQIGMKRLKVQLK-------RSKNDSKSGP 112

>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 = 84.6 bits (210), Expect = 3e-20
 Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 3/98 (3%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVS-FRLVIDRETGKPKGYGFCEYKDEET 60
           SS    +F+GN+  +  E+ L +     G ++   +++ D +TG  KGY F  +   + 
Sbjct: 1  GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 61 ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRG 98
          + +A   + G  +  R + V +A   K   +      G
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSYAF--KKDSKGSGPSSG 96

>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 = 85.0 bits (211), Expect = 3e-20
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 11/102 (10%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
             ++ + +FV N+    TEE L +   + G +   +        K K Y F  + + + A
Sbjct: 7   GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGA 58

Query: 62  LSARRNLQGYEINGRQLRVDFA---ENDKGADRNREQGRGGP 100
           + A   + G ++ G  + + FA   +  +   + + Q   GP
Sbjct: 59  VKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 86.8 bits (215), Expect = 4e-20
 Identities = 15/94 (15%), Positives = 37/94 (39%), Gaps = 1/94 (1%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
                  + V N+ +  ++  + E+  E G +    +  DR +G+  G     ++    A
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADA 142

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQ 95
           L A +  +G  ++GR + +    +    + +   
Sbjct: 143 LKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 176

>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 = 86.0 bits (214), Expect = 6e-20
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FVG I  D   ++  E   + G ++  +L++D++TG+ +G+GF  Y   +         
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV-CQN 148

Query: 69  QGYEINGRQLRVDFAE 84
           +  +   R++ +  AE
Sbjct: 149 KFIDFKDRKIEIKRAE 164

>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 = 76.8 bits (190), Expect = 1e-16
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G + +D TE+ L E   + G V   +++ D  TG+ +G+GF  ++   +     +  
Sbjct: 6  MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT- 64

Query: 69 QGYEINGRQLRVDFAENDKGADRNR 93
            + ++G+ +    A      D+  
Sbjct: 65 -QHILDGKVIDPKRAIPRDEQDKTG 88

>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 = 84.4 bits (209), Expect = 6e-20
 Identities = 22/103 (21%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            +S   C  + NIP+  T+  +++    +    +   V+    G+  G    ++K+E+ A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 62  LSARRNLQGYEINGRQLRVDFA---ENDKGADRNREQGRGGPG 101
             + R L   ++NGR+  V      +  +       QG+ GP 
Sbjct: 71  RKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPS 112

>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 = 83.8 bits (208), Expect = 7e-20
 Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           VFVG I     E ++       G V   +++ DR TG  KGYGF  + ++        + 
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES- 69

Query: 69  QGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
                +G++L++  A   +  + +    +  P
Sbjct: 70  -QINFHGKKLKLGPAI--RKQNLSTYHVQPRP 98

>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 = 83.0 bits (206), Expect = 9e-20
 Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 15/101 (14%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
            +S     +FVGN+    T ++L  +    G V+   +V        K Y F   + E  
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEAD 55

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           A +A   L G E+ G+++ V+ +          ++  G   
Sbjct: 56  AKAAIAQLNGKEVKGKRINVELS-------TKGQKKSGPSS 89

>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 = 86.6 bits (215), Expect = 1e-19
 Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FVG I  D  E  L +   + G +    ++ DR +GK +G+ F  + D ++        
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ- 165

Query: 69  QGYEINGRQLRVDFAE--NDKGADRNREQGR 97
           + + +NG    V  A    +  +  + ++GR
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 78.5 bits (194), Expect = 5e-17
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
             Q R +F+G + ++ T+E L     + G +    ++ D  T + +G+GF  Y   E  
Sbjct: 9  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68

Query: 62 LSARRNLQGYEINGRQLRVDFA 83
           +A    + ++++GR +    A
Sbjct: 69 DAAMNA-RPHKVDGRVVEPKRA 89

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 82.7 bits (205), Expect = 2e-19
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          A  +    ++GNIP+ ATE  LI + +  G ++ F+          KG  F +Y   E A
Sbjct: 23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH------YPEKGCCFIKYDTHEQA 76

Query: 62 LSARRNLQGYEINGRQLRVDFA 83
                L  +   GR LR  + 
Sbjct: 77 AVCIVALANFPFQGRNLRTGWG 98

>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 = 82.3 bits (204), Expect = 3e-19
 Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+ N+      + L +     G ++S ++V D      KGYGF  ++ +E A  A   +
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65

Query: 69 QGYEINGRQLRVDFAENDKGADRNREQG 96
           G  +N R++ V   ++ K  +R  E G
Sbjct: 66 NGMLLNDRKVFVGRFKSRK--EREAELG 91

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 81.8 bits (202), Expect = 5e-19
 Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 11/94 (11%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
            ++R + + N+P   + + L ++ RE     +F       T    G G  E+  EE  + 
Sbjct: 27  KRYR-ITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILVE 82

Query: 64  ARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
           A   L   E  G  + V+        D N    R
Sbjct: 83  ALERLNNIEFRGSVITVE-------RDDNPPPIR 109

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 81.2 bits (201), Expect = 7e-19
 Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 4/103 (3%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           A      VFV N+ Y    ++L E+    G VV   ++ D++ GK +G G   ++    A
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEA 69

Query: 62  LSARRNLQGYEINGRQLRVDFAE--NDKGADRNREQ-GRGGPG 101
           + A     G  +  R + V   E    KG     E+  + GP 
Sbjct: 70  VQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPS 112

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 79.4 bits (196), Expect = 3e-18
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 5/95 (5%)

Query: 5   QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
           ++R V++   P DAT + + E   + G V++ ++         KG  F  +   E+A   
Sbjct: 10  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKF 68

Query: 65  RRNLQGYEINGRQLRVDFAENDKGADRN--REQGR 97
                G +     L + F + D  A +N  R+Q +
Sbjct: 69  -VETPGQKYKETDLLILFKD-DYFAKKNEERKQNK 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 = 79.5 bits (196), Expect = 3e-18
 Identities = 21/95 (22%), Positives = 34/95 (35%), Gaps = 8/95 (8%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
           S++R V V  +P   + + L +  RE G V    +  D       G G  E+  +E    
Sbjct: 14  SENR-VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTY 65

Query: 64  ARRNLQGYEINGRQLRVDFAENDKGADRNREQGRG 98
           A R L   +    +    +        R+   GR 
Sbjct: 66  AVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRS 100

>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 = 82.8 bits (204), Expect = 3e-18
 Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 3/104 (2%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGP--VVSFRLVIDRETGKPKGYGFCEYKDEET 60
           + +   +++GN+ +  T+E L E    +G   ++  +   +R  G+ KG+       E +
Sbjct: 65  TGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEAS 124

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAA 104
           +      L   E++G+   V    N +   +   Q R       
Sbjct: 125 SKKLMDLLPKRELHGQNPVVTPV-NKQFLSQFEMQSRKTTQSGQ 167

>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 = 78.4 bits (194), Expect = 5e-18
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            ++VG +  + +   L       G + +   V      K   + + +Y+  + A +A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

Query: 67 NLQGYEING--RQLRVDFAENDKGA 89
           ++G+ + G  R+LRVDFA++   +
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 78.2 bits (193), Expect = 5e-18
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRL-----VIDRETGKPKGYGFCEYKDEE 59
            R ++VGNIP+  TEE +++       +          V+  +  + K + F E++  +
Sbjct: 5  SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64

Query: 60 TALSARRNLQGYEINGRQLRV 80
              A     G    G+ L++
Sbjct: 65 ETTQA-MAFDGIIFQGQSLKI 84

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 78.3 bits (193), Expect = 6e-18
 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 3/87 (3%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
            + R + + NIP     E L  +  + G V S   V               Y  ++ A 
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQAR 68

Query: 63 SARRNLQGYEINGRQLRVDFAENDKGA 89
           A   L G+++    L+V +  ++  A
Sbjct: 69 QALDKLNGFQLENFTLKVAYIPDEMAA 95

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 78.0 bits (193), Expect = 7e-18
 Identities = 27/95 (28%), Positives = 50/95 (52%), Gaps = 1/95 (1%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          + S+   +FVG IP++  E +L E  ++ G V    ++ D E  +P+G+GF  ++DE++ 
Sbjct: 6  SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSV 65

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQG 96
            A  N+  ++I G+++ V  AE           G
Sbjct: 66 DQA-VNMHFHDIMGKKVEVKRAEPRDSKSSGPSSG 99

>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 = 78.0 bits (193), Expect = 9e-18
 Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 9/100 (9%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
           +   Q   ++V N+     +E+L +     G + S +++   E G+ KG+GF  +   E 
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEE 67

Query: 61  ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           A  A   + G  +  + L V  A       + +E+ + GP
Sbjct: 68  ATKAVTEMNGRIVATKPLYVALA-------QRKEERQSGP 100

>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 = 78.1 bits (193), Expect = 1e-17
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
              +    +FVG +PY  T+  L +     G +    ++ DR+TGK +GYGF    D   
Sbjct: 12  QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71

Query: 61  ALSARRNLQGYEINGRQLRVDFA---ENDKGADRNREQGRGGP 100
           A  A ++     I+GR+  V+ A      +        G  GP
Sbjct: 72  AERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113

>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 = 82.0 bits (203), Expect = 1e-17
 Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           +Q   +FVGN+P D TEE    +    G      +  DR      G+GF   +    A 
Sbjct: 19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAE 72

Query: 63 SARRNLQGYEINGRQLRVDFAENDK 87
           A+  L G  +  R LR+ FA +  
Sbjct: 73 IAKAELDGTILKSRPLRIRFATHGA 97

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 68.9 bits (169), Expect = 3e-13
 Identities = 24/123 (19%), Positives = 41/123 (33%), Gaps = 10/123 (8%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
             ++    + V N+    + E L +   + GPV    +V+D + G+  G GF E+  +  
Sbjct: 91  RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPP 149

Query: 61  ALSARRNLQGYEI----NGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPA 116
           A  A               R + V+  E       + E G     M       K+   P 
Sbjct: 150 ARKALERCGDGAFLLTTTPRPVIVEPMEQ-----FDDEDGLPEKLMQKTQQYHKEREQPP 204

Query: 117 IHG 119
              
Sbjct: 205 RFA 207

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 10/85 (11%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +FV   P D  E +L EI    GP+   ++          G+ F E+++ E+A  A   +
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85

Query: 69  QGYEINGRQLRVDFAENDKGADRNR 93
            G     + L V +++    A R R
Sbjct: 86  HGKSFANQPLEVVYSK--LPAKRYR 108

>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 = 77.0 bits (190), Expect = 2e-17
 Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 12/92 (13%)

Query: 9   VFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           VF+GN+      +  +  I  + G V    +         KGY F +Y +E  A +A   
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLG 81

Query: 68  LQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
             G  + G+ L ++ A        +R     G
Sbjct: 82  ENGRVLAGQTLDINMA---GEPKPDRSGPSSG 110

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 11/92 (11%)

Query: 9  VFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +F+GN+P  + ++E L  I    G ++   +           +GF ++ + ++   A   
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEC 64

Query: 68 LQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
                 G++L ++ + ++     +   G  G
Sbjct: 65 ESQEMNFGKKLILEVSSSNARPQFDH--GDHG 94

>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 = 78.8 bits (195), Expect = 2e-17
 Identities = 22/96 (22%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP--KGYGFCEYKDEETA 61
          S    +FVG +P   +E+ L E+  + G V    ++ DR    P  KG  F  +   + A
Sbjct: 1  SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
          L A+  L   ++          +       N  + R
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR 96

>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 = 69.2 bits (170), Expect = 6e-14
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           + + R +F+G I    TE  +  +    G +   R++     G  +G  F  +     A 
Sbjct: 92  AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQ 150

Query: 63  SARRNLQGYEI---NGRQLRVDFAE 84
           +A + +   +        + V FA+
Sbjct: 151 TAIKAMHQAQTMEGCSSPMVVKFAD 175

>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 = 77.0 bits (190), Expect = 2e-17
 Identities = 19/100 (19%), Positives = 39/100 (39%), Gaps = 13/100 (13%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           +S ++  V+ G I    T++ + +     G ++  R+  +      KGY F  +   E+A
Sbjct: 21  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESA 74

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
             A  ++ G  I G  ++  +        +       GP 
Sbjct: 75  AHAIVSVNGTTIEGHVVKCYWG-------KESPDMTSGPS 107

>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 = 83.4 bits (205), Expect = 3e-17
 Identities = 31/118 (26%), Positives = 50/118 (42%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           + +FV  + YD TE +L       GP+    +V  + +GKP+GY F EY+ E    SA +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHH 124
           +  G +I+GR++ VD             +  GG G          +        S + 
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 75.5 bits (186), Expect = 4e-17
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 8  CVFVGNIP------YDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           + V N+P       +  +  + +I  + G + +       E GK KGY F EY     A
Sbjct: 3  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAHA 60

Query: 62 LSARRNLQGYEINGR-QLRV 80
          + A +N  GY+++ +   RV
Sbjct: 61 VDAVKNADGYKLDKQHTFRV 80

>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 = 76.0 bits (187), Expect = 6e-17
 Identities = 21/102 (20%), Positives = 45/102 (44%), Gaps = 6/102 (5%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
                CV++  +P++A  + +I+  +++  V     +     GK  G GF E+++E    
Sbjct: 22  HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 81

Query: 63  SA-RRNLQGYEINGRQLRVDFA---ENDKGADRNREQGRGGP 100
           +A  R+     +  R ++V         +  D  R++ + GP
Sbjct: 82  AALCRH--KQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGP 121

>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 = 76.0 bits (187), Expect = 1e-16
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSF-----RLVIDRETGKPKGYGFCEYKDEETALS 63
           ++V N+     E+ L  I        S        +   + G+ KG  F    +E+ A  
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 64  ARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
           A +   GY + G+ + V FA + +     +E  R
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141

>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 = 77.8 bits (191), Expect = 1e-16
 Identities = 16/80 (20%), Positives = 27/80 (33%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
                 +   N P + TEE   EIC E+G      + +     +    G  E+  +  AL
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 63  SARRNLQGYEINGRQLRVDF 82
                L  Y++        +
Sbjct: 180 ETLGFLNHYQMKNPNGPYPY 199

>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 = 57.0 bits (137), Expect = 2e-09
 Identities = 11/92 (11%), Positives = 27/92 (29%), Gaps = 6/92 (6%)

Query: 9  VFVGNIPYDA-TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          + V  +       +++  +    G V   + +  +      G    E  D      A  +
Sbjct: 7  LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61

Query: 68 LQGYEINGRQLRVDFAENDKGADRNREQGRGG 99
          L    + G+++ V  ++              G
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDG 93

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 74.5 bits (183), Expect = 2e-16
 Identities = 21/97 (21%), Positives = 34/97 (35%), Gaps = 8/97 (8%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
           S++R V V  +P   + + L +  RE G V    +  D       G G  E+  +E    
Sbjct: 15  SENR-VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTY 66

Query: 64  ARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           A R L   +    +    +        R+   GR   
Sbjct: 67  AVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 4/102 (3%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S     +FVG++  D  +  L E   +V P      V+  +TG  KGYGF ++ DE    
Sbjct: 6   SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQK 65

Query: 63  SARRNLQG-YEINGRQLRVDFAENDKGADRNREQGRGGPGMA 103
            A    QG   +  + +R+  A          +    GP   
Sbjct: 66  RALTECQGAVGLGSKPVRLSVAIPK---ASRVKPVESGPSSG 104

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 73.1 bits (180), Expect = 3e-16
 Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 6/97 (6%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS  R VFV   P      QL E     GPV    +V+D++ G    +   E  D    
Sbjct: 4  GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKGV---FAIVEMGDVGAR 58

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRG 98
           +   +   + + G +LRV   E  +      +  +G
Sbjct: 59 EAV-LSQSQHSLGGHRLRVRPREQKEFQSPASKSPKG 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 = 73.1 bits (180), Expect = 4e-16
 Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 9/80 (11%)

Query: 9  VFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +F+GN+P  + ++E L  I    G ++   +           +GF ++ + ++   A   
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76

Query: 68 LQGYEINGRQLRVDFAENDK 87
                 G++L ++ + ++ 
Sbjct: 77 ESQEMNFGKKLILEVSSSNA 96

>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 = 73.1 bits (180), Expect = 6e-16
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
           +++ N+P    E++L  + +  G V+S R++ D  +G  +G GF   +  E   +   + 
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 69  QGYEINGRQLRVDFAE 84
            G  I          E
Sbjct: 87  NGKFIKTPPGVSAPTE 102

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 71.3 bits (176), Expect = 8e-16
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  + T E +     + G V    L+ D+ T + +G+GF  ++ E+         
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 69 QGYEINGRQLRVDFA 83
            +EIN + +    A
Sbjct: 61 HFHEINNKMVECKKA 75

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 72.2 bits (177), Expect = 1e-15
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 9/95 (9%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R + +  +P D TE ++I +    G V +  ++      K K   F E   EE A +   
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 70

Query: 67  NLQ--GYEINGRQLRVDFAEN-DKGADRNREQGRG 98
                   + G+ + + F+ + +   D +  Q R 
Sbjct: 71  YYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQARA 105

>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 = 70.6 bits (174), Expect = 1e-15
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  D  EE++ E     G V S  L +D +T K +G+ F  +K+EE         
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 69 QGYEINGRQLRVDFA 83
          + + +   +  +  A
Sbjct: 61 KYHNVGLSKCEIKVA 75

>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 = 71.4 bits (175), Expect = 2e-15
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 5  QHRCVFVGNIPYDATEEQLI---EICREVGPVVSFRLVIDRETGK---PKGYGFCEYKDE 58
          Q   VFV  +     + +++   E   + G +    +           P    +  Y   
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 59 ETALSARRNLQGYEINGRQLRVDFA 83
          E AL A + +    ++GR L+    
Sbjct: 74 EDALRAIQCVNNVVVDGRTLKASLG 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 70.9 bits (174), Expect = 2e-15
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 8/83 (9%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            V +  +     E  L+E  +E GP+    ++        K     E++D   A +A  
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVN 75

Query: 67 NLQG--YEINGRQLRVDFAENDK 87
                  I G    V+++ + K
Sbjct: 76 YAADNQIYIAGHPAFVNYSTSQK 98

>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 = 71.0 bits (174), Expect = 2e-15
 Identities = 14/95 (14%), Positives = 31/95 (32%), Gaps = 9/95 (9%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             V V  +     E  L+E   + G +    ++        K     E+++ ++A     
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVEFENIDSAKECVT 69

Query: 67  NLQ--GYEINGRQLRVDFAENDK-GADRNREQGRG 98
                   I G+Q   +++ + +     N     G
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 73.4 bits (180), Expect = 3e-15
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
                  + + NIP   +EE L  +    G VV       +   K +     +    E A
Sbjct: 116 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEA 171

Query: 62  LSARRNLQGYEI-NGRQLRVDFAEN 85
           + A  +L  +++     LRV F+++
Sbjct: 172 VQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 61.5 bits (149), Expect = 4e-11
 Identities = 20/119 (16%), Positives = 42/119 (35%), Gaps = 6/119 (5%)

Query: 9   VFVGNI-PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
           + V N+ P   T + L  +    G V   +++ ++     K     +  D   A  A  +
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 68  LQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHGESVHHQP 126
           L G++++G+ +R+  +++         Q   G        P  +   P          P
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

>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 = 71.1 bits (174), Expect = 3e-15
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 9/94 (9%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R + +  +P D TE ++I +    G V +  ++      K K   F E   EE A +   
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 85

Query: 67  --NLQGYEINGRQLRVDFAEN-DKGADRNREQGR 97
                   + G+ + + F+ + +   D +  Q R
Sbjct: 86  YYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQAR 119

>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 = 69.9 bits (172), Expect = 4e-15
 Identities = 15/82 (18%), Positives = 41/82 (50%), Gaps = 7/82 (8%)

Query: 9  VFVGNIPYDATEEQLIEICREV----GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          +++ N+     +++L +    +    G ++   +     + K +G  F  +K+  +A +A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 67

Query: 65 RRNLQGYEINGRQLRVDFAEND 86
           R++QG+    + +R+ +A+ D
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTD 89

>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 = 69.9 bits (171), Expect = 6e-15
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 8/79 (10%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R + +  +P + TE ++I +    G V +  ++      K K   F E   EE A++   
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVN 69

Query: 67 --NLQGYEINGRQLRVDFA 83
            +     +  + + + ++
Sbjct: 70 YYSAVTPHLRNQPIYIQYS 88

>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 = 69.2 bits (170), Expect = 7e-15
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA-R 65
            ++VG +    TE  L     + G + +  +V        +   F ++   + A  A  
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAE 66

Query: 66 RNLQGYEINGRQLRVDFA 83
          ++     +NGR+L V + 
Sbjct: 67 KSFNKLIVNGRRLNVKWG 84

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 67.5 bits (166), Expect = 2e-14
 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G + +  T+E L E   + G V    ++ D  T + +G+GF  + D+          
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 69 QGYEINGRQLRVDFA 83
            +E++ + +    A
Sbjct: 62 SRHELDSKTIDPKVA 76

>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 = 68.6 bits (168), Expect = 2e-14
 Identities = 12/79 (15%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          ++    V +  +P+  ++E++++    +  V +   +     G+  G  F ++  +E A 
Sbjct: 12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 63 SA-RRNLQGYEINGRQLRV 80
           A +++     I  R + +
Sbjct: 72 KALKKH--KERIGHRYIEI 88

>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 = 68.0 bits (167), Expect = 2e-14
 Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 9/100 (9%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           A  +   + V  +P+  TE+ L E     G V+  ++  D +TG  KG+GF  + + ET 
Sbjct: 11  AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           +          I+GR               +++    GP 
Sbjct: 71  VKVMSQRH--MIDGRWCDCKLPN-------SKQSQDSGPS 101

>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 = 71.6 bits (175), Expect = 2e-14
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 5/86 (5%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
                   + + NIP   +EE L  +    G VV       +   K +     +    E 
Sbjct: 146 NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEE 201

Query: 61  ALSARRNLQGYEI-NGRQLRVDFAEN 85
           A+ A  +L  +++     LRV F+++
Sbjct: 202 AVQALIDLHNHDLGENHHLRVSFSKS 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 = 58.5 bits (141), Expect = 7e-10
 Identities = 21/127 (16%), Positives = 46/127 (36%), Gaps = 6/127 (4%)

Query: 1   MASSQHRCVFVGNI-PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
           +A + +  + V N+ P   T + L  +    G V   +++ ++     K     +  D  
Sbjct: 29  LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGN 83

Query: 60  TALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGMAAIVDPQKQLGGPAIHG 119
            A  A  +L G++++G+ +R+  +++         Q   G        P  +   P    
Sbjct: 84  QAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKN 143

Query: 120 ESVHHQP 126
                 P
Sbjct: 144 FQNIFPP 150

>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 = 67.7 bits (166), Expect = 3e-14
 Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 6/96 (6%)

Query: 4   SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
            + R +FVG +    +EE ++ + +  G +    ++     G  KG  F ++     A +
Sbjct: 13  GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQA 71

Query: 64  ARRNLQGYEI---NGRQLRVDFAENDKGADRNREQG 96
           A   L G +        L V FA+ DK  +     G
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFADTDK--ESGPSSG 105

>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 = 67.3 bits (165), Expect = 4e-14
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           +    V +   P++ TE+ ++E    + P V+ R+V +   G   GY F ++ +EE   
Sbjct: 7  GTTCHTVKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNAH-GNKTGYIFVDFSNEEEVK 64

Query: 63 SA-RRNLQGYEINGRQLRV 80
           A + N     + GR + V
Sbjct: 65 QALKCN--REYMGGRYIEV 81

>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 = 67.9 bits (166), Expect = 4e-14
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 5/86 (5%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          +     V V  +P+ A E  + +    +  V +  L+ D   G+  G G  ++   +   
Sbjct: 13 NPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTF 70

Query: 63 SA-RRNLQGYEINGRQLRVDFAENDK 87
           A +RN     +  R + V  A   +
Sbjct: 71 EALKRN--RMLMIQRYVEVSPATERQ 94

>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 = 66.4 bits (163), Expect = 5e-14
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET-- 60
                +FVG + +D +++ L +   + G VV   + +D  TG+ +G+GF  +KD  +  
Sbjct: 8  EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVE 67

Query: 61 -ALSARRNLQGYEINGRQLRVDFA 83
            L  + +     ++GR +    A
Sbjct: 68 KVLDQKEH----RLDGRVIDPKKA 87

>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 = 68.3 bits (167), Expect = 5e-14
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 6/101 (5%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S+   CV +  +PY ATE  +      + P V   + I  + G+  G    E+   E A+
Sbjct: 43  STTGHCVHMRGLPYKATENDIYNFFSPLNP-VRVHIEIGPD-GRVTGEADVEFATHEEAV 100

Query: 63  SA-RRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM 102
           +A  ++     +  R + + F  +  GA       +   GM
Sbjct: 101 AAMSKD--RANMQHRYIEL-FLNSTTGASNGAYSSQVMQGM 138

>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 = 66.5 bits (162), Expect = 1e-13
 Identities = 19/105 (18%), Positives = 33/105 (31%), Gaps = 8/105 (7%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEI---CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
             +   V +  +P+  + E +      C     V     +  RE G+  G  F E + E+
Sbjct: 14  GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESED 72

Query: 60  TALSARRNLQGYEINGRQLRV---DFAENDKGADRNREQGRGGPG 101
               A +      +  R + V      E D     +      GP 
Sbjct: 73  DVKLALK-KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPS 116

>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 = 70.3 bits (171), Expect = 1e-13
 Identities = 30/221 (13%), Positives = 70/221 (31%), Gaps = 18/221 (8%)

Query: 9   VFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
           +++ N+     +++L +    I  + G ++    ++   + K +G  F  +K+  +A +A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNA 68

Query: 65  RRNLQGYEINGRQLRVDFAENDK-------GADRNREQGRGGPGMAAIVDPQKQLGGPAI 117
            R++QG+    + +R+ +A+ D        G    R++ R      +   P  +      
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 118 HGE----SVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLA 173
                  +V     G+     A  +M    G                      P  +   
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 174 KMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQ 214
           ++   Q+       +                   +L  LF 
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFN 229

>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 = 56.8 bits (136), Expect = 4e-09
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 5   QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
            +  +F+ N+P +  E  L  +  +       RLV  R         F E+ +E  A +A
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAA 260

Query: 65  RRNLQGYEI-NGRQLRVDFA 83
           R  LQG++I     +++ FA
Sbjct: 261 RDALQGFKITQNNAMKISFA 280

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 66.5 bits (162), Expect = 2e-13
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 7/85 (8%)

Query: 7   RCVFVGNIPYDATEEQLIEICREV----GPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           + V + NI  +  +E+L  +   +    G ++   +     +    G  +  +  +E+A 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDNSGKAYIVFATQESAQ 86

Query: 63  SARRNLQGYEINGRQLRVDFAENDK 87
           +     QGY   G  L + F+E  +
Sbjct: 87  AFVEAFQGYPFQGNPLVITFSETPQ 111

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 21/100 (21%), Positives = 34/100 (34%), Gaps = 15/100 (15%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           A  +   ++V     D T   L       G ++            P+   F  Y+  E+A
Sbjct: 11  APRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLS------MDPPRNCAFVTYEKMESA 62

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
             A   L G ++   QL+V+ A       R +     GP 
Sbjct: 63  DQAVAELNGTQVESVQLKVNIA-------RKQPMLDSGPS 95

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 65.6 bits (160), Expect = 2e-13
 Identities = 16/107 (14%), Positives = 34/107 (31%), Gaps = 16/107 (14%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
             +   N+P      ++ E     G +    L       +       E+ +   A  A R
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64

Query: 67  NLQGYEINGRQLRVDFA----------ENDKGADRNREQGRGGPGMA 103
           +L   + +   L +++A          + D   ++  E+   GP   
Sbjct: 65  HLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSSG 111

>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 = 64.3 bits (157), Expect = 4e-13
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          S+   CV +  +PY ATE  +      + P +   + I  + G+  G    E+   E A+
Sbjct: 12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPD-GRVTGEADVEFATHEDAV 69

Query: 63 SA-RRNLQGYEINGRQLRVDFAENDKGADR 91
          +A  ++     +  R + + F  +  G   
Sbjct: 70 AAMAKD--KANMQHRYVEL-FLNSTAGTSG 96

>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 = 65.3 bits (159), Expect = 4e-13
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S+    V +  +P+  T+E++++    +  V +   +     GK  G  F ++  +E A 
Sbjct: 39  SANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAE 98

Query: 63  SA-RRNLQGYEINGRQLRV 80
            A  ++     I  R + V
Sbjct: 99  KALGKH--KERIGHRYIEV 115

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 64.6 bits (158), Expect = 6e-13
 Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 8/99 (8%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
             Q R +F+G + ++ TEE L     + G +    ++ D  + + +G+GF  +       
Sbjct: 24  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 83

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           +A    + + I+GR +    A         RE+   GP 
Sbjct: 84  AAMAA-RPHSIDGRVVEPKRAV-------AREESGSGPS 114

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 64.5 bits (157), Expect = 8e-13
 Identities = 22/108 (20%), Positives = 39/108 (36%), Gaps = 9/108 (8%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYK 56
           ++      V +  +P+ AT E+++      C   G       V   + G+P G  F  + 
Sbjct: 18  LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFA 76

Query: 57  DEETALSARRNLQGYEINGRQLRVDF---AENDKGADRNREQGRGGPG 101
            EE A +A R      +  R + +     AE  +  +R         G
Sbjct: 77  CEEYAQNALR-KHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSSG 123

>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 = 63.4 bits (155), Expect = 1e-12
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 8/99 (8%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           + +   +FVG + +  T+E L     + G VV   ++ D+ T + +G+GF ++KD     
Sbjct: 13  ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
           +   + + + ++GR +              R     GP 
Sbjct: 73  TVLAS-RPHTLDGRNIDPKPCT-------PRGMQPSGPS 103

>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 = 63.0 bits (154), Expect = 1e-12
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
              S    +F+G + +  T+E L E   + G V    ++ D  T + +G+GF  + D+  
Sbjct: 20  HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79

Query: 61  ALSARRNLQGYEINGRQLRVDFA 83
                     +E++ + +    A
Sbjct: 80  VDKVLAQ-SRHELDSKTIDPKVA 101

>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 = 62.6 bits (152), Expect = 3e-12
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 6/102 (5%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEI---CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
                 +    +P+  T E ++     CR          +++R+ GK +G    E + E+
Sbjct: 8   VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQ 66

Query: 60  TALSARRNLQGYEINGRQLRVDFAEN-DKGADRNREQGRGGP 100
               A        +  R + V    N D  A     Q +  P
Sbjct: 67  DVQKALE-KHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSP 107

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 61.6 bits (149), Expect = 1e-11
 Identities = 16/101 (15%), Positives = 31/101 (30%), Gaps = 8/101 (7%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEI---CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
             +   V +  +P+  + E +      C           +  RE G+  G  F E   E+
Sbjct: 41  GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSED 99

Query: 60  TALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
               A +      +  R + V  +      + +      GP
Sbjct: 100 DVKMALK-KDRESMGHRYIEVFKS---HRTEMDWVLKHSGP 136

>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 = 59.6 bits (144), Expect = 3e-11
 Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 11/88 (12%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           ++Q   V  G +    +  QL+ +  + G V +  +  +      K Y F  Y+  E + 
Sbjct: 24  ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESK 77

Query: 63  SARRNLQGYEINGRQ-----LRVDFAEN 85
            A   L G E+         L ++F E 
Sbjct: 78  RAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 7/95 (7%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS    VFVG    D TE++L E   + G V+   +         + + F  + D++ A
Sbjct: 1  GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIA 55

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQG 96
           S     +   I G  + +  AE    ++     G
Sbjct: 56 QSLCG--EDLIIKGISVHISNAEPKHNSNSGPSSG 88

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          VFVG    D T E+L +   + G VV   +         + + F  + D++ A S     
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCG-- 66

Query: 69 QGYEINGRQLRVDFAE 84
          +   I G  + +  AE
Sbjct: 67 EDLIIKGISVHISNAE 82

>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 = 56.8 bits (136), Expect = 2e-09
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 5   QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
           ++R V++   P DAT + + E   + G V++ ++         KG  F  +   E+A   
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKF 166

Query: 65  RRNLQGYEINGRQLRVDFAE 84
                G +     L + F +
Sbjct: 167 VETP-GQKYKETDLLILFKD 185

>4eba_G RNA15, KLLA0F09383P; HAT domain, heat repeat, monkeytail, CLP1, PCF11, structural RNA binding protein complex; 3.30A {Kluyveromyces lactis} Length = 174

 Score = 55.2 bits (132), Expect = 4e-09
 Identities = 27/150 (18%), Positives = 49/150 (32%), Gaps = 7/150 (4%)

Query: 119 GESVHHQPIGLHIAITAAAVMTGALGAAQVGVQSNQNGIQSQLASPNDPLTLHLAKMSRN 178
               HH      +   +  V         VGV  N N     + +P   ++  L K+ ++
Sbjct: 3   SSHHHHHHSSGLVPRGSHMVEDVKFPWLPVGVDVNIN-----MTTPAMCISSELGKLQKD 57

Query: 179 QLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQMPILRQGPGH 238
           Q   ++  ++     +KE    LL   P L  A+ +  +  G+ +   L    +      
Sbjct: 58  QQMALLKVIQHFCKDDKETFVALLEEAPQLSYAIAELLLSNGVCSVDQLTQLAMASKQRP 117

Query: 239 PAQPLFQDGQQQVAQLPGLPPLAQKMQLMP 268
             Q           +   L  L Q +QL  
Sbjct: 118 EEQTDNTVEDGLDEEKVDL--LRQVLQLQD 145

>4eba_G RNA15, KLLA0F09383P; HAT domain, heat repeat, monkeytail, CLP1, PCF11, structural RNA binding protein complex; 3.30A {Kluyveromyces lactis} Length = 174

 Score = 42.1 bits (98), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 30/65 (46%)

Query: 483 LVPVNQVPKVEEVQYSEKQIPQISPDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQA 542
           L  +    K    + ++  +     + +  LL+QVL L    +  LP +++  V +L+Q 
Sbjct: 106 LTQLAMASKQRPEEQTDNTVEDGLDEEKVDLLRQVLQLQDSDIAMLPQDEKMAVWELKQR 165

Query: 543 LLRDQ 547
            ++ +
Sbjct: 166 AMKGE 170

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 52.2 bits (125), Expect = 9e-09
 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 20  EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR 79
           EE   E+  + G V     V D       G  + +++ EE A  A  +L     NG+ + 
Sbjct: 41  EEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 80  VDF 82
            + 
Sbjct: 100 AEL 102

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 51.5 bits (123), Expect = 2e-08
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVID--RETGKPKGYGFCEYKDEET---ALS 63
          VFVG +P D  E+++    R  GP+V         +    PKGY F  +++E +    + 
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 64 ARRNLQG---YEINGRQLRVDFAE 84
          A     G     ++   ++    +
Sbjct: 71 ACLEEDGKLYLCVSSPTIKDKPVQ 94

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.4 bits (120), Expect = 6e-08
 Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 15/94 (15%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
            + V N+ Y  T + L +I  + G V+           +       +Y D  +A  A+ +
Sbjct: 30  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 85

Query: 68  LQGYEI--NGRQLRVDFA---------ENDKGAD 90
           L G  I      LR+DF+          NDK  D
Sbjct: 86  LDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRD 119

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 51.3 bits (122), Expect = 7e-08
 Identities = 26/121 (21%), Positives = 43/121 (35%), Gaps = 15/121 (12%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
            + V N+ Y  T + L +I  + G V+           +       +Y D  +A  A+ +
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 103

Query: 68  LQGYEI--NGRQLRVDFA---------ENDKGADRNREQGRGGPGMAAIVDPQKQLGGPA 116
           L G  I      LR+DF+          NDK  D  R     G    ++        G +
Sbjct: 104 LDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGLS 163

Query: 117 I 117
           +
Sbjct: 164 V 164

>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 = 45.7 bits (108), Expect = 3e-06
 Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 9/93 (9%)

Query: 7   RCVFVGNIPYDA-TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
           R + + N+P+   ++  ++++    G + ++ L+      + K   F E +  E A++  
Sbjct: 26  RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETREDAMAMV 79

Query: 66  RNLQGY--EINGRQLRVDFAENDKGADRNREQG 96
            +         GR ++VD +E  K        G
Sbjct: 80  DHCLKKALWFQGRCVKVDLSEKYKKLVSGPSSG 112

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 44.4 bits (105), Expect = 5e-06
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 10/89 (11%)

Query: 7  RCVFVGNI--P---YDATEEQLIEICREVGPVVSFRLVIDRETGKPK---GYGFCEYKDE 58
          + V + N+       +  E +  E C + G V   + VI    G P       F E++  
Sbjct: 9  KVVLLRNMVGAGEVDEDLEVETKEECEKYGKVG--KCVIFEIPGAPDDEAVRIFLEFERV 66

Query: 59 ETALSARRNLQGYEINGRQLRVDFAENDK 87
          E+A+ A  +L G    GR ++  F   DK
Sbjct: 67 ESAIKAVVDLNGRYFGGRVVKACFYNLDK 95

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 4/63 (6%)

Query: 20 EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR 79
           E L   C + G +   +L++      P G     ++D E A    + L G    GRQ+ 
Sbjct: 40 REDLRVECSKFGQIR--KLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95

Query: 80 VDF 82
             
Sbjct: 96 AQA 98

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 44.8 bits (105), Expect = 3e-05
 Identities = 13/93 (13%), Positives = 32/93 (34%), Gaps = 15/93 (16%)

Query: 3   SSQHRCVFVGNIPYDAT---------EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFC 53
             +++ ++VG I              E ++  +   +G +   R V      + K  GF 
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFV 184

Query: 54  EYKDEETALSARRNLQGYEINGRQLRVDFAEND 86
           ++K +  A  A+  +    +     +      +
Sbjct: 185 KFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.4 bits (99), Expect = 5e-05
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 8   CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
            + + N  Y  T + L  +C  VG V            +       E++    A  A+  
Sbjct: 27  LLSIQNPLYPITVDVLYTVCNPVGKVQR-----IVIFKRNGIQAMVEFESVLCAQKAKAA 81

Query: 68  LQGYEINGR--QLRVDFAENDK 87
           L G +I      L++++A   +
Sbjct: 82  LNGADIYAGCCTLKIEYARPTR 103

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 45.2 bits (106), Expect = 6e-05
 Identities = 36/173 (20%), Positives = 54/173 (31%), Gaps = 10/173 (5%)

Query: 214 QAQIMLGMATPQVLQMPILR--QGPGHPAQPLFQDGQQQVAQLPGLPPLAQKMQLMPKVQ 271
           QAQ+  G     + Q       Q P          GQ  +     +P + Q+  L P   
Sbjct: 11  QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSY---GQMGMPPQGAVPSMGQQQFLTP--- 64

Query: 272 EAQIQLHNQFSAATQPTLHPQIQLPQNAKNQALQQASLPGQSGIPMLPSMHPSVRPQIQL 331
            AQ QLH Q   AT       +         A  Q  +P Q G P+     P   P    
Sbjct: 65  -AQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG- 122

Query: 332 ANSSSLNQQVHPPSLENQVQVSASNLGQNTWTKLPNSAMRSSFLPHPPSSDAG 384
             S+++ Q + P +    + +        T   LP   +          S+  
Sbjct: 123 QPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELS 175

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 14/86 (16%)

Query: 7  RCVFVGNI--PYDATEEQLI-EICREV-------GPVVSFRLVIDRETGKPKGYGFCEYK 56
          +C  + N+  P    E     EI  +V       G V+   + +D+ +   +G  + +  
Sbjct: 8  QCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVI--HIYVDKNS--AQGNVYVKCP 63

Query: 57 DEETALSARRNLQGYEINGRQLRVDF 82
              A++A   L G    G+ +   +
Sbjct: 64 SIAAAIAAVNALHGRWFAGKMITAAY 89

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 13 NIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE 72
          N+        L  +C + GP+VSF   +       +G   C+Y   E A  A+  L    
Sbjct: 14 NLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCV 67

Query: 73 INGRQLRVDFA 83
          +    +  +  
Sbjct: 68 LANTTIFAESP 78

>2j8p_A Cleavage stimulation factor 64 kDa subunit; cleavage/polyadenylation, alternative splicing RNA15, PCF11, CSTF-64, RNA-binding, nuclear protein; NMR {Homo sapiens} Length = 49

 Score = 37.1 bits (85), Expect = 6e-04
 Identities = 17/41 (41%), Positives = 28/41 (68%)

Query: 510 ESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQMQP 550
           ++AL+ QVL LT +Q+  LPPEQRQ ++ L++ + +    P
Sbjct: 9   KAALIMQVLQLTADQIAMLPPEQRQSILILKEQIQKSTGAP 49

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	551
4eba_G	174	RNA15, KLLA0F09383P; HAT domain, heat repeat, monk	99.87
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.79
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.78
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.78
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.78
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.78
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.77
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.77
2div_A	99	TRNA selenocysteine associated protein; structural	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.76
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.76
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.75
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.75
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.75
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.75
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.75
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.74
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.74
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.74
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.74
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.74
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.73
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.72
2l9b_A	109	MRNA 3'-END-processing protein RNA15; 3' END mRNA	99.72
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.72
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.72
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.72
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.55
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.71
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.7
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.7
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.69
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.69
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.69
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.69
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.69
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.68
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.68
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.67
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.67
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.67
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.67
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.67
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.67
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.67
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.67
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.66
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.66
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.66
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.66
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.66
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.66
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.65
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.65
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.65
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.63
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.63
1x5p_A	97	Negative elongation factor E; structure genomics,	99.63
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.62
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.62
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.62
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.62
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.61
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.61
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.6
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.6
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.6
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.59
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.58
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.58
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.58
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.57
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.57
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.57
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.57
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.56
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.56
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.55
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.54
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.52
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.52
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.51
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.51
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.5
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.5
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.49
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.49
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.48
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.48
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.47
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.46
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.45
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.42
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.41
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.41
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.4
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.4
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.4
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.39
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.39
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.38
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.37
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.37
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.19
2j8p_A	49	Cleavage stimulation factor 64 kDa subunit; cleava	99.18
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.13
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.91
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.88
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.8
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.7
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.15
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.08
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.65
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.57
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.99
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.09
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	94.72
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	94.4
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.95
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.71
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	92.92
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	89.41

>4eba_G RNA15, KLLA0F09383P; HAT domain, heat repeat, monkeytail, CLP1, PCF11, structural RNA binding protein complex; 3.30A {Kluyveromyces lactis}

Probab=99.87  E-value=3.1e-23  Score=196.45  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=69.2

Q ss_pred             CCCCCcccccCC-CCc-hhhHhhhcCChHHHHHHHHHHHHHHhhCHHHHHHHHHhCCChHHHHHHHHHHhCCCChhhhhc
Q 008851          152 SNQNGIQSQLAS-PND-PLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQM  229 (551)
Q Consensus       152 ~~~~glp~~~~~-a~D-~IS~~Lakl~p~QL~eiLsqLK~l~~~~P~~Ar~LL~~NPQLa~AL~QA~llLgmid~~v~q~  229 (551)
                      .++.|++..... ++| .|+++|++|+++||+|+|++||.|+.+||++||+||.+||||+||+|||+|+||+||+++++.
T Consensus        29 ~LP~G~~~~~~~t~pd~~IS~~Ls~lpp~QL~eiL~qmK~l~~~nP~~ar~LL~~nPQLayAl~QAlL~mgivd~~~l~~  108 (174)
T 4eba_G           29 WLPVGVDVNINMTTPAMCISSELGKLQKDQQMALLKVIQHFCKDDKETFVALLEEAPQLSYAIAELLLSNGVCSVDQLTQ  108 (174)
T ss_dssp             CCCCCBCCCTTTCCHHHHHHHHHTTSCHHHHHHHHHHHHHGGGC--CCHHHHHHSCTHHHHHHHHHHHHTSCCSSSTHHH
T ss_pred             CCCCCCCCCCCcCCcHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCHHHHHHHHHHCchHHHHHHHHHHHhCCCCHHHHHH
Confidence            444555443333 578 999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ccc
Q 008851          230 PIL  232 (551)
Q Consensus       230 ~~~  232 (551)
                      +..
T Consensus       109 v~~  111 (174)
T 4eba_G          109 LAM  111 (174)
T ss_dssp             HC-
T ss_pred             HHH
Confidence            866

>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=99.83  E-value=3.1e-20  Score=159.48  Aligned_cols=81  Identities=27%  Similarity=0.527  Sum_probs=78.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++++|||+|||+++||++|+++|+.||.|++|++++|+.||+++|||||+|.+.++|.+|++.|||..|+|+.|+|+||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.82  E-value=6.5e-20  Score=164.31  Aligned_cols=86  Identities=31%  Similarity=0.561  Sum_probs=81.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||++++|++|+++|+.||.|++|++++|+.||+++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 008851           84 ENDKGA   89 (551)
Q Consensus        84 ~~~~~~   89 (551)
                      +.+..+
T Consensus       120 ~~~~~~  125 (139)
T 1u6f_A          120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
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=99.80  E-value=2.8e-19  Score=156.60  Aligned_cols=84  Identities=17%  Similarity=0.246  Sum_probs=80.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+||+++++|++|+++|++||.|++|+|++|+.||+++|||||+|.+.++|++|++.||+..|+|+.|+|++
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +..+
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            9754

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.7e-19  Score=150.14  Aligned_cols=85  Identities=24%  Similarity=0.447  Sum_probs=81.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~v-rLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ..++++|||+|||+++++++|+++|+.||.|.++ +++.|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4578999999999999999999999999999999 999999999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      ++.+..
T Consensus        82 ~a~~~~   87 (96)
T 1x5t_A           82 YAFKKD   87 (96)
T ss_dssp             ESCCCC
T ss_pred             EecccC
Confidence            998754

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.5e-19  Score=149.17  Aligned_cols=85  Identities=34%  Similarity=0.609  Sum_probs=81.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+++++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +..+.
T Consensus        82 a~~~~   86 (95)
T 2dnz_A           82 VTERL   86 (95)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            98643

>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=99.79  E-value=4.8e-19  Score=162.09  Aligned_cols=85  Identities=26%  Similarity=0.462  Sum_probs=81.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||++++|++|+++|+.||.|++|+|+.|+.|++++|||||+|.+.++|++|++.||++.|+|+.|+|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            36799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      ++...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87544

>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=99.79  E-value=4.4e-19  Score=154.25  Aligned_cols=86  Identities=23%  Similarity=0.512  Sum_probs=81.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|++|+|++|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      ++++..
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            987543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.79  E-value=1.4e-18  Score=150.90  Aligned_cols=87  Identities=33%  Similarity=0.523  Sum_probs=82.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+|++|+.+|+++|||||+|.+.++|++|++.|++..|+|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 008851           83 AENDKGA   89 (551)
Q Consensus        83 A~~~~~~   89 (551)
                      ++.....
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9876543

>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=99.79  E-value=6.4e-19  Score=148.86  Aligned_cols=86  Identities=33%  Similarity=0.475  Sum_probs=81.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
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            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=9.1e-19  Score=152.49  Aligned_cols=85  Identities=29%  Similarity=0.516  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|++|+|++|+.|++++|||||+|.+.++|++|++.+++ .|+|+.|+|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            44689999999999999999999999999999999999999999999999999999999999999998 89999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      +.....
T Consensus        93 a~~~~~   98 (116)
T 2cqd_A           93 AYLGAK   98 (116)
T ss_dssp             STTTCC
T ss_pred             cccCCC
Confidence            986543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.9e-19  Score=149.84  Aligned_cols=85  Identities=29%  Similarity=0.537  Sum_probs=80.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++ +++..|+|+.|+|++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            4578999999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            987543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=1.3e-19  Score=152.88  Aligned_cols=82  Identities=18%  Similarity=0.384  Sum_probs=76.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCEEEEEEee
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL-QGYEINGRQLRVDFA   83 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L-ng~~I~GR~LrV~~A   83 (551)
                      +++|||+|||+++||++|+++|+.|| .|++|+|++|+.||++||||||+|.+.++|.+|++.+ ++..|+||+|+|+||
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            57899999999999999999999999 8999999999999999999999999999999999877 456899999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4e-19  Score=150.87  Aligned_cols=85  Identities=26%  Similarity=0.467  Sum_probs=81.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|++|+++.|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      +....
T Consensus        90 ~~~~~   94 (102)
T 2cqb_A           90 KPMRI   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.79  E-value=7.8e-19  Score=144.49  Aligned_cols=83  Identities=31%  Similarity=0.518  Sum_probs=77.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|++|++.||+..++|+.|+|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      +.+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            753

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7.2e-19  Score=149.83  Aligned_cols=85  Identities=26%  Similarity=0.459  Sum_probs=81.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            44689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +..+.
T Consensus        92 a~~~~   96 (103)
T 2cq0_A           92 AKPST   96 (103)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98754

>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=99.78  E-value=7.2e-19  Score=151.24  Aligned_cols=86  Identities=30%  Similarity=0.556  Sum_probs=81.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCCEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ------GYEINGRQ   77 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln------g~~I~GR~   77 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+|++|+.||+++|||||+|.+.++|.+|++.|+      +..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            468899999999999999999999999999999999999999999999999999999999999999      99999999


Q ss_pred             EEEEeecCCCCC
Q 008851           78 LRVDFAENDKGA   89 (551)
Q Consensus        78 LrV~~A~~~~~~   89 (551)
                      |+|+++..+...
T Consensus        93 l~v~~a~~~~~~  104 (111)
T 1x4h_A           93 LKVDLAVTRDEA  104 (111)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEECCCCccC
Confidence            999999875443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.8e-19  Score=150.44  Aligned_cols=85  Identities=31%  Similarity=0.592  Sum_probs=81.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||++++|++|+++|+.||.|.+|+++.|+.+++++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      +....
T Consensus        90 ~~~~~   94 (102)
T 1x5s_A           90 GKSSD   94 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.78  E-value=5.7e-19  Score=150.72  Aligned_cols=85  Identities=33%  Similarity=0.522  Sum_probs=81.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|||+++++++|+++|+.||.|++|+++.|+.+|+++|||||+|.+.++|++|++.|++..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +....
T Consensus        92 a~~~~   96 (105)
T 1x5u_A           92 ASAHN   96 (105)
T ss_dssp             TTTTS
T ss_pred             CCCCC
Confidence            98754

>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=99.78  E-value=8.2e-19  Score=154.27  Aligned_cols=86  Identities=22%  Similarity=0.522  Sum_probs=81.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         1 ma~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      ++..+.++|||+|||+++++++|+++|+.||.|++|+++.|+ +|+++|||||+|.+.++|++|++.|++..|+|+.|+|
T Consensus         2 ~e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V   80 (116)
T 2fy1_A            2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKV   80 (116)
T ss_dssp             CTTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            456678999999999999999999999999999999999998 9999999999999999999999999999999999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      ++++...
T Consensus        81 ~~a~~~~   87 (116)
T 2fy1_A           81 EQAKKPS   87 (116)
T ss_dssp             EECCCSS
T ss_pred             EECCCCC
Confidence            9998654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=8.2e-19  Score=147.95  Aligned_cols=85  Identities=32%  Similarity=0.523  Sum_probs=80.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRE---TGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~---TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|.+|+++.|+.   |++++|||||+|.+.++|++|++.||+..|+|+.|+
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            45789999999999999999999999999999999999987   779999999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 008851           80 VDFAENDK   87 (551)
Q Consensus        80 V~~A~~~~   87 (551)
                      |++++...
T Consensus        82 V~~a~~~~   89 (98)
T 2cpf_A           82 VRISERAT   89 (98)
T ss_dssp             EECSSCSS
T ss_pred             EEEccCCC
Confidence            99998654

>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=99.78  E-value=1.3e-18  Score=142.03  Aligned_cols=81  Identities=28%  Similarity=0.561  Sum_probs=78.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +++|||+|||+++++++|+++|+.||.|.+++++.|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=4.3e-19  Score=151.20  Aligned_cols=85  Identities=25%  Similarity=0.462  Sum_probs=81.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.||+++|||||+|.+.++|++|++.||+..|+|+.|+|+++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      +....
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87543

>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=99.78  E-value=1.1e-18  Score=147.08  Aligned_cols=83  Identities=43%  Similarity=0.933  Sum_probs=79.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.|+|..|+|+.|+|+++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>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=99.78  E-value=1e-18  Score=149.35  Aligned_cols=84  Identities=32%  Similarity=0.606  Sum_probs=79.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRET-GKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~T-GksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ..+.++|||+|||++++|++|+++|+.|| |.+|+|+.|+.| |+++|||||+|.+.++|++|+ .|++..|+|+.|+|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            34679999999999999999999999999 999999999998 999999999999999999999 999999999999999


Q ss_pred             eecCCCC
Q 008851           82 FAENDKG   88 (551)
Q Consensus        82 ~A~~~~~   88 (551)
                      ++..+..
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987544

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.6e-18  Score=147.94  Aligned_cols=83  Identities=30%  Similarity=0.562  Sum_probs=78.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.|| |++|++++|+.||+++|||||+|.+.++|.+|+ .||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            45689999999999999999999999997 999999999999999999999999999999999 8999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98654

>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=99.78  E-value=1e-18  Score=143.23  Aligned_cols=82  Identities=27%  Similarity=0.511  Sum_probs=79.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+++++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
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            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.4e-18  Score=145.29  Aligned_cols=83  Identities=24%  Similarity=0.510  Sum_probs=79.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            875

>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=99.77  E-value=8.2e-19  Score=149.96  Aligned_cols=85  Identities=28%  Similarity=0.470  Sum_probs=80.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI---NGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I---~GR~Lr   79 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|.+|+++.|+.||+++|||||+|.+.++|.+|++.||+..+   +|+.|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999988   899999


Q ss_pred             EEeecCCC
Q 008851           80 VDFAENDK   87 (551)
Q Consensus        80 V~~A~~~~   87 (551)
                      |++++...
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99998754

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.2e-18  Score=149.01  Aligned_cols=86  Identities=24%  Similarity=0.499  Sum_probs=81.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVID-RETGKPKGYGFCEYKDEETALSARRNL-QGYEINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~D-r~TGksKGyAFVEF~d~e~A~sAi~~L-ng~~I~GR~LrV   80 (551)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++.| +.+|+++|||||+|.+.++|.+|++.| |+..|+|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            346789999999999999999999999999999999999 889999999999999999999999999 999999999999


Q ss_pred             EeecCCCC
Q 008851           81 DFAENDKG   88 (551)
Q Consensus        81 ~~A~~~~~   88 (551)
                      +|++.+..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.4e-18  Score=150.29  Aligned_cols=85  Identities=28%  Similarity=0.498  Sum_probs=80.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVV--------SFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~--------~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.        .|+|+.|+.+|+++|||||+|.+.++|.+|++.||+..|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            44689999999999999999999999999999        6999999999999999999999999999999999999999


Q ss_pred             CEEEEEEeecCCC
Q 008851           75 GRQLRVDFAENDK   87 (551)
Q Consensus        75 GR~LrV~~A~~~~   87 (551)
                      |+.|+|++++...
T Consensus        92 g~~l~V~~a~~~~  104 (113)
T 2cpe_A           92 GSKLKVSLARKKP  104 (113)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CCEEEEEECCCCC
Confidence            9999999998754

>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=99.77  E-value=8.1e-19  Score=154.68  Aligned_cols=85  Identities=29%  Similarity=0.448  Sum_probs=80.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+|+.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      .....
T Consensus       100 ~~~~~  104 (126)
T 3ex7_B          100 FVRGP  104 (126)
T ss_dssp             EESSS
T ss_pred             cCCCC
Confidence            87544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.2e-18  Score=148.42  Aligned_cols=85  Identities=27%  Similarity=0.428  Sum_probs=80.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHc-CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-eCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICRE-VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE-INGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~-~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~-I~GR~LrV   80 (551)
                      ..+.++|||+|||+++++++|+++|+. ||.|.+|+++.|+ +|+++|||||+|.+.++|.+|++.|++.. |+|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            457899999999999999999999999 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             EeecCCCC
Q 008851           81 DFAENDKG   88 (551)
Q Consensus        81 ~~A~~~~~   88 (551)
                      +++.....
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99976543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=146.87  Aligned_cols=85  Identities=24%  Similarity=0.439  Sum_probs=80.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCee-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE----
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVV-SFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ----   77 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~-~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~----   77 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|+ +|++++|+.+|+++|||||+|.+.++|++|++.||+..|+|+.    
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            45789999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEEeecCCC
Q 008851           78 LRVDFAENDK   87 (551)
Q Consensus        78 LrV~~A~~~~   87 (551)
                      |+|+||+...
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999997643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.8e-18  Score=144.58  Aligned_cols=81  Identities=27%  Similarity=0.516  Sum_probs=78.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ++.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+||
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.77  E-value=5e-19  Score=151.75  Aligned_cols=81  Identities=22%  Similarity=0.413  Sum_probs=76.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCC--eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCCEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGP--VVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY----EINGRQL   78 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~--V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~----~I~GR~L   78 (551)
                      .=.+|||+|||+++||++|+++|+.||.  |++|++++|+.||++||||||+|.+.++|.+|++.||+.    .|+||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            4578999999999999999999999995  679999999999999999999999999999999999986    5999999


Q ss_pred             EEEeecC
Q 008851           79 RVDFAEN   85 (551)
Q Consensus        79 rV~~A~~   85 (551)
                      +|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999974

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2.6e-18  Score=145.66  Aligned_cols=83  Identities=33%  Similarity=0.655  Sum_probs=79.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+++.|+ +|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            467899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +++.
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=7.5e-18  Score=145.75  Aligned_cols=84  Identities=25%  Similarity=0.379  Sum_probs=79.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|++|+|+.|+ +|+++|||||+|.+.++|++|++.||++.|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3467899999999999999999999999999999999998 599999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++...
T Consensus        91 a~~~~   95 (114)
T 2do0_A           91 DERAL   95 (114)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            97643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.76  E-value=1.2e-18  Score=152.01  Aligned_cols=82  Identities=22%  Similarity=0.500  Sum_probs=78.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|++||.|++|++++|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.2e-18  Score=146.84  Aligned_cols=84  Identities=23%  Similarity=0.411  Sum_probs=79.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++.|  +|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            457899999999999999999999999999999999998  899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      ++....
T Consensus        90 a~~~~~   95 (103)
T 2d9p_A           90 AQRKEE   95 (103)
T ss_dssp             CSSCCC
T ss_pred             eccccc
Confidence            987543

>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=99.76  E-value=2.8e-18  Score=147.78  Aligned_cols=84  Identities=32%  Similarity=0.528  Sum_probs=80.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.|++..|+|+.|+|+++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ..+.
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            8654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.3e-18  Score=147.17  Aligned_cols=83  Identities=30%  Similarity=0.469  Sum_probs=79.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .++++|||+|||+++++++|+++|+.||.|.+|+++.|+.||+++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ..+
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            864

>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=99.76  E-value=6.6e-18  Score=143.85  Aligned_cols=83  Identities=25%  Similarity=0.549  Sum_probs=77.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|++|+++.|+.+  ++|||||+|.+.++|.+|++.|++..|+|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            456899999999999999999999999999999999998643  689999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++...
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            98754

>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=99.76  E-value=4.6e-19  Score=148.20  Aligned_cols=81  Identities=20%  Similarity=0.392  Sum_probs=73.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G--~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+|||+|||++++|++|+++|+.||  .|.+++++.|+.||+++|||||+|.+.++|++|++.|||..|+||.|+|+++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            653

>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=99.76  E-value=3.8e-18  Score=145.59  Aligned_cols=84  Identities=25%  Similarity=0.436  Sum_probs=79.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC---EEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING---RQLRV   80 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G---R~LrV   80 (551)
                      .+.++|||+|||++++|++|+++|+.||.|.+|+|+.|+ +|+++|||||+|.+.++|.+|++.||+..+.|   +.|+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            467999999999999999999999999999999999998 79999999999999999999999999999988   99999


Q ss_pred             EeecCCCC
Q 008851           81 DFAENDKG   88 (551)
Q Consensus        81 ~~A~~~~~   88 (551)
                      ++++....
T Consensus        92 ~~a~~~~~   99 (105)
T 2dnh_A           92 KFADTDKE   99 (105)
T ss_dssp             EESCSSCC
T ss_pred             EECccCcc
Confidence            99987653

>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=99.76  E-value=7e-18  Score=143.70  Aligned_cols=84  Identities=25%  Similarity=0.430  Sum_probs=78.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|++|+++.|+.||+++|||||+|.+.++|.+|++  +++.|+|+.|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            3467899999999999999999999999999999999999999999999999999999999998  46799999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      +..+..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            987544

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.76  E-value=3.3e-18  Score=149.83  Aligned_cols=81  Identities=25%  Similarity=0.444  Sum_probs=75.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+++|||+|||+++||++|+++|+.||.|++|+|++|+  +++||||||+|.+.++|++|++.|++..|+|+.|+|+++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46789999999999999999999999999999999986  4589999999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus        82 ~~~   84 (115)
T 4f25_A           82 SRK   84 (115)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            643

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=147.50  Aligned_cols=84  Identities=21%  Similarity=0.417  Sum_probs=79.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|++|+++.|+.+|+++|||||+|.+.++|.+|++. +++.|+|+.|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999998 99999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +.++.
T Consensus        92 a~~~~   96 (105)
T 2dh8_A           92 CTPRG   96 (105)
T ss_dssp             SCCSS
T ss_pred             ccCCC
Confidence            98654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.76  E-value=2.2e-18  Score=146.00  Aligned_cols=82  Identities=29%  Similarity=0.475  Sum_probs=78.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~--------vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      ....++|||+|||+++++++|+++|++||.|.+        ++++.|++||+++|||||+|.+.++|.+|++.|||..|+
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            346899999999999999999999999999999        999999999999999999999999999999999999999


Q ss_pred             CEEEEEEeec
Q 008851           75 GRQLRVDFAE   84 (551)
Q Consensus        75 GR~LrV~~A~   84 (551)
                      |+.|+|++|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999984

>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=99.75  E-value=3.4e-18  Score=140.64  Aligned_cols=84  Identities=19%  Similarity=0.417  Sum_probs=79.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGK-PKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGk-sKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...++|||+|||+++++++|+++|+.||.|.+++++.|+.++. ++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            3578999999999999999999999999999999999998877 999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            97643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.75  E-value=7.7e-19  Score=150.23  Aligned_cols=84  Identities=21%  Similarity=0.340  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCC------CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-
Q 008851            3 SSQHRCVFVGNIPY------DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING-   75 (551)
Q Consensus         3 ~~~srtVFVGNLP~------d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G-   75 (551)
                      ...+++|||+|||+      ++++++|+++|+.||.|.+|+|++|+.||+++|||||+|.+.++|.+|++.|||..|+| 
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34578999999999      99999999999999999999999999999999999999999999999999999999999 


Q ss_pred             EEEEEEeecCC
Q 008851           76 RQLRVDFAEND   86 (551)
Q Consensus        76 R~LrV~~A~~~   86 (551)
                      +.|+|+++.+.
T Consensus        83 r~l~V~~a~~~   93 (100)
T 3ns6_A           83 HRLFLYTMKDV   93 (100)
T ss_dssp             CBCEEEESHHH
T ss_pred             eEEEEEECchh
Confidence            99999999763

>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=99.75  E-value=5e-18  Score=142.11  Aligned_cols=82  Identities=35%  Similarity=0.575  Sum_probs=78.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|||+++++++|+++|+.||.|++|++..|+. |+++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            34679999999999999999999999999999999999986 99999999999999999999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.4e-18  Score=148.12  Aligned_cols=82  Identities=21%  Similarity=0.396  Sum_probs=78.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||+++++++|+++|+.||.|++|+|+.|+.||+++|||||+|.+.++|.+|++. +++.|+|+.|+|+++..
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            58999999999999999999999999999999999999999999999999999999999987 99999999999999987


Q ss_pred             CCC
Q 008851           86 DKG   88 (551)
Q Consensus        86 ~~~   88 (551)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            543

>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=99.75  E-value=6.3e-18  Score=139.51  Aligned_cols=80  Identities=24%  Similarity=0.485  Sum_probs=75.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|.+|+++.|+.||+++|||||+|.+.++|.+|++ +++..|+|+.|+|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4578999999999999999999999999999999999999999999999999999999999996 588899999999998


Q ss_pred             e
Q 008851           83 A   83 (551)
Q Consensus        83 A   83 (551)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.75  E-value=7.2e-19  Score=149.58  Aligned_cols=85  Identities=73%  Similarity=1.129  Sum_probs=80.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 008851           85 NDKGA   89 (551)
Q Consensus        85 ~~~~~   89 (551)
                      .....
T Consensus        87 ~~~~~   91 (104)
T 1p1t_A           87 SEKNK   91 (104)
T ss_dssp             CTTHH
T ss_pred             Cccch
Confidence            76543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=9e-19  Score=156.52  Aligned_cols=84  Identities=20%  Similarity=0.374  Sum_probs=79.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCCE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVS--FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY----EINGR   76 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~--vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~----~I~GR   76 (551)
                      ....++|||+|||+++||++|+++|+.||.|..  |+|++|+.||++||||||+|.+. +|.+|++.||+.    .|+||
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            346789999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEeecCCC
Q 008851           77 QLRVDFAENDK   87 (551)
Q Consensus        77 ~LrV~~A~~~~   87 (551)
                      .|+|+++++.+
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998653

>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=99.75  E-value=6.5e-18  Score=139.52  Aligned_cols=81  Identities=30%  Similarity=0.546  Sum_probs=77.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+++++.|+.+|+++|||||+|.+.++|++|+ .||+..|+|+.|+|++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4689999999999999999999999999999999999999999999999999999999999 999999999999999987


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            63

>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=99.75  E-value=1.5e-17  Score=141.64  Aligned_cols=85  Identities=24%  Similarity=0.495  Sum_probs=78.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|.+|+++.|+.  .++|||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34679999999999999999999999999999999998864  4899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 008851           83 AENDKGA   89 (551)
Q Consensus        83 A~~~~~~   89 (551)
                      +......
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
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=99.75  E-value=7.2e-18  Score=148.21  Aligned_cols=81  Identities=25%  Similarity=0.501  Sum_probs=77.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||+++++++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.++|.+|+ .|++..|+|+.|+|++++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            589999999999999999999999999999999999999999999999999999999999 8999999999999999986


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.75  E-value=5.5e-18  Score=157.30  Aligned_cols=81  Identities=28%  Similarity=0.491  Sum_probs=77.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G--~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..++|||||||++++|++|+++|+.||  .|++|+|+.|+.||+++|||||+|.+.++|++|++.|||..|+|+.|+|++
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  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            975

>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=99.75  E-value=1.2e-17  Score=143.76  Aligned_cols=83  Identities=24%  Similarity=0.472  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      +..+.++|||+|||++++|++|+++|+.||.|++|++..+   ++++|||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456799999999999999999999999999999999654   5689999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      +++...
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            998754

>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=99.74  E-value=6.5e-18  Score=145.07  Aligned_cols=86  Identities=30%  Similarity=0.475  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCC-eeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGP-VVSFRLV-IDRETGKPKGYGFCEYKDEETALSARRNLQ--GYEINGRQL   78 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~-V~~vrLv-~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln--g~~I~GR~L   78 (551)
                      +.+.++|||+|||+++++++|+++|+.||. |.+|+++ .|+.||+++|||||+|.+.++|.+|++.|+  +..|+|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            346889999999999999999999999998 9999998 899999999999999999999999999996  589999999


Q ss_pred             EEEeecCCCC
Q 008851           79 RVDFAENDKG   88 (551)
Q Consensus        79 rV~~A~~~~~   88 (551)
                      +|+|++++..
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.74  E-value=1.1e-17  Score=143.08  Aligned_cols=80  Identities=19%  Similarity=0.417  Sum_probs=77.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||++++|++|+++|+.||.|++|+++.|+ +|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            357899999999999999999999999999999999998 9999999999999999999999999999999999999998


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.74  E-value=3.9e-18  Score=143.77  Aligned_cols=83  Identities=14%  Similarity=0.284  Sum_probs=78.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||++++|++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ...
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            753

>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=99.74  E-value=2.5e-18  Score=143.95  Aligned_cols=82  Identities=15%  Similarity=0.280  Sum_probs=77.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +..++|||+|||+++++++|+++|+.||.|.+++++.|+.+|+++|||||+|.+.++|++|++.||+..|+||.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            64

>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=99.74  E-value=4.9e-18  Score=147.53  Aligned_cols=84  Identities=35%  Similarity=0.648  Sum_probs=80.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.++|.+|++.|++..|+|+.|+|++
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      ++++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9764

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.74  E-value=6.8e-18  Score=146.68  Aligned_cols=83  Identities=20%  Similarity=0.343  Sum_probs=76.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||++++|++|+++|+.||.|.+|++++|+.||+++|||||+|.+.++|.+|++.+ +..|+|+.|+|+++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            36789999999999999999999999999999999999999999999999999999999999876 49999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ..+.
T Consensus       102 ~~~~  105 (109)
T 2rs2_A          102 FPRR  105 (109)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>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=99.74  E-value=2.9e-18  Score=168.26  Aligned_cols=81  Identities=20%  Similarity=0.408  Sum_probs=77.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G--~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..++|||+||++++||++|+++|+.||  .|++|+|++|+.||++||||||+|.+.++|++||+.||++.|+|+.|+|++
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            467899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      ++.
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            874

>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=99.74  E-value=3.6e-18  Score=153.34  Aligned_cols=85  Identities=26%  Similarity=0.565  Sum_probs=81.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|++|++++|+.+|+++|||||+|.+.++|++|++.|++..|+|+.|+|+|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +..++
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            98653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.73  E-value=1.1e-17  Score=139.18  Aligned_cols=83  Identities=31%  Similarity=0.510  Sum_probs=78.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|++..+  +|+++|||||+|.+.++|++|++.|++..|+|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457899999999999999999999999999999999874  799999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +++..
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98654

>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=99.73  E-value=2.9e-18  Score=148.83  Aligned_cols=82  Identities=23%  Similarity=0.386  Sum_probs=78.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|++|+|+.|+.||+++|||||+|.+.++|++|+ .||++.|+|+.|+|+++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3579999999999999999999999999999999999999999999999999999999999 999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            643

>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=99.73  E-value=1.1e-17  Score=152.69  Aligned_cols=83  Identities=25%  Similarity=0.456  Sum_probs=79.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|++++
T Consensus        69 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  148 (158)
T 2kn4_A           69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  148 (158)
T ss_dssp             BCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      +.+
T Consensus       149 ~~~  151 (158)
T 2kn4_A          149 YGR  151 (158)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>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=99.73  E-value=1.6e-17  Score=140.61  Aligned_cols=80  Identities=23%  Similarity=0.292  Sum_probs=75.7

Q ss_pred             CCcEEEEecCCCCCCHHHHH----HHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLI----EICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLr----e~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      +.++|||+|||++++|++|+    ++|+.||.|++|+++.|+++   +|||||+|.+.++|.+|++.||+..|+||.|+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            57899999999999999999    99999999999999999876   899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      +++++..
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9997643

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-18  Score=142.67  Aligned_cols=82  Identities=23%  Similarity=0.473  Sum_probs=77.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.8e-17  Score=136.90  Aligned_cols=82  Identities=22%  Similarity=0.382  Sum_probs=77.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|||+++++++|+++|+.| .|.+|++++| .+|+++|||||+|.+.++|.+|++ +|+..|+||.|+|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3467899999999999999999999999 9999999999 789999999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +....
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.9e-17  Score=140.51  Aligned_cols=81  Identities=30%  Similarity=0.503  Sum_probs=74.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|   +++.+ .+|+++|||||+|.+.++|++|++.||+..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3468999999999999999999999999977   56666 6899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++.+.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98753

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.1e-17  Score=140.27  Aligned_cols=82  Identities=37%  Similarity=0.609  Sum_probs=75.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.|   .+|+++.|+.+++++|||||+|.+.++|.+|++.||++.|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3468899999999999999999999977   4788889999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++++.
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98654

>2l9b_A MRNA 3'-END-processing protein RNA15; 3' END mRNA maturation, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.72  E-value=3.9e-18  Score=149.62  Aligned_cols=82  Identities=16%  Similarity=0.136  Sum_probs=72.2

Q ss_pred             CCCCCCccccc-CCCCc-hhhHhhhcCChHHHHHHHHHHHHHHhhCHHHHHHHHHhCCChHHHHHHHHHHhCCCChhhhh
Q 008851          151 QSNQNGIQSQL-ASPND-PLTLHLAKMSRNQLNEIMSEMKLMATQNKEQARQLLLAKPPLLKALFQAQIMLGMATPQVLQ  228 (551)
Q Consensus       151 ~~~~~glp~~~-~~a~D-~IS~~Lakl~p~QL~eiLsqLK~l~~~~P~~Ar~LL~~NPQLa~AL~QA~llLgmid~~v~q  228 (551)
                      ++++.|++... ..++| .|+++|++++++|++|||++||.|+..||++||+||.+||||+||||||+|+||+||+++++
T Consensus        23 p~lP~G~~v~~~~~ap~~~IS~~Laslpp~Ql~eiL~qmK~~~~~nP~~a~~LL~q~PQLAyAl~QalL~m~ivd~~~l~  102 (109)
T 2l9b_A           23 PELPSGIDVNINMTTPAMMISSELAKKPKEVQLKFLQKFQEWTRAHPEDAASLLELCPQLSFVTAELLLTNGICKVDDLI  102 (109)
T ss_dssp             TTCCCCBCCCTTTSCHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHHHHHHHHTSSCHHHHT
T ss_pred             CCCCCCCCCCCCCCchHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCHHHHHHHHHHCchHHHHHHHHHHHhCCCCHHHHH
Confidence            34445554422 35789 99999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q 008851          229 MPIL  232 (551)
Q Consensus       229 ~~~~  232 (551)
                      ..+.
T Consensus       103 ~ll~  106 (109)
T 2l9b_A          103 PLAS  106 (109)
T ss_dssp             TTC-
T ss_pred             HHhc
Confidence            8765

>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=99.72  E-value=1.8e-17  Score=143.99  Aligned_cols=83  Identities=18%  Similarity=0.313  Sum_probs=77.4

Q ss_pred             CCcEEEEecCCCCCCHHHHH---HHHHcCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLI---EICREVGPVVSFRLVIDRETG---KPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLr---e~Fs~~G~V~~vrLv~Dr~TG---ksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      ..++|||+|||++++|++|+   ++|++||.|.+|+++.|+.++   +++|||||+|.+.++|++|++.||+..|+|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            57899999999999999999   999999999999999998755   556999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q 008851           79 RVDFAENDK   87 (551)
Q Consensus        79 rV~~A~~~~   87 (551)
                      +|++|..+.
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999998754

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.72  E-value=2.6e-17  Score=145.09  Aligned_cols=83  Identities=18%  Similarity=0.397  Sum_probs=78.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++|||+|||+++++++|+++|+.||.|++|+++.|+ +|+++|||||+|.+.++|.+|++.|++..|+|+.|+|++|
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            357899999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ....
T Consensus       112 ~~~~  115 (124)
T 2kt5_A          112 ASQI  115 (124)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8643

>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=99.72  E-value=5e-17  Score=140.36  Aligned_cols=77  Identities=23%  Similarity=0.299  Sum_probs=72.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-----EEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING-----RQLR   79 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G-----R~Lr   79 (551)
                      ..++|||+|||++++|++|+++|+.||.|++|+|+.|       |||||+|.+.++|++|++.||+..|+|     +.|+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            5789999999999999999999999999999999875       899999999999999999999999999     9999


Q ss_pred             EEeecCCCC
Q 008851           80 VDFAENDKG   88 (551)
Q Consensus        80 V~~A~~~~~   88 (551)
                      |+++.++..
T Consensus        87 V~~a~~~~~   95 (108)
T 1x4c_A           87 VKVDGPRSP   95 (108)
T ss_dssp             EEESSCCSC
T ss_pred             EEeCCCCCC
Confidence            999987543

>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=99.72  E-value=2.8e-17  Score=152.34  Aligned_cols=84  Identities=32%  Similarity=0.526  Sum_probs=79.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||+|||+++++++|+++|+.||.|..|.|+.++.||+++|||||+|.+.++|.+|++.||+..|+|+.|+|.|+.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  150 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  150 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ....
T Consensus       151 ~~~~  154 (165)
T 1rk8_A          151 VKGP  154 (165)
T ss_dssp             ECC-
T ss_pred             CCCC
Confidence            7554

>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=99.72  E-value=1.1e-17  Score=146.12  Aligned_cols=83  Identities=20%  Similarity=0.420  Sum_probs=77.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCe-eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPV-VSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V-~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ..+.++|||+|||++++|++|+++|+.||.| .+|+|++|+ +|+++|||||+|.+.++|++|++. |+..|+||.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3467899999999999999999999999999 899999998 999999999999999999999987 9999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            998643

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.72  E-value=6.2e-18  Score=135.83  Aligned_cols=75  Identities=24%  Similarity=0.436  Sum_probs=72.6

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|++|++ +++..|+|+.|+|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999999999999999999999999999997 9999999999999986

>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=99.72  E-value=6.3e-17  Score=138.21  Aligned_cols=79  Identities=22%  Similarity=0.450  Sum_probs=72.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|++|+++        +|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            357899999999999999999999999999999986        569999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 008851           84 ENDKGAD   90 (551)
Q Consensus        84 ~~~~~~~   90 (551)
                      +......
T Consensus        81 ~~~~~~~   87 (103)
T 2dgu_A           81 KPPDQKR   87 (103)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccc
Confidence            8765443

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=5.2e-19  Score=154.27  Aligned_cols=86  Identities=28%  Similarity=0.455  Sum_probs=81.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~--------vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      +..+.++|||+|||+++++++|+++|+.||.|.+        |+++.|+.+|+++|||||+|.+.++|.+|++.||+..|
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            3457899999999999999999999999999999        99999999999999999999999999999999999999


Q ss_pred             CCEEEEEEeecCCC
Q 008851           74 NGRQLRVDFAENDK   87 (551)
Q Consensus        74 ~GR~LrV~~A~~~~   87 (551)
                      +|+.|+|+++..+.
T Consensus        83 ~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           83 SGNPIKVSFATRRA   96 (116)
Confidence            99999999998654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.71  E-value=2.6e-17  Score=146.52  Aligned_cols=80  Identities=28%  Similarity=0.515  Sum_probs=76.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|++++++.|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|++|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999986

>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=99.71  E-value=5.8e-18  Score=144.34  Aligned_cols=81  Identities=35%  Similarity=0.631  Sum_probs=75.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR-ETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr-~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...++|||+|||+++++++|+++|+.|| |.+|++++|+ .+|+++|||||+|.+.++|.+|+ .|++..|+|+.|+|++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            4579999999999999999999999999 9999999998 69999999999999999999999 8999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      ++.+
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            9764

>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=99.71  E-value=1.5e-17  Score=143.33  Aligned_cols=80  Identities=19%  Similarity=0.342  Sum_probs=74.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++||++|+++|+.|| +++|+|++|+ +|+++|||||+|.+.++|++|++ +|+..|+||.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            4678999999999999999999999999 5599999998 89999999999999999999994 7999999999999998


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ...
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.71  E-value=3.7e-18  Score=141.76  Aligned_cols=80  Identities=41%  Similarity=0.687  Sum_probs=74.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ++|||+|||++++|++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.+ |.+|++.||+..++|+.|+|++|...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999999999999999999999999999 99999999999999999999999864


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=6.5e-18  Score=135.92  Aligned_cols=76  Identities=21%  Similarity=0.392  Sum_probs=73.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ++|||+|||+++++++|+++|++||.|.+++++.|+.+|+++|||||+|.+.++|++|++.++ ..++|+.|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            579999999999999999999999999999999999999999999999999999999999999 9999999999987

>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=99.70  E-value=8.2e-18  Score=145.73  Aligned_cols=85  Identities=21%  Similarity=0.412  Sum_probs=74.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .++++|||+|||+++++++|+++|+.||.|..+.+..+..+|+++|||||+|.+.++|.+|++.|++..|+|+.|+|+|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            35789999999999999999999999999954433333338999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      +....
T Consensus       103 ~~~~~  107 (115)
T 2cpx_A          103 KNKKQ  107 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            87543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.70  E-value=9.9e-18  Score=151.42  Aligned_cols=84  Identities=25%  Similarity=0.444  Sum_probs=80.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||+|||+++++++|+++|+.||.|++|+++.|+.+|+++|||||+|.+.++|++|++.|++..|+|+.|+|+|++
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ....
T Consensus       126 ~~~~  129 (135)
T 2lea_A          126 YGRP  129 (135)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.70  E-value=3.5e-17  Score=140.65  Aligned_cols=81  Identities=17%  Similarity=0.334  Sum_probs=75.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVS-FRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~-vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...++|||+|||++++|++|+++|+.||.|.+ |+|++| .+|+++|||||+|.+.++|++|++. ++..|+||.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            45789999999999999999999999999998 889888 7999999999999999999999987 99999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +...
T Consensus        91 ~~~~   94 (104)
T 1wg5_A           91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2e-17  Score=143.31  Aligned_cols=80  Identities=21%  Similarity=0.309  Sum_probs=76.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++|+++|+++|+.||.|.+|++++|+. |+++|||||+|.+.++|.+|+. ++++.|+|+.|+|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4578999999999999999999999999999999999987 9999999999999999999998 8999999999999998


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            75

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.9e-17  Score=134.16  Aligned_cols=78  Identities=32%  Similarity=0.591  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|++.        +|||||+|.+.++|++|++.||+..|+|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4578999999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      ++....
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

>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=99.70  E-value=5e-17  Score=140.78  Aligned_cols=82  Identities=22%  Similarity=0.436  Sum_probs=77.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--------CC
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI--------NG   75 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I--------~G   75 (551)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+++.|+ +|+++|||||+|.+.++|.+|++.||+..|        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            467899999999999999999999999999999999998 999999999999999999999999999999        57


Q ss_pred             EEEEEEeecCC
Q 008851           76 RQLRVDFAEND   86 (551)
Q Consensus        76 R~LrV~~A~~~   86 (551)
                      +.|+|+|+++.
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999999854

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.70  E-value=1.1e-16  Score=171.21  Aligned_cols=84  Identities=32%  Similarity=0.608  Sum_probs=80.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||+|||+++|+++|+++|+.||.|+.|.|+.|+.||+++|||||+|.+.++|.+||..||++.|+|+.|+|+|+.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 008851           85 NDKG   88 (551)
Q Consensus        85 ~~~~   88 (551)
                      ....
T Consensus       181 ~~~~  184 (437)
T 3pgw_S          181 GRTV  184 (437)
T ss_pred             CCCC
Confidence            7544

>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=99.69  E-value=1.1e-16  Score=137.96  Aligned_cols=80  Identities=21%  Similarity=0.440  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++.+      +|||||+|.+.++|.+|++.|++..|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            346789999999999999999999999999999999875      79999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      ++....
T Consensus        96 a~~~~~  101 (109)
T 1x4g_A           96 GKESPD  101 (109)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.69  E-value=4.3e-17  Score=143.66  Aligned_cols=81  Identities=17%  Similarity=0.277  Sum_probs=76.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGP---VVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~---V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      ...++|||+|||+++||++|+++|+.||.   |.+|+|++|++ |+++|||||+|.+.++|++|++ +|+..|+||.|+|
T Consensus        15 ~~~~~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           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45789999999999999999999999999   89999999987 9999999999999999999998 9999999999999


Q ss_pred             EeecCC
Q 008851           81 DFAEND   86 (551)
Q Consensus        81 ~~A~~~   86 (551)
                      .++...
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            999753

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.5e-17  Score=142.42  Aligned_cols=79  Identities=20%  Similarity=0.369  Sum_probs=72.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ--GYEINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln--g~~I~GR~LrV   80 (551)
                      ..+.++|||+|||+++||++|+++|+.||.|++|+|++|      ||||||+|.+.++|.+|++.|+  +..|+||.|+|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            357899999999999999999999999999999999865      7999999999999999999886  47899999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      +||+.+.
T Consensus        87 ~~A~~~~   93 (105)
T 1sjq_A           87 QFSNHKE   93 (105)
T ss_dssp             CCCSSSS
T ss_pred             EEcCCCC
Confidence            9998654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=5.7e-18  Score=143.74  Aligned_cols=82  Identities=18%  Similarity=0.353  Sum_probs=76.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|.. .++.|+.+|+++|||||+|.+.++|.+|++ ||+..|+|+.|+|+++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            36789999999999999999999999999988 777888899999999999999999999998 9999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ..+.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8643

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.2e-17  Score=140.41  Aligned_cols=82  Identities=26%  Similarity=0.537  Sum_probs=76.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|||+++++++|+++|+.||.|.+|++++|+  ++++|||||+|.+.++|++|++.|++..|+|+.|+|++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3468999999999999999999999999999999999886  45899999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      ++.+
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.69  E-value=5.2e-17  Score=139.81  Aligned_cols=80  Identities=26%  Similarity=0.444  Sum_probs=75.1

Q ss_pred             CCcEEEEecCCCCC------CHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCE-E
Q 008851            5 QHRCVFVGNIPYDA------TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGR-Q   77 (551)
Q Consensus         5 ~srtVFVGNLP~d~------TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR-~   77 (551)
                      .+++|||+|||+++      ++++|+++|+.||.|.+|+++  +.+|+++|||||+|.+.++|.+|++.|||..|+|+ .
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            47899999999999      789999999999999999988  47899999999999999999999999999999998 9


Q ss_pred             EEEEeecCC
Q 008851           78 LRVDFAEND   86 (551)
Q Consensus        78 LrV~~A~~~   86 (551)
                      |+|+++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999999754

>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=1.6e-16  Score=137.69  Aligned_cols=80  Identities=16%  Similarity=0.314  Sum_probs=72.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL--QGYEINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L--ng~~I~GR~LrV   80 (551)
                      ..++++|||+|||++++|++|+++|+.||.|++|+++.+      ||||||+|.+.++|.+|++.|  ++..|+||.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            346899999999999999999999999999999998864      799999999999999999976  567899999999


Q ss_pred             EeecCCCC
Q 008851           81 DFAENDKG   88 (551)
Q Consensus        81 ~~A~~~~~   88 (551)
                      +|++.+..
T Consensus        86 ~~a~~~~~   93 (101)
T 2cq1_A           86 QYSNHKEL   93 (101)
T ss_dssp             EECSCSSC
T ss_pred             EEcCcccC
Confidence            99986543

>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=99.68  E-value=4.3e-17  Score=136.87  Aligned_cols=84  Identities=19%  Similarity=0.429  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHH----HHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCE
Q 008851            1 MASSQHRCVFVGNIPYDATEEQLI----EICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGR   76 (551)
Q Consensus         1 ma~~~srtVFVGNLP~d~TEEeLr----e~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR   76 (551)
                      ++..++++|||+|||+++++++|+    ++|+.||.|.+|++..   +|+++|||||+|.+.++|.+|++.|||..|+|+
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   79 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCc
Confidence            356788999999999999999999    9999999999999873   688899999999999999999999999999999


Q ss_pred             EEEEEeecCCC
Q 008851           77 QLRVDFAENDK   87 (551)
Q Consensus        77 ~LrV~~A~~~~   87 (551)
                      .|+|++++.+.
T Consensus        80 ~l~v~~a~~~~   90 (97)
T 1nu4_A           80 PMRIQYAKTDS   90 (97)
T ss_dssp             ECEEEECSSCC
T ss_pred             EEEEEEccCCC
Confidence            99999998754

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=6.4e-17  Score=140.88  Aligned_cols=79  Identities=18%  Similarity=0.236  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCEEEE
Q 008851            3 SSQHRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG--YEINGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng--~~I~GR~Lr   79 (551)
                      ..++++|||+|||+ +++|++|+++|+.||.|.+|+|+++      +|||||+|.+.++|.+|++.|++  ..|+||+|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34789999999999 9999999999999999999999865      58999999999999999999885  469999999


Q ss_pred             EEeecCCC
Q 008851           80 VDFAENDK   87 (551)
Q Consensus        80 V~~A~~~~   87 (551)
                      |+||...+
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99998644

>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=1.4e-16  Score=136.15  Aligned_cols=76  Identities=20%  Similarity=0.378  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+.+..||||||++.+||++|+++|.+||+|++|++..      +||||||||.+.++|.+|++.||+.+++||.|+|++
T Consensus         4 ~~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~   77 (89)
T 2wbr_A            4 AWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAES   77 (89)
T ss_dssp             CCCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEE
Confidence            45678899999999999999999999999999999875      589999999999999999999999999999999999


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      |.
T Consensus        78 A~   79 (89)
T 2wbr_A           78 PS   79 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            95

>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=3.9e-16  Score=130.47  Aligned_cols=77  Identities=29%  Similarity=0.478  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++        ++||||+|.+.++|.+|++.||++.|+|+.|+|++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4568999999999999999999999999999999987        44999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++.+.
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            98654

>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=99.67  E-value=2.1e-17  Score=132.48  Aligned_cols=75  Identities=27%  Similarity=0.423  Sum_probs=71.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|++|++. ++..|+|+.|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999984 889999999999885

>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=1.5e-16  Score=138.40  Aligned_cols=78  Identities=17%  Similarity=0.221  Sum_probs=70.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCEEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG--YEINGRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng--~~I~GR~LrV~   81 (551)
                      .++++|||+|||++++|++|+++|+.||.|.+|+++.+      ||||||+|.+.++|.+|++.|++  ..|+|+.|+|+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            46899999999999999999999999999999998753      79999999999999999998865  45999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      |++.+.
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            998654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.2e-16  Score=135.62  Aligned_cols=76  Identities=29%  Similarity=0.519  Sum_probs=71.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++|||+|||+++++++|+++|+.||.|.+|++.      +++|||||+|.+.++|.+|++.||+..|+|+.|+|+|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            357899999999999999999999999999999987      45899999999999999999999999999999999998


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ++
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.7e-16  Score=131.63  Aligned_cols=76  Identities=22%  Similarity=0.454  Sum_probs=70.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREV--GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~--G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      .+.++|||+|||+++++++|+++|+.|  |.|.+|++.        +|||||+|.+.++|.+|++.||+..|+|+.|+|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            357899999999999999999999999  999998864        6899999999999999999999999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      ++++..
T Consensus        85 ~a~~~~   90 (99)
T 2cpd_A           85 LAKPVD   90 (99)
T ss_dssp             CCCCCC
T ss_pred             ECCCCC
Confidence            998654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.5e-16  Score=132.30  Aligned_cols=78  Identities=29%  Similarity=0.427  Sum_probs=71.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||++++|++|+++|+.||.|.+|  +.|+.+|+   ||||+|.+.++|.+|++ |+++.|+|+.|+|+++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            356899999999999999999999999999987  67777777   99999999999999999 9999999999999988


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ..+.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7544

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.67  E-value=6.1e-17  Score=137.62  Aligned_cols=80  Identities=25%  Similarity=0.465  Sum_probs=76.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++.|+ +|+++|||||+|.+.++|++|++  +++.++|+.|+|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            56899999999999999999999999999999999998 99999999999999999999998  9999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.7e-17  Score=145.43  Aligned_cols=81  Identities=20%  Similarity=0.374  Sum_probs=76.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||.|.++.++.+..+|+++|||||+|.+.++|.+|++ +|+..|+||.|+|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            56899999999999999999999999999997777788899999999999999999999999 99999999999999997


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus       103 ~~  104 (124)
T 1wel_A          103 KK  104 (124)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.67  E-value=1.5e-16  Score=140.38  Aligned_cols=80  Identities=20%  Similarity=0.272  Sum_probs=72.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...++|||+|||++++|++|+++|+.|| .|..+++..    ++++|||||+|.+.++|++|++.|||..|+||.|+|++
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3568999999999999999999999999 899998853    35799999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++...
T Consensus       102 a~~~p  106 (111)
T 2jvr_A          102 DDNPP  106 (111)
T ss_dssp             SCC--
T ss_pred             CCCCC
Confidence            97543

>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=99.67  E-value=1.6e-16  Score=132.90  Aligned_cols=78  Identities=27%  Similarity=0.501  Sum_probs=70.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCC-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGP-VVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG-YEINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~-V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng-~~I~GR~LrV   80 (551)
                      ....++|||+|||++++|++|+++|+.||. |..+.+.       ++|||||+|.+.++|++|++.||+ ..|+|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            456789999999999999999999999999 5555552       379999999999999999999999 9999999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      ++++++.
T Consensus        78 ~~a~~~~   84 (93)
T 2cqh_A           78 DYSVSKK   84 (93)
T ss_dssp             EECCCCC
T ss_pred             EEccCcc
Confidence            9998654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=2.1e-16  Score=134.06  Aligned_cols=76  Identities=29%  Similarity=0.482  Sum_probs=72.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ++|||+|||+++++++|+++|+.||.|.+|+++.|     ++|||||+|.+.++|.+|++.|++..++|+.|+|++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999876     6899999999999999999999999999999999999876


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.67  E-value=1.7e-17  Score=151.87  Aligned_cols=81  Identities=20%  Similarity=0.367  Sum_probs=75.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++||++|+++|+.|| |++|+|++|++ |+++|||||+|.+.++|++|+ .+|+..|+||.|+|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            3578999999999999999999999999 77999999986 999999999999999999999 78999999999999998


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ....
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=137.21  Aligned_cols=78  Identities=19%  Similarity=0.286  Sum_probs=71.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce--eCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE--INGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~--I~GR~LrV   80 (551)
                      ..++++|||+|||+++||++|+++|+.||.|.++++++      .||||||+|.+.++|.+|++.|++..  |+||+|+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            35789999999999999999999999999999999974      37999999999999999999998864  88999999


Q ss_pred             EeecCC
Q 008851           81 DFAEND   86 (551)
Q Consensus        81 ~~A~~~   86 (551)
                      +|++.+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            999764

>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=99.67  E-value=8.7e-17  Score=146.60  Aligned_cols=80  Identities=16%  Similarity=0.257  Sum_probs=76.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGP---VVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~---V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      ...++|||+|||+++||++|+++|+.||.   |.+|+|++|++ |+++|||||+|.+.++|++|++ +|+..|+||.|+|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            45789999999999999999999999999   89999999987 9999999999999999999999 9999999999999


Q ss_pred             EeecC
Q 008851           81 DFAEN   85 (551)
Q Consensus        81 ~~A~~   85 (551)
                      .++..
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            99864

>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=2.1e-16  Score=133.30  Aligned_cols=78  Identities=21%  Similarity=0.431  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC--CEEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN--GRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~--GR~LrV~   81 (551)
                      .+.++|||+|||++++|++|+++|+.||.|++|++..+      +|||||+|.+.++|++|++.||+..|+  |+.|+|+
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            46789999999999999999999999999999998753      789999999999999999999999999  9999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      |++++.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.66  E-value=4.6e-17  Score=133.25  Aligned_cols=73  Identities=29%  Similarity=0.498  Sum_probs=68.6

Q ss_pred             CcEEEEecCCCCC------CHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCE-EE
Q 008851            6 HRCVFVGNIPYDA------TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGR-QL   78 (551)
Q Consensus         6 srtVFVGNLP~d~------TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR-~L   78 (551)
                      +++|||+|||+++      ++++|+++|++||.|.+|++.  +.+|+++|||||+|.+.++|.+|++.|||..|+|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4789999999999      789999999999999999987  46899999999999999999999999999999999 88


Q ss_pred             EE
Q 008851           79 RV   80 (551)
Q Consensus        79 rV   80 (551)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.1e-16  Score=135.23  Aligned_cols=78  Identities=17%  Similarity=0.396  Sum_probs=71.7

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            3 SSQHRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         3 ~~~srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      .++.++|||+|||+ ++++++|+++|+.||.|.+|++.        +|||||+|.+.++|.+|++.|++..++|+.|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34789999999999 99999999999999999999984        7999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 008851           82 FAENDKG   88 (551)
Q Consensus        82 ~A~~~~~   88 (551)
                      ++.....
T Consensus        79 ~a~~~~~   85 (96)
T 2kvi_A           79 VSSSNAR   85 (96)
T ss_dssp             EEECCCC
T ss_pred             EcCcCCC
Confidence            9987543

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.1e-16  Score=141.49  Aligned_cols=79  Identities=20%  Similarity=0.369  Sum_probs=72.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ--GYEINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln--g~~I~GR~LrV   80 (551)
                      ..++++|||+|||++++|++|+++|+.||.|++|+|+.+      ||||||+|.+.++|.+|++.|+  +..|+|+.|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            457899999999999999999999999999999999875      7999999999999999999887  46899999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      +|++.+.
T Consensus       102 ~~a~~k~  108 (119)
T 2ad9_A          102 QFSNHKE  108 (119)
T ss_dssp             EECSSSS
T ss_pred             EEccCCC
Confidence            9998654

>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=99.66  E-value=2.9e-16  Score=145.70  Aligned_cols=84  Identities=23%  Similarity=0.406  Sum_probs=76.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++. ++..|+|+.|+|+++.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            458999999999999999999999999999999999999999999999999999999999976 7999999999999998


Q ss_pred             CCCCC
Q 008851           85 NDKGA   89 (551)
Q Consensus        85 ~~~~~   89 (551)
                      ++...
T Consensus       182 ~k~~~  186 (196)
T 1l3k_A          182 SKQEM  186 (196)
T ss_dssp             -----
T ss_pred             ChhHh
Confidence            76543

>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=99.66  E-value=5.2e-16  Score=139.56  Aligned_cols=81  Identities=28%  Similarity=0.543  Sum_probs=78.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +++|||+|||++++|++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|.+|++.|++..++|+.|+|.++.+
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            68999999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.66  E-value=3.6e-16  Score=149.71  Aligned_cols=82  Identities=26%  Similarity=0.454  Sum_probs=78.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||||||+++||++|+++|++||.|++|+|++|+.||+++|||||+|.+.++|.+|++.+++..+.|+.|+|.++.
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            57899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=2.2e-16  Score=133.67  Aligned_cols=78  Identities=33%  Similarity=0.531  Sum_probs=72.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|++|++..+      +|||||+|.+.++|.+|++.|++..|+|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            46789999999999999999999999999999999754      799999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +...
T Consensus        87 ~~~~   90 (99)
T 2cpj_A           87 CHSA   90 (99)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            8643

>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=99.66  E-value=2.9e-16  Score=135.61  Aligned_cols=75  Identities=27%  Similarity=0.454  Sum_probs=70.4

Q ss_pred             CCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..++|||+|||++ ++|++|+++|+.||.|.+|++        ++|||||+|.+.++|++|++.|++..|+|+.|+|+++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4589999999999 999999999999999999998        4899999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +..+
T Consensus        98 ~~~~  101 (110)
T 1wf1_A           98 GEPK  101 (110)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8643

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=5e-16  Score=139.51  Aligned_cols=81  Identities=28%  Similarity=0.580  Sum_probs=78.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|.+++++.|+.+|+++|||||+|.+.++|.+|++.|||..|+|+.|+|+||
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      +
T Consensus       165 ~  165 (166)
T 3md3_A          165 A  165 (166)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.66  E-value=1.2e-16  Score=134.06  Aligned_cols=79  Identities=25%  Similarity=0.452  Sum_probs=72.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++++++|+++|+.||.|..+     ..+|+++|||||+|.+.++|.+|++.|++..|+|+.|+|+++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            357899999999999999999999999988766     357999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      .++.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=2.2e-16  Score=133.45  Aligned_cols=79  Identities=34%  Similarity=0.503  Sum_probs=72.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|. ++++.    ++++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3478999999999999999999999999997 67765    467999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ++++
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>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=5.4e-16  Score=129.07  Aligned_cols=77  Identities=27%  Similarity=0.507  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+++        ++||||+|.+.++|.+|++.||+..|+|+.|+|++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4568999999999999999999999999999999997        45999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +....
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.66  E-value=2.4e-16  Score=141.96  Aligned_cols=82  Identities=20%  Similarity=0.392  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHH----HHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLI----EICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLr----e~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      ..++++|||+||++++++++|+    ++|++||.|++|.+.   .+|+++|||||+|.+.++|.+|++.|||..|.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3467899999999999999876    699999999998875   368999999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q 008851           79 RVDFAENDK   87 (551)
Q Consensus        79 rV~~A~~~~   87 (551)
                      +|+||+.+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999998654

>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=3.3e-16  Score=136.13  Aligned_cols=77  Identities=25%  Similarity=0.485  Sum_probs=72.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|++|+++        +|||||+|.+.++|.+|++.|||..|+|+.|+|+++
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            467999999999999999999999999999999987        799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      +....
T Consensus       101 ~~~~~  105 (108)
T 2jvo_A          101 KLPAK  105 (108)
T ss_dssp             SCCC-
T ss_pred             cCCCC
Confidence            87543

>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=99.66  E-value=4.7e-16  Score=140.56  Aligned_cols=83  Identities=27%  Similarity=0.548  Sum_probs=79.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++++|||+|||+++++++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|.+|++.|++..++|+.|+|.++.
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            57899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>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=7e-16  Score=131.29  Aligned_cols=76  Identities=18%  Similarity=0.430  Sum_probs=71.5

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            3 SSQHRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         3 ~~~srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      .+++++|||+|||+ ++++++|+++|+.||.|.+|++.        +|||||+|.+.++|.+|++.||+..++|+.|+|+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45789999999998 99999999999999999999983        7999999999999999999999999999999999


Q ss_pred             eecCC
Q 008851           82 FAEND   86 (551)
Q Consensus        82 ~A~~~   86 (551)
                      +++.+
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99764

>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=99.65  E-value=4.3e-16  Score=127.71  Aligned_cols=76  Identities=20%  Similarity=0.334  Sum_probs=71.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCEEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL-QGYEINGRQLRVD   81 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L-ng~~I~GR~LrV~   81 (551)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++.+      +|||||+|.+.++|.+|++.| ++..++|+.|+|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            346789999999999999999999999999999999864      799999999999999999988 9999999999999


Q ss_pred             eec
Q 008851           82 FAE   84 (551)
Q Consensus        82 ~A~   84 (551)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>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=99.65  E-value=8.6e-17  Score=145.08  Aligned_cols=85  Identities=22%  Similarity=0.320  Sum_probs=74.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEE--E---eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFR--L---VIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vr--L---v~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      .++++|||+|||+++|+++|+++|+.||.|..|.  +   +....+|+++|||||+|.+.++|.+|++.||+..|+|+.|
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            4678999999999999999999999999987751  1   1123579999999999999999999999999999999999


Q ss_pred             EEEeecCCCC
Q 008851           79 RVDFAENDKG   88 (551)
Q Consensus        79 rV~~A~~~~~   88 (551)
                      +|++|+....
T Consensus       123 ~V~~a~~~~~  132 (143)
T 3egn_A          123 VVQFARSARP  132 (143)
T ss_dssp             EEEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999986543

>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=99.65  E-value=4.8e-17  Score=140.47  Aligned_cols=82  Identities=16%  Similarity=0.263  Sum_probs=76.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGP---VVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~---V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      ....++|||+|||+++||++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++|++ +++..|+||.|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            346789999999999999999999999988   89999999987 9999999999999999999998 999999999999


Q ss_pred             EEeecCC
Q 008851           80 VDFAEND   86 (551)
Q Consensus        80 V~~A~~~   86 (551)
                      |.++...
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998753

>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=99.65  E-value=4.9e-16  Score=134.74  Aligned_cols=82  Identities=24%  Similarity=0.492  Sum_probs=75.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...+++|||+|||+++++++|+++|+.||.|.+|+++.|   ++++|||||+|.+.++|.+|++.|||..|+|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456899999999999999999999999999999999865   55699999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +.+..
T Consensus        82 a~~~~   86 (115)
T 3lqv_A           82 YNANR   86 (115)
T ss_dssp             CCHHH
T ss_pred             ecCCh
Confidence            98643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=5e-16  Score=136.34  Aligned_cols=78  Identities=19%  Similarity=0.301  Sum_probs=73.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||++++|++|+++|+.| .|++|+|++|++ |+++|||||+|.+.++|++|+ .+|+..|+||.|+|..+..
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-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            5789999999999999999999999 899999999986 999999999999999999999 6999999999999998865


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      .
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.63  E-value=9.2e-16  Score=144.38  Aligned_cols=83  Identities=27%  Similarity=0.492  Sum_probs=79.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+|+.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus       204 ~~~  206 (216)
T 2qfj_A          204 TPP  206 (216)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            753

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.63  E-value=1.2e-15  Score=141.84  Aligned_cols=84  Identities=32%  Similarity=0.572  Sum_probs=80.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|.+|++..|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
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            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      .++.
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.63  E-value=5.2e-16  Score=146.63  Aligned_cols=82  Identities=18%  Similarity=0.411  Sum_probs=78.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++|||+|||+++++++|+++|+.||.|++|+|++|+ +|+++|||||+|.+.++|.+|++.|++..|+|+.|+|+||
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            357899999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.2e-15  Score=127.24  Aligned_cols=77  Identities=22%  Similarity=0.346  Sum_probs=70.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|+  ++++++|+++|+.||.|.+|++.      +++|||||+|.+.++|.+|++.|++..|+|+.|+|+|+
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            36789999995  99999999999999999999984      56899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      ..+..
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.63  E-value=1.2e-15  Score=141.51  Aligned_cols=82  Identities=23%  Similarity=0.427  Sum_probs=77.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++||++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|.+|++. ++..|+|+.|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            4578999999999999999999999999999999999999999999999999999999999976 889999999999998


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ...
T Consensus        90 ~~~   92 (196)
T 1l3k_A           90 VSR   92 (196)
T ss_dssp             CC-
T ss_pred             cCc
Confidence            754

>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=99.62  E-value=1.1e-15  Score=138.90  Aligned_cols=80  Identities=34%  Similarity=0.603  Sum_probs=77.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.++++..|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|+||.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            36889999999999999999999999999999999999999999999999999999999999999999999999999973

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.62  E-value=7.3e-16  Score=140.44  Aligned_cols=79  Identities=18%  Similarity=0.202  Sum_probs=72.2

Q ss_pred             cEEEEecC----CCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HhCCce
Q 008851            7 RCVFVGNI----PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKD----EET----ALSARR--NLQGYE   72 (551)
Q Consensus         7 rtVFVGNL----P~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d----~e~----A~sAi~--~Lng~~   72 (551)
                      +.||||||    +|.++|++|+++|+.||+|.+|+++.|++||+++|||||+|.|    .++    |.+|++  .+++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999996    333    888988  789999


Q ss_pred             eCCEEEEEEeecC
Q 008851           73 INGRQLRVDFAEN   85 (551)
Q Consensus        73 I~GR~LrV~~A~~   85 (551)
                      |+||.|+|++.+.
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=3.9e-16  Score=140.03  Aligned_cols=80  Identities=21%  Similarity=0.310  Sum_probs=74.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCe----eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPV----VSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V----~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      .+.++|||+||||++||++|+++|+.||.|    .+|+|++|+ +|+++|||||+|.+.++|++|++. |+..|+||.|+
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            457899999999999999999999999986    689999995 899999999999999999999986 99999999999


Q ss_pred             EEeecC
Q 008851           80 VDFAEN   85 (551)
Q Consensus        80 V~~A~~   85 (551)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            999864

>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=99.62  E-value=6.9e-16  Score=140.23  Aligned_cols=79  Identities=28%  Similarity=0.515  Sum_probs=74.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|.+|+++.|     ++|||||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  145 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS  145 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            35789999999999999999999999999999999876     5899999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      .+++
T Consensus       146 ~~~~  149 (150)
T 2i2y_A          146 NGEK  149 (150)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>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=99.62  E-value=5.9e-16  Score=135.63  Aligned_cols=75  Identities=24%  Similarity=0.334  Sum_probs=66.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE-----EE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ-----LR   79 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~-----Lr   79 (551)
                      ..++|||+|||++++|++|+++|+.||.|++|.|+.|       |||||+|.+.++|++|++.||+..|+|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4688999999999999999999999999999999865       99999999999999999999999999988     77


Q ss_pred             EEeecCC
Q 008851           80 VDFAEND   86 (551)
Q Consensus        80 V~~A~~~   86 (551)
                      |+.+...
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            7776653

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=5.2e-16  Score=137.58  Aligned_cols=79  Identities=20%  Similarity=0.369  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCEEEE
Q 008851            3 SSQHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ--GYEINGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln--g~~I~GR~Lr   79 (551)
                      ..++++|||+|||++ ++|++|+++|+.||.|.+|+|++      .||||||+|.+.++|.+|++.|+  +..|+||.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            457899999999998 99999999999999999999973      37999999999999999999885  4569999999


Q ss_pred             EEeecCCC
Q 008851           80 VDFAENDK   87 (551)
Q Consensus        80 V~~A~~~~   87 (551)
                      |+|+....
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99997643

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=8.6e-16  Score=128.88  Aligned_cols=78  Identities=24%  Similarity=0.314  Sum_probs=72.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEE-EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFR-LVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vr-Lv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|+ ++.|+.+|+    |||+|.+.++|.+|++.||+..|+|+.|+|+++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            478999999999999999999999999999994 888876544    999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            875

>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=99.61  E-value=1.6e-15  Score=126.14  Aligned_cols=77  Identities=21%  Similarity=0.334  Sum_probs=71.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +..+++|||+|||++++|++|+++|++| .|.++++.      +++|||||+|.+.++|++|++.||+..++|+.|+|++
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   74 (88)
T 1wg1_A            2 SSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEE
Confidence            3467899999999999999999999999 99999884      5689999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +..+
T Consensus        75 a~~~   78 (88)
T 1wg1_A           75 QPTD   78 (88)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9754

>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=99.60  E-value=8.8e-16  Score=127.29  Aligned_cols=79  Identities=27%  Similarity=0.357  Sum_probs=68.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..++++|||+|||++++|++|+++|+.||.|.+|+++.+     ++|||||+|.+.++|++|+..  .+.++|+.|+|++
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~   74 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISN   74 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEe
Confidence            457899999999999999999999999999999999865     689999999999999865432  3566999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      +.++..
T Consensus        75 a~~~~~   80 (88)
T 1wf0_A           75 AEPKHN   80 (88)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            986543

>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=99.60  E-value=9.1e-16  Score=138.82  Aligned_cols=80  Identities=23%  Similarity=0.475  Sum_probs=76.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||+++++++|+++|+.||.|.++++..|+.+|+++|||||+|.+.++|.+|++ +++..|+|+.|+|+||.+
T Consensus        87 ~~~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           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCC
Confidence            5789999999999999999999999999999999999999999999999999999999997 899999999999999976


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.60  E-value=6.7e-16  Score=139.30  Aligned_cols=79  Identities=23%  Similarity=0.378  Sum_probs=72.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCee--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVV--SFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~--~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ...++|||+|||+++||++|+++|+.| .|+  +|+|++|++ |+++|||||+|.+.++|++|++. ++..|+||.|+|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEE
Confidence            357899999999999999999999999 677  999999987 99999999999999999999985 7799999999999


Q ss_pred             eecC
Q 008851           82 FAEN   85 (551)
Q Consensus        82 ~A~~   85 (551)
                      ++..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8864

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=1.3e-15  Score=132.92  Aligned_cols=76  Identities=16%  Similarity=0.155  Sum_probs=71.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|++..      .+|||||+|.+.++|.+|++.||+..|+|+.|+|+|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999999864      47899999999999999999999999999999999998


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=1.6e-15  Score=132.26  Aligned_cols=80  Identities=29%  Similarity=0.430  Sum_probs=72.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRET---GKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~T---GksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      ....++|||+|||++++|++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.|+  .++|+.+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            34679999999999999999999999999999 889988887   8999999999999999999999985  68899888


Q ss_pred             EEeecC
Q 008851           80 VDFAEN   85 (551)
Q Consensus        80 V~~A~~   85 (551)
                      +..+..
T Consensus        82 ~~~~~~   87 (114)
T 2dnl_A           82 CVSSPT   87 (114)
T ss_dssp             EECCSS
T ss_pred             eccCCC
Confidence            876553

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.59  E-value=4.9e-15  Score=133.00  Aligned_cols=80  Identities=28%  Similarity=0.530  Sum_probs=74.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      ++|||+|||++++|++|+++|+.||.|.+++++.|+ +|+++|||||+|.+.++|.+|++.|++..+.|+.|+|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            689999999999999999999999999999999997 4889999999999999999999999999999999999998754


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.59  E-value=2.6e-15  Score=141.31  Aligned_cols=81  Identities=30%  Similarity=0.465  Sum_probs=74.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||+|||+++||++|+++|+.||.|++|++++|+.+|+++|||||+|.+.++|.+|++.|++..|+|+.|+|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus       107 ~  107 (216)
T 2qfj_A          107 N  107 (216)
T ss_dssp             C
T ss_pred             C
Confidence            4

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.58  E-value=4.3e-15  Score=142.24  Aligned_cols=80  Identities=24%  Similarity=0.429  Sum_probs=75.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||.|++|+|++|+  +.++|||||+|.+.++|.+|++.|||..|+|+.|+|++|.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            35789999999999999999999999999999999986  4579999999999999999999999999999999999998


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ++
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.58  E-value=5.1e-15  Score=133.71  Aligned_cols=80  Identities=30%  Similarity=0.489  Sum_probs=76.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~   81 (551)
                      ...++|||+|||+++++++|+++|+.||.|.++++..|+.+|+++|||||+|.+.++|.+|++.||+..++|  ++|+|+
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            357899999999999999999999999999999999999999999999999999999999999999999988  999999


Q ss_pred             ee
Q 008851           82 FA   83 (551)
Q Consensus        82 ~A   83 (551)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.58  E-value=3.2e-15  Score=125.57  Aligned_cols=76  Identities=28%  Similarity=0.376  Sum_probs=63.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc--eeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY--EINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~--~I~GR~LrV   80 (551)
                      ....++|||||||+++||++|+++|++||.|++|++++|     +||||||+|.+.++|++    +++.  .++|+.|+|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            456789999999999999999999999999999999874     69999999999999884    3444  457999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      ++|.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9998653

>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=99.57  E-value=6.6e-15  Score=132.28  Aligned_cols=79  Identities=25%  Similarity=0.526  Sum_probs=75.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE--EEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ--LRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~--LrV~~   82 (551)
                      ..++|||+|||+++++++|+++|+.||.|.++++..|+.+|+++|||||+|.+.++|.+|++.|||..++|+.  |+|+|
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4688999999999999999999999999999999999999999999999999999999999999999999975  88888


Q ss_pred             e
Q 008851           83 A   83 (551)
Q Consensus        83 A   83 (551)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.57  E-value=6.1e-15  Score=121.11  Aligned_cols=73  Identities=27%  Similarity=0.587  Sum_probs=67.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREV----G-------PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY   71 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~----G-------~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~   71 (551)
                      +.+.++|||+|||+++++++|+++|+.|    |       .|.++++..+      +|||||+|.+.++|.+|+ .||+.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            3467999999999999999999999999    8       8999998754      799999999999999999 99999


Q ss_pred             eeCCEEEEEEe
Q 008851           72 EINGRQLRVDF   82 (551)
Q Consensus        72 ~I~GR~LrV~~   82 (551)
                      .|+|+.|+|++
T Consensus        76 ~~~g~~l~V~r   86 (87)
T 2hzc_A           76 IFQGQSLKIRR   86 (87)
T ss_dssp             EETTEECEEEC
T ss_pred             EECCeEEEEeC
Confidence            99999999974

>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=99.57  E-value=7.4e-15  Score=133.23  Aligned_cols=83  Identities=24%  Similarity=0.434  Sum_probs=76.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCceeC---CEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETG--KPKGYGFCEYKDEETALSARRNLQGYEIN---GRQL   78 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TG--ksKGyAFVEF~d~e~A~sAi~~Lng~~I~---GR~L   78 (551)
                      +++++|||+|||++++|++|+++|+.||.|.+|++++|+.+|  +++|||||+|.+.++|.+|++.|++..+.   ++.+
T Consensus         1 s~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            367999999999999999999999999999999999999887  89999999999999999999999998775   6778


Q ss_pred             EEEeecCC
Q 008851           79 RVDFAEND   86 (551)
Q Consensus        79 rV~~A~~~   86 (551)
                      .+.++...
T Consensus        81 ~~~~~~~~   88 (175)
T 3nmr_A           81 QMKPADSE   88 (175)
T ss_dssp             EEEECGGG
T ss_pred             EEcccccc
Confidence            88887654

>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=99.57  E-value=3.8e-15  Score=134.70  Aligned_cols=79  Identities=22%  Similarity=0.458  Sum_probs=74.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++++|||+|||+++||++|+++|+.||.|.+|++++|+.+|+++|||||+|.+.++|.+|++.  +..++|+.|+|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            578999999999999999999999999999999999999999999999999999999999985  569999999999986


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.56  E-value=1.1e-14  Score=137.27  Aligned_cols=78  Identities=24%  Similarity=0.324  Sum_probs=70.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEEee
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVDFA   83 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~~A   83 (551)
                      ..+|||+||++++||++|+++|++||.|++|++..+    +.+|||||+|.+.++|++|++.|||..|.|  +.|+|+|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            356899999999999999999999999999998643    257999999999999999999999999965  99999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +.+.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8754

>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=99.56  E-value=1.2e-14  Score=143.37  Aligned_cols=83  Identities=19%  Similarity=0.449  Sum_probs=76.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH----HHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLI----EICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ   77 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLr----e~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~   77 (551)
                      +..++++|||+|||++++|++|+    ++|+.||.|++|++++   +|+++|||||+|.+.++|.+|++.||+..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            44678999999999999999976    8999999999999875   7899999999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q 008851           78 LRVDFAENDK   87 (551)
Q Consensus        78 LrV~~A~~~~   87 (551)
                      |+|+|++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997543

>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=99.55  E-value=1e-14  Score=129.85  Aligned_cols=79  Identities=24%  Similarity=0.397  Sum_probs=71.2

Q ss_pred             CCCCcEEEE--ecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-----CC
Q 008851            3 SSQHRCVFV--GNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI-----NG   75 (551)
Q Consensus         3 ~~~srtVFV--GNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I-----~G   75 (551)
                      ..+.++|||  |||+++++|++|+++|++||.|.+|.+..+      ||||||+|.+.++|++|++.|||.+|     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            446789999  779999999999999999999999987632      79999999999999999999999998     78


Q ss_pred             EEEEEEeecCCC
Q 008851           76 RQLRVDFAENDK   87 (551)
Q Consensus        76 R~LrV~~A~~~~   87 (551)
                      +.|.|+|+....
T Consensus        96 ~~l~v~~a~~~p  107 (114)
T 2cq2_A           96 ITLYLNFVEKVQ  107 (114)
T ss_dssp             EECEEEEESCCC
T ss_pred             cEEEEEecccCc
Confidence            999999998543

>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=99.55  E-value=1.2e-14  Score=131.82  Aligned_cols=79  Identities=20%  Similarity=0.390  Sum_probs=74.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---CEEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN---GRQLRVD   81 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~---GR~LrV~   81 (551)
                      ..++|||+|||+++++++|+++|+.||.|.++++..|+ +|+++|||||+|.+.++|.+|++.|||..+.   |++|+|+
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            56899999999999999999999999999999999996 5999999999999999999999999998775   4999999


Q ss_pred             eec
Q 008851           82 FAE   84 (551)
Q Consensus        82 ~A~   84 (551)
                      ||+
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>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=3.3e-14  Score=129.26  Aligned_cols=76  Identities=25%  Similarity=0.388  Sum_probs=69.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--EEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGY-GFCEYKDEETALSARRNLQGYEING--RQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGy-AFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~~A   83 (551)
                      -+|||+||++.+||++|+++|++||.|.+|++..+.     +|| |||+|.+.++|++|++.|||..|.|  +.|+|+|+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            457899999999999999999999999999887542     687 9999999999999999999999988  99999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +...
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            8753

>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=99.54  E-value=1.8e-14  Score=138.71  Aligned_cols=79  Identities=13%  Similarity=0.180  Sum_probs=73.6

Q ss_pred             CCCcEEEEecCC-CCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIP-YDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP-~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .++++|||+||+ +++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|++|++.|||..+.|+.|+|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            467899999999 899999999999999999999998763     79999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      ++...
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            97543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.54  E-value=3.7e-14  Score=123.53  Aligned_cols=84  Identities=21%  Similarity=0.251  Sum_probs=75.3

Q ss_pred             CCCCcEEEEecCCC-----CCCHHHHHHHHHcCCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCE
Q 008851            3 SSQHRCVFVGNIPY-----DATEEQLIEICREVGPVVSFRLVIDRET-GKPKGYGFCEYKDEETALSARRNLQGYEINGR   76 (551)
Q Consensus         3 ~~~srtVFVGNLP~-----d~TEEeLre~Fs~~G~V~~vrLv~Dr~T-GksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR   76 (551)
                      ..++++|+|.|+-.     +-++++|+++|++||.|.+|+|.+|+++ ++++|||||+|.+.++|.+|++.|||..++||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            35789999999963     2368999999999999999999998765 68999999999999999999999999999999


Q ss_pred             EEEEEeecCC
Q 008851           77 QLRVDFAEND   86 (551)
Q Consensus        77 ~LrV~~A~~~   86 (551)
                      .|+|+++...
T Consensus        85 ~i~v~~a~~~   94 (105)
T 2pe8_A           85 VVKACFYNLD   94 (105)
T ss_dssp             ECEEEECCHH
T ss_pred             EEEEEEcCHH
Confidence            9999999753

>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=99.52  E-value=2.8e-14  Score=130.52  Aligned_cols=77  Identities=26%  Similarity=0.469  Sum_probs=71.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|..+     ..+|+++|||||+|.+.++|.+|++.|||..|+|+.|+|+||.
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            46899999999999999999999999988766     4689999999999999999999999999999999999999997


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ++
T Consensus       173 ~k  174 (175)
T 1fje_B          173 EK  174 (175)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.51  E-value=5.5e-14  Score=134.37  Aligned_cols=78  Identities=21%  Similarity=0.278  Sum_probs=72.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||+++++++|+++|+.||.|.+|++.+|+ +|+++|||||+|.+.++|.+|++.++ ..|+|+.|+|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            4789999999999999999999999999999999987 59999999999999999999997654 599999999999764

>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=5.1e-14  Score=121.70  Aligned_cols=75  Identities=20%  Similarity=0.415  Sum_probs=67.2

Q ss_pred             CCCcE-EEEecCCCCCCHHH----HHHHHHcC-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE
Q 008851            4 SQHRC-VFVGNIPYDATEEQ----LIEICREV-GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ   77 (551)
Q Consensus         4 ~~srt-VFVGNLP~d~TEEe----Lre~Fs~~-G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~   77 (551)
                      +++.+ |||+|||+++++++    |+++|+.| |+|.+|       ||   |+|||+|.+.++|.+|++.|+|..+.||.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            35666 99999999999988    55899999 599998       34   99999999999999999999999999999


Q ss_pred             EEEEeecCCCC
Q 008851           78 LRVDFAENDKG   88 (551)
Q Consensus        78 LrV~~A~~~~~   88 (551)
                      |+|+||+.+..
T Consensus        76 i~v~~A~~~sd   86 (96)
T 2diu_A           76 IIVSFTPKNRE   86 (96)
T ss_dssp             CEEESSCCSCC
T ss_pred             EEEEecCCCcc
Confidence            99999987643

>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=99.50  E-value=1e-13  Score=136.97  Aligned_cols=84  Identities=31%  Similarity=0.544  Sum_probs=79.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +..++|||+|||+++++++|+++|+.||.|.+++++.|+.+|+++|||||+|.+.++|.+|++.|++..|+|+.|+|+++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ....
T Consensus       173 ~~~~  176 (284)
T 3smz_A          173 DAGQ  176 (284)
T ss_dssp             CGGG
T ss_pred             CCCC
Confidence            7643

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=6.9e-14  Score=125.92  Aligned_cols=74  Identities=24%  Similarity=0.424  Sum_probs=66.9

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--EEEEEEeec
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGY-GFCEYKDEETALSARRNLQGYEING--RQLRVDFAE   84 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGy-AFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~~A~   84 (551)
                      .|||+||++.+++++|+++|+.||.|.+|++.. +     .|| |||+|.+.++|.+|++.|||..|.|  +.|+|++|+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            368999999999999999999999999999864 2     386 9999999999999999999999987  689999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            654

>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=99.49  E-value=6.2e-14  Score=139.01  Aligned_cols=82  Identities=15%  Similarity=0.274  Sum_probs=76.0

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            4 SQHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRE-TGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~-TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ...++|||+|||++ +++++|+++|+.||.|.+|+++.|.. ||+++|||||+|.+.++|.+|+ .|||..|+|+.|+|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS  286 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEE
Confidence            35689999999999 99999999999999999999999887 7999999999999999999999 999999999999999


Q ss_pred             eecCC
Q 008851           82 FAEND   86 (551)
Q Consensus        82 ~A~~~   86 (551)
                      |+.++
T Consensus       287 ~a~~k  291 (292)
T 2ghp_A          287 LADKK  291 (292)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99864

>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=99.49  E-value=9e-14  Score=137.17  Aligned_cols=75  Identities=28%  Similarity=0.488  Sum_probs=71.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-GRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-GR~LrV~~A   83 (551)
                      ++++|||+|||+++++++|+++|+.||.|++|+++.++     +|||||+|.+.++|.+|++.|||..|+ |+.|+|+|+
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            57899999999999999999999999999999998664     689999999999999999999999999 999999998


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      +
T Consensus       281 k  281 (282)
T 3pgw_A          281 K  281 (282)
T ss_pred             c
Confidence            6

>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=99.48  E-value=1.4e-14  Score=132.49  Aligned_cols=82  Identities=20%  Similarity=0.362  Sum_probs=74.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.+.. .++.+..+|+++|||||+|.+.++|.+|+ .|++..|+|+.|+|++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            457899999999999999999999999998776 44556678999999999999999999999 5999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +...
T Consensus        88 ~~~~   91 (175)
T 1fje_B           88 PKGR   91 (175)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            9764

>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=99.48  E-value=1.2e-13  Score=136.55  Aligned_cols=83  Identities=25%  Similarity=0.430  Sum_probs=78.1

Q ss_pred             CCCcEEEEecCCCCC-CHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDA-TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~-TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ...++|||+|||+++ ++++|+++|+.||.|.++++..|+ +|+++|||||+|.+.++|.+|++.|||..|+|+.|+|+|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            357899999999995 999999999999999999999987 799999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +.++.
T Consensus       261 a~~~~  265 (284)
T 3smz_A          261 CAPGP  265 (284)
T ss_dssp             CCSSS
T ss_pred             ecCCC
Confidence            98654

>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=99.47  E-value=1.2e-13  Score=133.47  Aligned_cols=78  Identities=18%  Similarity=0.371  Sum_probs=74.0

Q ss_pred             CCCcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .++++|||+|||+ +++|++|+++|+.||.|.+|++++|+     +|||||+|.+.++|.+|++.|++..|+|+.|+|++
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4689999999999 99999999999999999999999875     89999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +...
T Consensus       107 a~~~  110 (229)
T 2adc_A          107 SKHQ  110 (229)
T ss_dssp             CSCC
T ss_pred             ecCc
Confidence            9865

>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=99.46  E-value=3.8e-13  Score=117.02  Aligned_cols=81  Identities=25%  Similarity=0.381  Sum_probs=70.3

Q ss_pred             CCCCcEEEEecCCCCCC-----------HHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 008851            3 SSQHRCVFVGNIPYDAT-----------EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY   71 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~T-----------EEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~   71 (551)
                      ..++++|+|.||-...+           +++|+++|++||.|.+|.| .|+   .++|||||+|.+.++|.+|++.|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34689999999944332           5899999999999999965 564   37999999999999999999999999


Q ss_pred             eeCCEEEEEEeecCCC
Q 008851           72 EINGRQLRVDFAENDK   87 (551)
Q Consensus        72 ~I~GR~LrV~~A~~~~   87 (551)
                      .|+||.|+|+++.+..
T Consensus        88 ~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           88 WFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCcEEEEEEeCCCC
Confidence            9999999999998654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.45  E-value=2.1e-13  Score=127.60  Aligned_cols=78  Identities=18%  Similarity=0.369  Sum_probs=73.1

Q ss_pred             CCcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+++|||+|||+ ++++++|+++|+.||.|.+|++++|+     +|||||+|.+.++|.+|++.|++..|+|+.|+|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            358999999999 99999999999999999999998875     789999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ....
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8653

>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=6.1e-14  Score=130.19  Aligned_cols=75  Identities=25%  Similarity=0.577  Sum_probs=66.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREV----G-------PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~----G-------~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      .+++|||+|||++++|++|+++|+.|    |       .|.++++      ++++|||||+|.+.++|.+|+ .|++..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            57999999999999999999999999    4       5555554      566899999999999999999 8999999


Q ss_pred             CCEEEEEEeecCC
Q 008851           74 NGRQLRVDFAEND   86 (551)
Q Consensus        74 ~GR~LrV~~A~~~   86 (551)
                      +|+.|+|+++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998764

>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=99.41  E-value=4.1e-13  Score=133.11  Aligned_cols=83  Identities=17%  Similarity=0.295  Sum_probs=71.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..++|||+|||+++++++|+++|+.|| .|.+|+++.|+. |+++|||||+|.+.++|.+|++.|++..|+|+.|+|+++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 999999999876 889999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 008851           84 ENDKG   88 (551)
Q Consensus        84 ~~~~~   88 (551)
                      .+...
T Consensus       195 ~~~~~  199 (292)
T 2ghp_A          195 NPLEK  199 (292)
T ss_dssp             CCC--
T ss_pred             CCCcc
Confidence            86543

>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=99.41  E-value=6.2e-13  Score=131.17  Aligned_cols=82  Identities=24%  Similarity=0.314  Sum_probs=74.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CceeC---CEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ-GYEIN---GRQLRV   80 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln-g~~I~---GR~LrV   80 (551)
                      ++++|||+|||+++|+++|+++|+.||.|.+|+++.| .+|+++|||||+|.+.++|.+|++.|+ +..+.   ||.|+|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            4689999999999999999999999999999999999 589999999999999999999999995 44444   999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      +++....
T Consensus       174 ~~~~~~~  180 (261)
T 3sde_A          174 EPMEQFD  180 (261)
T ss_dssp             EECCCEE
T ss_pred             eeccccC
Confidence            9998643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.40  E-value=3.2e-13  Score=134.31  Aligned_cols=79  Identities=23%  Similarity=0.399  Sum_probs=70.7

Q ss_pred             CCCcEEEEecCCCCC---------CHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-
Q 008851            4 SQHRCVFVGNIPYDA---------TEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI-   73 (551)
Q Consensus         4 ~~srtVFVGNLP~d~---------TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I-   73 (551)
                      ...++||||||++++         +|++|+++|+.||.|.+|+|+.+      ||||||+|.+.++|+.|++.|++..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            357899999999998         79999999999999999999853      79999999999999999999999999 


Q ss_pred             -----------CCEEEEEEeecCCCC
Q 008851           74 -----------NGRQLRVDFAENDKG   88 (551)
Q Consensus        74 -----------~GR~LrV~~A~~~~~   88 (551)
                                 +|+.|+|+||+.+..
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccccCCCCEEEEEEccCCCC
Confidence                       899999999987543

>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=99.40  E-value=4e-13  Score=129.23  Aligned_cols=77  Identities=22%  Similarity=0.416  Sum_probs=69.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCe--eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCE----EE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPV--VSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGR----QL   78 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V--~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR----~L   78 (551)
                      ++++|||+|||+++||++|+++|+.||.|  +++++..|+  |+.+|||||+|.+.++|.+|+..||++.|+|+    ++
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            56789999999999999999999999999  899988775  66679999999999999999999999999886    56


Q ss_pred             EEEee
Q 008851           79 RVDFA   83 (551)
Q Consensus        79 rV~~A   83 (551)
                      .|++|
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            77765

>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=99.40  E-value=8.2e-13  Score=114.88  Aligned_cols=83  Identities=18%  Similarity=0.248  Sum_probs=73.5

Q ss_pred             CCCcEEEEecC--CCCCC--------HHHHHHHHHcCCCeeEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCc
Q 008851            4 SQHRCVFVGNI--PYDAT--------EEQLIEICREVGPVVSFRLVIDRET--GKPKGYGFCEYKDEETALSARRNLQGY   71 (551)
Q Consensus         4 ~~srtVFVGNL--P~d~T--------EEeLre~Fs~~G~V~~vrLv~Dr~T--GksKGyAFVEF~d~e~A~sAi~~Lng~   71 (551)
                      .++++|.|.|+  +.+..        +++|++.|++||.|.+|+|.+|+++  ++++|||||+|.+.++|.+|++.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            47899999998  44443        3689999999999999999998865  478999999999999999999999999


Q ss_pred             eeCCEEEEEEeecCC
Q 008851           72 EINGRQLRVDFAEND   86 (551)
Q Consensus        72 ~I~GR~LrV~~A~~~   86 (551)
                      .++||.|+|+++...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998754

>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=4.1e-13  Score=125.56  Aligned_cols=76  Identities=22%  Similarity=0.377  Sum_probs=71.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CEEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-GRQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-GR~LrV~~   82 (551)
                      ++++|||+|||+++++++|+++|+.|| .|.+++++.+.     +|||||+|.+.++|.+|++.|||..|+ |+.|+|+|
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            478999999999999999999999999 99999997542     799999999999999999999999999 99999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +++
T Consensus       194 a~~  196 (198)
T 1qm9_A          194 SKS  196 (198)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            975

>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=99.39  E-value=2.3e-13  Score=118.10  Aligned_cols=72  Identities=15%  Similarity=0.252  Sum_probs=64.2

Q ss_pred             EecCCCCCCHHHHHHHH------------HcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851           11 VGNIPYDATEEQLIEIC------------REVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus        11 VGNLP~d~TEEeLre~F------------s~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      +.||++++++++|++.|            ++||.|.+|+|++|+. |+++|||||+|.+.++|.+|++.|||..++||.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777887777666            9999999999998874 8999999999999999999999999999999999


Q ss_pred             EEEee
Q 008851           79 RVDFA   83 (551)
Q Consensus        79 rV~~A   83 (551)
                      +|+|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=8.3e-13  Score=127.63  Aligned_cols=76  Identities=22%  Similarity=0.375  Sum_probs=71.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CEEEEEEe
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN-GRQLRVDF   82 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G-~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~-GR~LrV~~   82 (551)
                      ++++|||+|||+++++++|+++|+.|| .|.+|+++.+     .+|||||+|.+.++|.+|++.|+|..|+ |+.|+|+|
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            468999999999999999999999999 9999999653     3799999999999999999999999999 99999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +++
T Consensus       225 a~~  227 (229)
T 2adc_A          225 SKS  227 (229)
T ss_dssp             CSS
T ss_pred             ecC
Confidence            975

>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=99.38  E-value=1.1e-12  Score=129.42  Aligned_cols=75  Identities=31%  Similarity=0.503  Sum_probs=70.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++|+++|+++|+.||.|.+|++.+      .+|||||+|.+.++|.+|++.|++..|+|+.|+|.++.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~   94 (261)
T 3sde_A           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            468999999999999999999999999999999864      37999999999999999999999999999999999987


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus        95 ~   95 (261)
T 3sde_A           95 H   95 (261)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.37  E-value=1.5e-12  Score=118.10  Aligned_cols=75  Identities=25%  Similarity=0.571  Sum_probs=67.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREV----G-------PVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~----G-------~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      ++++|||+|||+++||++|+++|+.|    |       .|.++++.      +++|||||+|.+.++|.+|+ .+++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            57899999999999999999999999    6       67777654      45899999999999999999 8999999


Q ss_pred             CCEEEEEEeecCC
Q 008851           74 NGRQLRVDFAEND   86 (551)
Q Consensus        74 ~GR~LrV~~A~~~   86 (551)
                      +|+.|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987643

>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=99.37  E-value=1.8e-12  Score=115.39  Aligned_cols=83  Identities=17%  Similarity=0.260  Sum_probs=73.4

Q ss_pred             CCCcEEEEecCC--CCC---CHHHHHHHHHcCCCeeEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            4 SQHRCVFVGNIP--YDA---TEEQLIEICREVGPVVSFRLVIDRE----TGKPKGYGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         4 ~~srtVFVGNLP--~d~---TEEeLre~Fs~~G~V~~vrLv~Dr~----TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      +++++|+|.|+-  .++   -+++|++.|++||.|.+|+|..|+.    +++++||+||+|.+.++|.+|++.|||..++
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            368999999983  222   3689999999999999999999875    4678899999999999999999999999999


Q ss_pred             CEEEEEEeecCC
Q 008851           75 GRQLRVDFAEND   86 (551)
Q Consensus        75 GR~LrV~~A~~~   86 (551)
                      ||.|+|+++...
T Consensus        98 GR~i~v~~~~~~  109 (118)
T 3ue2_A           98 GRKVVAEVYDQE  109 (118)
T ss_dssp             TEECEEEEECHH
T ss_pred             CcEEEEEEcChH
Confidence            999999998753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=3.1e-11  Score=104.58  Aligned_cols=75  Identities=16%  Similarity=0.185  Sum_probs=63.6

Q ss_pred             CcEEEEecCC-------CCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            6 HRCVFVGNIP-------YDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         6 srtVFVGNLP-------~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      .++|-|....       .+++|++|+++|++||.|++|+|+     ++++|||||+|.+.++|++|++.++  .+.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            4566665543       458999999999999999999987     4779999999999999999999865  4689999


Q ss_pred             EEEeecCCC
Q 008851           79 RVDFAENDK   87 (551)
Q Consensus        79 rV~~A~~~~   87 (551)
                      +|+|++...
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999988654

>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=99.19  E-value=3.2e-11  Score=125.64  Aligned_cols=76  Identities=26%  Similarity=0.425  Sum_probs=66.7

Q ss_pred             CCCCcEEEEec--CCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCE-
Q 008851            3 SSQHRCVFVGN--IPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI---NGR-   76 (551)
Q Consensus         3 ~~~srtVFVGN--LP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I---~GR-   76 (551)
                      +.++++|||||  |++++||++|+++|++||.|.+|.+..      .||||||+|.+.++|++|++.|||.++   .|+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45789999999  689999999999999999999987642      479999999999999999999999988   245 


Q ss_pred             -EEEEEeec
Q 008851           77 -QLRVDFAE   84 (551)
Q Consensus        77 -~LrV~~A~   84 (551)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57888875

>2j8p_A Cleavage stimulation factor 64 kDa subunit; cleavage/polyadenylation, alternative splicing RNA15, PCF11, CSTF-64, RNA-binding, nuclear protein; NMR {Homo sapiens}

Probab=99.18  E-value=1.3e-11  Score=94.04  Aligned_cols=42  Identities=38%  Similarity=0.611  Sum_probs=39.3

Q ss_pred             chHHHHHHHHHHhcCHHHHhcCChHHHHHHHHHHHHHHhhhc
Q 008851          507 PDVESALLQQVLSLTPEQLNSLPPEQRQQVIQLQQALLRDQM  548 (551)
Q Consensus       507 p~~~~~~~~qv~~l~~~q~~~lp~~q~~~v~~~~~~~~~~~~  548 (551)
                      +++|.+||+|||+||||||..|||++|++|++||++|.+...
T Consensus         6 ~~~q~~Li~QVLsLt~eQI~~LPp~qR~qI~~LR~q~~~~~~   47 (49)
T 2j8p_A            6 DHEKAALIMQVLQLTADQIAMLPPEQRQSILILKEQIQKSTG   47 (49)
T ss_dssp             HHTHHHHHHHHHTSCHHHHHTSCHHHHTHHHHHHHHHHCCCC
T ss_pred             cccHHHHHHHHHhCCHHHHHhCCHHHHHHHHHHHHHHHhccC
Confidence            578999999999999999999999999999999999998654

>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=99.13  E-value=1.7e-10  Score=102.09  Aligned_cols=79  Identities=18%  Similarity=0.325  Sum_probs=67.3

Q ss_pred             CCCcEEEEecCCCCCC----------HHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            4 SQHRCVFVGNIPYDAT----------EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         4 ~~srtVFVGNLP~d~T----------EEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      -++++|.+.|+=....          +++|++.|++||.|.+|.|.++.    .+|||||+|.+.++|.+|++.|||..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4688899998733221          35789999999999999986542    489999999999999999999999999


Q ss_pred             CCEEEEEEeecCC
Q 008851           74 NGRQLRVDFAEND   86 (551)
Q Consensus        74 ~GR~LrV~~A~~~   86 (551)
                      +||.|+|+|+...
T Consensus        81 ~GR~i~v~~~~~~   93 (114)
T 3s6e_A           81 AGKMITAAYVPLP   93 (114)
T ss_dssp             TTEECEEEEECHH
T ss_pred             CCEEEEEEEEcHH
Confidence            9999999999754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=3.9e-09  Score=90.44  Aligned_cols=74  Identities=20%  Similarity=0.341  Sum_probs=63.6

Q ss_pred             CCCcEEEEecCC----CCCCH----HHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 008851            4 SQHRCVFVGNIP----YDATE----EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING   75 (551)
Q Consensus         4 ~~srtVFVGNLP----~d~TE----EeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G   75 (551)
                      +++-+|+|.-.+    .++-.    .+|.+.|+.||.|+.++++.|+        +||+|.+.+.|.+|++ |||..++|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            567788888766    23433    5789999999999999999775        7999999999999998 99999999


Q ss_pred             EEEEEEeecCC
Q 008851           76 RQLRVDFAEND   86 (551)
Q Consensus        76 R~LrV~~A~~~   86 (551)
                      |.|+|++++++
T Consensus        76 r~LkV~lkt~d   86 (91)
T 2dnr_A           76 RTITIALKSPS   86 (91)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEeCCCC
Confidence            99999998864

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.88  E-value=2.9e-09  Score=95.64  Aligned_cols=76  Identities=13%  Similarity=0.176  Sum_probs=67.9

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHhC--CceeCCEEEE
Q 008851            4 SQHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKD-EETALSARRNLQ--GYEINGRQLR   79 (551)
Q Consensus         4 ~~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d-~e~A~sAi~~Ln--g~~I~GR~Lr   79 (551)
                      ..++.|||+||+++ +++++|+++|+.||.|.+|.+..|..      .|||+|.+ .++|..|++.++  +..|+|..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            36789999999999 99999999999999999999988764      59999999 899999999995  6788998888


Q ss_pred             EEeecC
Q 008851           80 VDFAEN   85 (551)
Q Consensus        80 V~~A~~   85 (551)
                      ++....
T Consensus        90 ~evL~G   95 (121)
T 1owx_A           90 WEVLEG   95 (121)
T ss_dssp             EEECCH
T ss_pred             EEECCC
Confidence            887653

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.80  E-value=7.6e-09  Score=99.32  Aligned_cols=69  Identities=19%  Similarity=0.260  Sum_probs=62.3

Q ss_pred             CCHHHHHHHHHcCCCeeEEEEeec----CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851           18 ATEEQLIEICREVGPVVSFRLVID----RETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus        18 ~TEEeLre~Fs~~G~V~~vrLv~D----r~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      -.+++|++.|++||.|.++.+..+    +++|+++|++||+|.+.++|.+|++.|||..++||.|+|.++...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~  213 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQE  213 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHH
Confidence            456889999999999999999855    456699999999999999999999999999999999999998753

>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=98.70  E-value=1.7e-08  Score=87.08  Aligned_cols=73  Identities=18%  Similarity=0.288  Sum_probs=62.5

Q ss_pred             CCCcEEEEecCCCC-----CCH----HHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            4 SQHRCVFVGNIPYD-----ATE----EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         4 ~~srtVFVGNLP~d-----~TE----EeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      +++-+|+|.-++.+     +..    .+|.+.|+.||.|+.++++.|+        +||+|.+.+.|.+|++ |+|..++
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            56788999887643     322    4688999999999999999875        8999999999999998 9999999


Q ss_pred             CEEEEEEeecC
Q 008851           75 GRQLRVDFAEN   85 (551)
Q Consensus        75 GR~LrV~~A~~   85 (551)
                      ||.|+|++..+
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.15  E-value=7.5e-06  Score=72.49  Aligned_cols=74  Identities=14%  Similarity=0.146  Sum_probs=67.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcC-----CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREV-----GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~-----G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      ..++|-+-|||..++++.|+.+++.+     |.++.+.++.|.      |-|+|+|.|..+|.+|.-.|+|.+|+||+|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            36889999999999999999999999     999999999874      6789999999999999999999999999999


Q ss_pred             EEeec
Q 008851           80 VDFAE   84 (551)
Q Consensus        80 V~~A~   84 (551)
                      |.-..
T Consensus        94 ~gTv~   98 (117)
T 2l9w_A           94 SGTIN   98 (117)
T ss_dssp             EECHH
T ss_pred             ecCHH
Confidence            87543

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.08  E-value=0.0018  Score=56.62  Aligned_cols=76  Identities=16%  Similarity=0.169  Sum_probs=64.2

Q ss_pred             CCCcEEEEecCCCCCC-----HHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            4 SQHRCVFVGNIPYDAT-----EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         4 ~~srtVFVGNLP~d~T-----EEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      .-.++++|.||+.++-     .+.++++|..|+++..+...+.-      .-..|.|.+.++|.+|-..||+..++|++|
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            3457899999988763     25789999999999998877543      235789999999999999999999999999


Q ss_pred             EEEeecC
Q 008851           79 RVDFAEN   85 (551)
Q Consensus        79 rV~~A~~   85 (551)
                      +|-++..
T Consensus        77 r~YFgq~   83 (104)
T 1wey_A           77 KLYFAQT   83 (104)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999874

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.65  E-value=0.012  Score=50.28  Aligned_cols=78  Identities=23%  Similarity=0.327  Sum_probs=61.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCc--ceEEEEEeCCHHHHHHHHHHhCCceeC---C--EEEE
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP--KGYGFCEYKDEETALSARRNLQGYEIN---G--RQLR   79 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGks--KGyAFVEF~d~e~A~sAi~~Lng~~I~---G--R~Lr   79 (551)
                      ++|.|++||...||+++.+.++....+.....+..+.+.+.  ..-|||.|.+.+++....+.++|+.+-   |  .+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            57899999999999999999999988877777654433332  356899999999999999999998772   2  2345


Q ss_pred             EEeec
Q 008851           80 VDFAE   84 (551)
Q Consensus        80 V~~A~   84 (551)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            77764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.57  E-value=0.016  Score=50.61  Aligned_cols=73  Identities=23%  Similarity=0.250  Sum_probs=59.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHc-----CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICRE-----VGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~-----~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      .-.++|.|.|||.+++++.|+-+|+.     -|+|.+++...        +-|+|+|.+.+.|++.++. ..+.|+|..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            45789999999999999999999986     25788877641        5689999999999999853 3578999889


Q ss_pred             EEEeecC
Q 008851           79 RVDFAEN   85 (551)
Q Consensus        79 rV~~A~~   85 (551)
                      .|.-..+
T Consensus        77 sV~P~~~   83 (104)
T 2dhx_A           77 SLRPAPP   83 (104)
T ss_dssp             EEEECCC
T ss_pred             EEEcCCC
Confidence            8866543

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.99  E-value=0.017  Score=50.06  Aligned_cols=54  Identities=15%  Similarity=0.233  Sum_probs=46.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL   68 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L   68 (551)
                      ...++| ++|.+|...||.++|+.|| -..|+++.|-       -|||.|.+.+.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            455666 9999999999999999999 5567777663       7999999999999999866

>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=95.09  E-value=0.023  Score=49.35  Aligned_cols=54  Identities=15%  Similarity=0.237  Sum_probs=46.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ   69 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln   69 (551)
                      ..++| ++|.+|...+|..+|+.|| -..|+++.|-       -|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            34555 9999999999999999999 6677777663       69999999999999998764

>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=94.72  E-value=0.17  Score=45.12  Aligned_cols=72  Identities=13%  Similarity=0.108  Sum_probs=57.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-EEEEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING-RQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G-R~LrV~~A   83 (551)
                      ..+.|.|-++|.+. -..|.+.|++||.|++....      ....+-.|.|.+..+|++|+. .||..|+| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            36778888999885 56677889999999988751      124578999999999999995 69999975 66777776


Q ss_pred             c
Q 008851           84 E   84 (551)
Q Consensus        84 ~   84 (551)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=94.40  E-value=0.032  Score=49.98  Aligned_cols=35  Identities=20%  Similarity=0.225  Sum_probs=29.5

Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 008851           35 SFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY   71 (551)
Q Consensus        35 ~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~   71 (551)
                      .++|+.+.  .+++|||||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            46677765  478999999999999999999888754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.95  E-value=0.083  Score=45.59  Aligned_cols=79  Identities=23%  Similarity=0.320  Sum_probs=55.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCc--ceEEEEEeCCHHHHHHHHHHhCCceeC---C--EEE
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP--KGYGFCEYKDEETALSARRNLQGYEIN---G--RQL   78 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGks--KGyAFVEF~d~e~A~sAi~~Lng~~I~---G--R~L   78 (551)
                      +-+|.|+.||...||+++.+.++.+-.+.....+..+.+-+.  -.-|||.|.+.++...-.+.++|+.+-   |  .+.
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            457889999999999998888776555433333222222221  245799999999999999999998772   2  245


Q ss_pred             EEEeec
Q 008851           79 RVDFAE   84 (551)
Q Consensus        79 rV~~A~   84 (551)
                      .|++|-
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            677764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.71  E-value=0.035  Score=59.93  Aligned_cols=55  Identities=18%  Similarity=0.309  Sum_probs=41.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR   66 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~   66 (551)
                      .++|||. .+.++++.+|.++|++||+|.++..-.++     .-|+.|||.+.+++.+++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            4789997 79999999999999999999998765543     3699999999999887754

>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=92.92  E-value=0.036  Score=49.46  Aligned_cols=41  Identities=22%  Similarity=0.159  Sum_probs=37.6

Q ss_pred             CCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCEEEEEEeecC
Q 008851           44 TGKPKGYGFCEYKDEETALSARRNL-QGYEINGRQLRVDFAEN   85 (551)
Q Consensus        44 TGksKGyAFVEF~d~e~A~sAi~~L-ng~~I~GR~LrV~~A~~   85 (551)
                      ..+.+|+++|||.+.++|++|++.+ |+..++| .++++++..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            4678999999999999999999999 9999999 999998765

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=89.41  E-value=0.48  Score=43.00  Aligned_cols=78  Identities=19%  Similarity=0.250  Sum_probs=54.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeE-EEEeec--------CCCCC-----cceEEEEEeCCHHHHHHHHHHhCCc
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVS-FRLVID--------RETGK-----PKGYGFCEYKDEETALSARRNLQGY   71 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~-vrLv~D--------r~TGk-----sKGyAFVEF~d~e~A~sAi~~Lng~   71 (551)
                      ...|.|-+.|.+.. ..+-+.|++||.|++ +....+        +.+.+     ...+-.|.|.+..+|.+|+. .||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45567778877754 456778999999876 321110        00011     24577899999999999995 6999


Q ss_pred             eeCCEEEEEEeecC
Q 008851           72 EINGRQLRVDFAEN   85 (551)
Q Consensus        72 ~I~GR~LrV~~A~~   85 (551)
                      .|+|..|-|...++
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888888764

---

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	551
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-22
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-22
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-21
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-21
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-21
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-20
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-20
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-20
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-20
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-20
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-20
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-19
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-19
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-19
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-19
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-19
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-19
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-19
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-19
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-19
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-19
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-18
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-18
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-18
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-18
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-18
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-18
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-18
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-18
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-18
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-18
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-18
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-17
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-17
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-17
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-17
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-17
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-17
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-17
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-17
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-17
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-17
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-17
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-17
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-17
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-17
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-17
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-17
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	9e-17
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-16
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-16
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-16
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-15
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-15
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-15
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-15
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-15
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-14
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-14
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-14
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-13
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-13
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-13
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-12
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-12
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-12
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-12
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-12
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-11
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-10
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-10
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-10
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-09
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-09
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	7e-08
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	2e-06

>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 = 88.4 bits (219), Expect = 3e-22
 Identities = 21/78 (26%), Positives = 39/78 (50%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VG++  D TE  L E     GP++S R+  D  T +  GY +  ++    A  A   +
Sbjct: 3  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 69 QGYEINGRQLRVDFAEND 86
              I G+ +R+ +++ D
Sbjct: 63 NFDVIKGKPVRIMWSQRD 80

>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 = 88.6 bits (219), Expect = 4e-22
 Identities = 26/94 (27%), Positives = 50/94 (53%), Gaps = 5/94 (5%)

Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          MA+++ R ++VG +  +  ++ L       G +   ++ +D ET K +G+ F E++  E 
Sbjct: 1  MATTK-RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 59

Query: 61 ALSARRNLQGYEINGRQLRVDFAENDKGADRNRE 94
          A +A  N+   E+ GR +RV+ A+      R +E
Sbjct: 60 AAAAIDNMNESELFGRTIRVNLAK----PMRIKE 89

>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 = 88.1 bits (218), Expect = 1e-21
 Identities = 21/97 (21%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          +    +R +++ N+PY  T E++ +I  + GP+   R      T + +G  +  Y+D   
Sbjct: 2  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFD 58

Query: 61 ALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
          A +A  +L G+ +  R L V +   ++   +   + +
Sbjct: 59 AKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKK 95

>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 = 86.9 bits (215), Expect = 1e-21
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 7/93 (7%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          +   ++VGN+ +  TEEQ+ E+  + G +    + +D+      G+ F EY     A +A
Sbjct: 6  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 65 RRNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
           R + G  ++ R +R D+           ++GR
Sbjct: 66 MRYINGTRLDDRIIRTDWD-------AGFKEGR 91

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 86.9 bits (215), Expect = 2e-21
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRE-TGKPKGYGFCEYKDEETALSAR 65
            + V NIP+ A + ++ E+    G + + RL      TG  +G+GF ++  ++ A  A 
Sbjct: 9  SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 66 RNL-QGYEINGRQLRVDFAENDK 87
            L     + GR+L +++A+++ 
Sbjct: 69 NALCHSTHLYGRRLVLEWADSEV 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 = 85.1 bits (210), Expect = 6e-21
 Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          H+ +F+G +P    ++Q+ E+    GP+ +F LV D  TG  KGY FCEY D      A 
Sbjct: 2  HK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 66 RNLQGYEINGRQLRVDFAE-NDKGA 89
            L G ++  ++L V  A    K A
Sbjct: 61 AGLNGMQLGDKKLLVQRASVGAKNA 85

>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 = 83.5 bits (206), Expect = 1e-20
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 8  C-VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          C +F+G + +  T+E L E   + G V    ++ D  T + +G+GF  + D+        
Sbjct: 1  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-L 59

Query: 67 NLQGYEINGRQLRVDFA 83
              +E++ + +    A
Sbjct: 60 AQSRHELDSKTIDPKVA 76

>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 = 84.4 bits (208), Expect = 2e-20
 Identities = 65/94 (69%), Positives = 74/94 (78%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VFVGNIPY+ATEEQL +I  EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           NL G E +GR LRVD A ++K  +  +  G G P
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 82.8 bits (204), Expect = 5e-20
 Identities = 28/85 (32%), Positives = 46/85 (54%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           +Q   V+VG +    +E  L E+  + GPVV+  +  DR TG+ +GYGF E+  EE A 
Sbjct: 6  RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 63 SARRNLQGYEINGRQLRVDFAENDK 87
           A + +   ++ G+ +RV+ A    
Sbjct: 66 YAIKIMDMIKLYGKPIRVNKASAHN 90

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.5 bits (203), Expect = 6e-20
 Identities = 28/87 (32%), Positives = 50/87 (57%), Gaps = 1/87 (1%)

Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          MAS + + +FVG + +D  E+ L ++  + G +    +V DRET + +G+GF  +++ + 
Sbjct: 1  MASDEGK-LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 59

Query: 61 ALSARRNLQGYEINGRQLRVDFAENDK 87
          A  A   + G  ++GRQ+RVD A    
Sbjct: 60 AKDAMMAMNGKSVDGRQIRVDQAGKSS 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 82.0 bits (202), Expect = 7e-20
 Identities = 12/77 (15%), Positives = 32/77 (41%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            + V N+P+  + +++++       +     +   E G P G     ++  + A +A  
Sbjct: 10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 67 NLQGYEINGRQLRVDFA 83
          +L    I  R++++   
Sbjct: 70 DLNDRPIGSRKVKLVLG 86

>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 = 81.9 bits (202), Expect = 8e-20
 Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          S +   ++V N+P   T++QL  I  + G +V   ++ D+ TG+P+G  F  Y   E A 
Sbjct: 3  SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 63 SARRNLQGYEING--RQLRVDFA 83
           A   L      G  + L V  A
Sbjct: 63 EAISALNNVIPEGGSQPLSVRLA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 81.6 bits (201), Expect = 1e-19
 Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 2/84 (2%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          AS +   ++V  +P   T+++L ++  + G +++ R+++D+ TG  +G GF  +     A
Sbjct: 2  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 61

Query: 62 LSARRNLQGYEINGR--QLRVDFA 83
            A + L G + +G    + V FA
Sbjct: 62 EEAIKGLNGQKPSGATEPITVKFA 85

>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 = 81.7 bits (201), Expect = 1e-19
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          ++VGN+P D   + + ++  + G +     +  +       + F E++D   A  A    
Sbjct: 17 IYVGNLPPDIRTKDIEDVFYKYGAIRD---IDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 69 QGYEINGRQLRVDFAENDKGA 89
           GY+ +G +LRV+F  + +G 
Sbjct: 74 DGYDYDGYRLRVEFPRSGRGT 94

>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 = 80.8 bits (199), Expect = 2e-19
 Identities = 22/75 (29%), Positives = 42/75 (56%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P D T+ +L  + R +GP+ + R++ D +TG   GY F ++  E  +  A + L
Sbjct: 5  LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 69 QGYEINGRQLRVDFA 83
           G  +  ++L+V +A
Sbjct: 65 NGITVRNKRLKVSYA 79

>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 = 80.6 bits (198), Expect = 2e-19
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEETALSARRN 67
          +F+GN+  +  E+ L +     G ++   +++ D +TG  KGY F  +   + + +A   
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 68 LQGYEINGRQLRVDFAE--NDKG 88
          + G  +  R + V +A   + KG
Sbjct: 61 MNGQYLCNRPITVSYAFKKDSKG 83

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 80.4 bits (198), Expect = 3e-19
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 2/89 (2%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          A  +   + V  +P+  TE+ L E     G V+  ++  D +TG  KG+GF  + + ET 
Sbjct: 4  AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGAD 90
          +        + I+GR        + +  D
Sbjct: 64 VKVMSQR--HMIDGRWCDCKLPNSKQSQD 90

>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 = 80.5 bits (198), Expect = 3e-19
 Identities = 28/81 (34%), Positives = 47/81 (58%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          S +   +FV +I  +A E+++ E   + G + +  L +DR TG  KGY   EY+  + AL
Sbjct: 4  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 63 SARRNLQGYEINGRQLRVDFA 83
          +A+  L G EI G+ ++VD+ 
Sbjct: 64 AAKEALNGAEIMGQTIQVDWC 84

>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 = 80.1 bits (197), Expect = 4e-19
 Identities = 21/84 (25%), Positives = 45/84 (53%), Gaps = 2/84 (2%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
           Q R ++VGN+  D TE  ++++  ++GP  S +++ +        Y F E+ +   A +
Sbjct: 6  GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAA 63

Query: 64 ARRNLQGYEINGRQLRVDFAENDK 87
          A   + G +I G++++V++A    
Sbjct: 64 ALAAMNGRKILGKEVKVNWATTPS 87

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 79.7 bits (196), Expect = 4e-19
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRE---TGKPKGYGFCEYKDEETALSARR 66
          F+ N+ +  TEE L  +  +VG + S  +   +         G+GF EYK  E A  A +
Sbjct: 2  FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 67 NLQGYEINGRQLRVDFAEN 85
           LQG+ ++G +L V  +E 
Sbjct: 62 QLQGHTVDGHKLEVRISER 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 79.4 bits (195), Expect = 6e-19
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V  +P + T+E+   +   +G + S +LV D+ TG+  GYGF  Y D + A  A   L
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 69 QGYEINGRQLRVDFAE 84
           G  +  + ++V +A 
Sbjct: 65 NGLRLQTKTIKVSYAR 80

>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 = 80.1 bits (197), Expect = 6e-19
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           R VF   +        L +    VG V   R++ DR + + KG  + E+ + ++      
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV-PLAI 77

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNR 93
            L G  + G  + V  ++    A++NR
Sbjct: 78  GLTGQRLLGVPIIVQASQ----AEKNR 100

>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 = 78.6 bits (193), Expect = 1e-18
 Identities = 20/74 (27%), Positives = 41/74 (55%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
           C+ V  +    TE  L E+  + GP+    +V D+++ + +G+ F  +++ + A  A+ 
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 67 NLQGYEINGRQLRV 80
             G E++GR++RV
Sbjct: 70 RANGMELDGRRIRV 83

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.1 bits (192), Expect = 2e-18
 Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + V N+ +  ++  + E+  E G +     V    +G+  G     ++ +  AL A +  
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 69 QGYEINGRQLRVDFA 83
           G  ++GR + +   
Sbjct: 62 NGVPLDGRPMNIQLV 76

>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 = 78.7 bits (193), Expect = 2e-18
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLV--------IDRETGKPKGYGFCE 54
           S +  ++V  +    T + L +  ++ G V   +          +D+ETGKPKG     
Sbjct: 5  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 55 YKDEETALSARRNLQGYEINGRQLRVDFAE 84
          Y+D  TA +A     G +  G +L+V  A 
Sbjct: 65 YEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 94

>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 = 78.0 bits (192), Expect = 3e-18
 Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 16/100 (16%)

Query: 3   SSQHRCVFVGNI-PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            S +  VF+GN+      +  +  I  + G +V   +         KG+ F +Y +E  A
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNA 63

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            +A     G  I G+ L ++ A          +  R GP 
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLA-------AEPKVNRSGPS 96

>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 = 77.0 bits (189), Expect = 4e-18
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 9/89 (10%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          S  + ++V N+    +EE + +    + P    R        K + Y F  + + E A+ 
Sbjct: 6  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVE 59

Query: 64 ARRNLQGYEINGRQLRVDFAENDKGADRN 92
          A + L G  ++G  + V  A   K  D++
Sbjct: 60 AMKALNGKVLDGSPIEVTLA---KPVDKD 85

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.0 bits (189), Expect = 4e-18
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          Q R +F+G + ++ T+E L     + G +    ++ D  T + +G+GF  Y   E   +A
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 65 RRNLQGYEINGRQLRVDFA 83
            N + ++++GR +    A
Sbjct: 65 -MNARPHKVDGRVVEPKRA 82

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.1 bits (189), Expect = 5e-18
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRL-----VIDRETGKPKGYGFCEYKDEETA 61
          R ++VGNIP+  TEE +++       +          V+  +  + K + F E++  +  
Sbjct: 2  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 62 LSARRNLQGYEINGRQLRV 80
            A     G    G+ L++
Sbjct: 62 TQA-MAFDGIIFQGQSLKI 79

>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 = 77.0 bits (189), Expect = 6e-18
 Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 4/91 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVI--DRETGKPKGYGFCEYKDEETALSARR 66
          +F+G IP     E+++E   +V   V   +V     +  K +G+ F EY+    A  ARR
Sbjct: 4  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 67 NLQG--YEINGRQLRVDFAENDKGADRNREQ 95
           L     ++ G Q+ VD+AE +   D +  +
Sbjct: 64 KLMPGRIQLWGHQIAVDWAEPEIDVDEDVME 94

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 76.6 bits (188), Expect = 7e-18
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R +   N+ ++ TE++L E+  +        + +  + GK KG  + E+K E  A     
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 67 NLQGYEINGRQLRVDFAENDKGADR 91
            QG EI+GR + + +   +KG  R
Sbjct: 72 EKQGAEIDGRSVSLYYT-GEKGGTR 95

>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 = 76.2 bits (187), Expect = 8e-18
 Identities = 14/81 (17%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREV-GPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
            +++ N+     +++L +    +         ++   + K +G  F  +K+  +A +A 
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 66 RNLQGYEINGRQLRVDFAEND 86
          R++QG+    + +R+ +A+ D
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTD 84

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.8 bits (186), Expect = 9e-18
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +F+G + +D T++ L +   + G VV   L +D  TG+ +G+GF  +K+ E+      + 
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV-MDQ 60

Query: 69 QGYEINGRQLRV 80
          + +++NG+ +  
Sbjct: 61 KEHKLNGKVIDP 72

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.4 bits (185), Expect = 1e-17
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  D  EE++ E     G V S  L +D +T K +G+ F  +K+EE         
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 69 QGYEINGRQLRVDFA 83
          + + +   +  +  A
Sbjct: 61 KYHNVGLSKCEIKVA 75

>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 = 78.9 bits (193), Expect = 1e-17
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 1   MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
            A    + +FVG I  D  E  L +   + G +    ++ DR +GK +G+ F  + D ++
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 61  ALSARRNLQGYEINGRQLRVDFAE 84
                   + + +NG    V  A 
Sbjct: 152 VDKIVI-QKYHTVNGHNCEVRKAL 174

>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 = 62.7 bits (151), Expect = 5e-12
 Identities = 16/60 (26%), Positives = 30/60 (50%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          Q R +F+G + ++ T+E L     + G +    ++ D  T + +G+GF  Y   E   +A
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

>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 = 75.9 bits (186), Expect = 1e-17
 Identities = 22/77 (28%), Positives = 35/77 (45%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            + V N+  D  E  L E+ R  G +    L  D+ TG+ KG+ F  +   E A  A  
Sbjct: 9  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 67 NLQGYEINGRQLRVDFA 83
           + G+  +   L V++A
Sbjct: 69 GVSGFGYDHLILNVEWA 85

>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 = 76.3 bits (187), Expect = 1e-17
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
            Q R +F+G + ++ TEE L     + G +    ++ D  + + +G+GF  +       
Sbjct: 17 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 63 SARRNLQGYEINGRQLRVDFA 83
          +A    + + I+GR +    A
Sbjct: 77 AA-MAARPHSIDGRVVEPKRA 96

>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 = 76.3 bits (187), Expect = 1e-17
 Identities = 30/99 (30%), Positives = 44/99 (44%), Gaps = 6/99 (6%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           SS    +FV N+ Y ++EE L ++    GP+      ID  T KPKG+ F  +   E A+
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
            A   + G    GR L V  +         +E  + GP 
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPST------IKKEASQSGPS 97

>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 = 75.2 bits (184), Expect = 1e-17
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +FVG +  + T E +     + G V    L+ D+ T + +G+GF  ++ E+        +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 69 QGYEINGRQLRVDFA 83
            +EIN + +    A
Sbjct: 61 HFHEINNKMVECKKA 75

>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 = 75.5 bits (185), Expect = 2e-17
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          + S  + + V NIP+   +  L ++  + G ++   ++ +      KG+GF  +++   A
Sbjct: 7  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADA 64

Query: 62 LSARRNLQGYEINGRQLRVDFAE 84
            AR  L G  + GR++ V+ A 
Sbjct: 65 DRAREKLHGTVVEGRKIEVNNAT 87

>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 = 75.0 bits (184), Expect = 2e-17
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          +Q   +FVGN+P D TEE++ ++  + G              K KG+GF   +    A  
Sbjct: 6  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEI 59

Query: 64 ARRNLQGYEINGRQLRVDFAEND 86
          A+  L    + G+QLRV FA + 
Sbjct: 60 AKVELDNMPLRGKQLRVRFACHS 82

>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 = 74.6 bits (183), Expect = 3e-17
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          +S ++  V+ G I    T++ + +     G ++  R+         KGY F  +   E+A
Sbjct: 14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESA 67

Query: 62 LSARRNLQGYEINGRQLRVDFAEND 86
            A  ++ G  I G  ++  + +  
Sbjct: 68 AHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 74.0 bits (181), Expect = 4e-17
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          + +FVG I  D  E  L +   + G +    ++ DR +GK +G+ F  + D + ++    
Sbjct: 3  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIV 61

Query: 67 NLQGYEINGRQLRVDFA 83
            + + +NG    V  A
Sbjct: 62 IQKYHTVNGHNCEVRKA 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 = 74.1 bits (181), Expect = 4e-17
 Identities = 11/76 (14%), Positives = 29/76 (38%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++ N P   T+  + ++ +++  V     +        + + + +   +E A      L
Sbjct: 4  LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 69 QGYEINGRQLRVDFAE 84
           G +I G  L    + 
Sbjct: 64 NGLKIEGYTLVTKVSN 79

>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 = 73.9 bits (181), Expect = 5e-17
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          S    +F+ N+      + L +     G ++S ++V   +    KGYGF  ++ +E A  
Sbjct: 6  SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAER 63

Query: 64 ARRNLQGYEINGRQLRVDFAENDK 87
          A   + G  +N R++ V   ++ K
Sbjct: 64 AIEKMNGMLLNDRKVFVGRFKSRK 87

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.6 bits (180), Expect = 6e-17
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++GN+    T + L ++  +    +        +     GY F +Y D+  A+ A   L
Sbjct: 4  LYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 69 QG-YEINGRQLRVDFAE 84
           G  E++G+ + VD++ 
Sbjct: 58 SGKVELHGKIMEVDYSV 74

>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 = 73.5 bits (180), Expect = 7e-17
 Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 7/95 (7%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
           SS    VFVG    D TE++L E   + G V+             + + F  + D++ A
Sbjct: 1  GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQIA 55

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQG 96
           S         I G  + +  AE    ++     G
Sbjct: 56 QSLCGE--DLIIKGISVHISNAEPKHNSNSGPSSG 88

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.9 bits (181), Expect = 8e-17
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 8/101 (7%)

Query: 1  MASSQH-RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
          MA       + V N+ Y  T + L +I  + G V+             +     +Y D  
Sbjct: 1  MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPV 56

Query: 60 TALSARRNLQGYEI--NGRQLRVDFAEN-DKGADRNREQGR 97
          +A  A+ +L G  I      LR+DF++        N ++ R
Sbjct: 57 SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSR 97

>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 = 74.0 bits (181), Expect = 9e-17
 Identities = 32/106 (30%), Positives = 47/106 (44%), Gaps = 7/106 (6%)

Query: 1   MASSQ----HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYK 56
           M  SQ       +FVG +PY  T+  L +     G +    ++ DR+TGK +GYGF    
Sbjct: 1   MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 60

Query: 57  DEETALSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPGM 102
           D   A  A ++     I+GR+  V+ A    GA     Q     G+
Sbjct: 61  DRAAAERACKDPNP-IIDGRKANVNLAY--LGAKPRSLQTGFAIGV 103

>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 = 73.7 bits (180), Expect = 9e-17
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 4/101 (3%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
            +S   C  + NIP+  T+  +++    +    +   V+    G+  G    ++K+E+ A
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNRE---QGRGG 99
             + R L   ++NGR+  V     +   +  +    QG+ G
Sbjct: 64  RKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>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 = 72.5 bits (177), Expect = 2e-16
 Identities = 18/81 (22%), Positives = 38/81 (46%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          + +++ N+    TE  L+ +           +     TG+ +G  F  + ++E A  A  
Sbjct: 19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 67 NLQGYEINGRQLRVDFAENDK 87
           + GY++ G+ L ++F +N K
Sbjct: 79 LVNGYKLYGKILVIEFGKNKK 99

>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 = 72.4 bits (177), Expect = 3e-16
 Identities = 20/80 (25%), Positives = 47/80 (58%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          +   +F+ ++P +  ++ L+++    G VVS ++ ID++T   K +GF  Y +  +A +A
Sbjct: 17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 65 RRNLQGYEINGRQLRVDFAE 84
           +++ G++I  ++L+V    
Sbjct: 77 IQSMNGFQIGMKRLKVQLKR 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 = 70.5 bits (172), Expect = 8e-16
 Identities = 11/84 (13%), Positives = 32/84 (38%), Gaps = 3/84 (3%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEI--CREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          + + R + + N+  +  +E L+                   +E        F  ++++++
Sbjct: 1  TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 61 ALSARRNLQGYEINGRQLRVDFAE 84
          A  A + +    +  R++ V  A+
Sbjct: 61 AERALQ-MNRSLLGNREISVSLAD 83

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (171), Expect = 9e-16
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 5  QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          ++R V++   P DAT + + E   + G V++ + +        KG  F  +   E+A   
Sbjct: 5  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 65 RRNLQGYEINGRQLRVDFAEN 85
               G +     L + F ++
Sbjct: 64 -VETPGQKYKETDLLILFKDD 83

>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 = 70.5 bits (172), Expect = 1e-15
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 7   RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
              F+GN+PYD TEE + E  R +               + KG+G+ E++D ++ LSA  
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-L 74

Query: 67  NLQGYEINGRQLRVDFAENDKGADRNREQG 96
           +L    +  +++RVD A+  +  D     G
Sbjct: 75  SLNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 69.9 bits (171), Expect = 2e-15
 Identities = 17/88 (19%), Positives = 27/88 (30%), Gaps = 15/88 (17%)

Query: 7  RCVFVGNI-----------PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEY 55
          R V + N+             +   E L   C + G +      +      P G     +
Sbjct: 9  RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRK----LLLFDRHPDGVASVSF 64

Query: 56 KDEETALSARRNLQGYEINGRQLRVDFA 83
          +D E A    + L G    GRQ+     
Sbjct: 65 RDPEEADYCIQTLDGRWFGGRQITAQAW 92

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.8 bits (170), Expect = 2e-15
 Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 6/88 (6%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           ++ + VF+ N+ +D+ EE L E+ ++ G +   R+V+  +T   KG  F ++  +E A 
Sbjct: 5  VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 63 SARRNLQ------GYEINGRQLRVDFAE 84
                       G +++GRQL+VD A 
Sbjct: 65 KCLAAASLEAEGGGLKLDGRQLKVDLAV 92

>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 = 68.9 bits (168), Expect = 5e-15
 Identities = 15/93 (16%), Positives = 31/93 (33%), Gaps = 12/93 (12%)

Query: 7  RCVFVGNI----------PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFC--E 54
            + + N+           Y+   E + + C + G V S  +    +  +  G G    E
Sbjct: 5  EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVE 64

Query: 55 YKDEETALSARRNLQGYEINGRQLRVDFAENDK 87
          +        A + L G +   R +   + + D 
Sbjct: 65 FTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97

>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 = 67.8 bits (165), Expect = 8e-15
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          SS    + V N+P D+  +++ ++ ++                + K   F    + E A 
Sbjct: 2  SSGSSGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQ 54

Query: 63 SARRNLQGYEINGRQLRVDFAEND 86
          +A +    Y   G+ L V     D
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 65.9 bits (160), Expect = 2e-14
 Identities = 17/71 (23%), Positives = 38/71 (53%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++  +    T++ L+++C+  G +VS + ++D+ T K KGYGF ++     A  A   L
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 69 QGYEINGRQLR 79
          +   +  +  +
Sbjct: 61 KASGVQAQMAK 71

>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 = 66.5 bits (161), Expect = 3e-14
 Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
          S+    +F+GN+  + +  +L     E+       +V  R TG  + +G+ +++  E   
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLE 68

Query: 63 SARRNLQGYEINGRQLRVDFAE 84
           A   L G ++ G +++++  +
Sbjct: 69 KA-LELTGLKVFGNEIKLEKPK 89

>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 = 66.3 bits (161), Expect = 3e-14
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            + + NIP   +EE L  +    G VV       +     +     +    E A+ A  
Sbjct: 11 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALI 66

Query: 67 NLQGYEI-NGRQLRVDFAEN 85
          +L  +++     LRV F+++
Sbjct: 67 DLHNHDLGENHHLRVSFSKS 86

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.1 bits (155), Expect = 2e-13
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 5  QHRCVFVGNIPYDATEEQLI---EICREVGPVVSFRLVIDRETGK---PKGYGFCEYKDE 58
          Q   VFV  +     + +++   E   + G +    +           P    +  Y   
Sbjct: 7  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 59 ETALSARRNLQGYEINGRQLRV 80
          E AL A + +    ++GR L+ 
Sbjct: 67 EDALRAIQCVNNVVVDGRTLKA 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 = 63.9 bits (155), Expect = 2e-13
 Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            ++VG +  + +   L       G + +          K   + + +Y+  + A +A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAAQAACA 71

Query: 67 NLQGYEING--RQLRVDFAENDKGA 89
           ++G+ + G  R+LRVDFA++   +
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSS 96

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.6 bits (154), Expect = 3e-13
 Identities = 18/98 (18%), Positives = 32/98 (32%), Gaps = 10/98 (10%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           S+   CV +  +PY ATE  +      + P+     +     G+  G    E+   E A+
Sbjct: 12  STTGHCVHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGEADVEFATHEDAV 69

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
           +A        +  R + +                  GP
Sbjct: 70  AA-MAKDKANMQHRYVELFLN-------STAGTSGSGP 99

>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 = 63.8 bits (154), Expect = 8e-13
 Identities = 32/100 (32%), Positives = 48/100 (48%), Gaps = 2/100 (2%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
                R + V  IP    E QL ++    GP+ S ++V DRET + +GYGF +++   +A
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 62  LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
             A   L G+ I  ++L+V  A    G  R    G  G G
Sbjct: 98  QQAIAGLNGFNILNKRLKVALAA--SGHQRPGIAGAVGDG 135

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 1e-12
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 1/81 (1%)

Query: 2   ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
             S    V +     +  EE   E+  + G V    +  D       G  + +++ EE A
Sbjct: 23  LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDA 81

Query: 62  LSARRNLQGYEINGRQLRVDF 82
             A  +L     NG+ +  + 
Sbjct: 82  EKAVIDLNNRWFNGQPIHAEL 102

>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 = 61.1 bits (147), Expect = 1e-12
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 7/78 (8%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          + +  +P D T +++ ++  +                K KG  F    + E A +A    
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 69 QGYEINGRQLRVDFAEND 86
              +  R+L V     D
Sbjct: 54 HQSRLRERELSVQLQPTD 71

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 60.6 bits (146), Expect = 2e-12
 Identities = 10/75 (13%), Positives = 24/75 (32%), Gaps = 3/75 (4%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V V N+P    + ++ +  +  GP++   +       K   +   E+        A    
Sbjct: 3  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFAR-YDGALAAITK 59

Query: 69 QGYEINGRQLRVDFA 83
              +   ++ V   
Sbjct: 60 THKVVGQNEIIVSHL 74

>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 = 61.0 bits (147), Expect = 3e-12
 Identities = 15/98 (15%), Positives = 36/98 (36%), Gaps = 8/98 (8%)

Query: 3   SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
           ++    V +  +P+  ++E++++    +  V +   +     G+  G  F ++  +E A 
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 63  SARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
            A        I  R + +  +          E    GP
Sbjct: 72  KA-LKKHKERIGHRYIEIFKS-------SRAEVRTSGP 101

>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 = 60.9 bits (147), Expect = 3e-12
 Identities = 17/97 (17%), Positives = 29/97 (29%), Gaps = 9/97 (9%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
                 V V  +P   + + L +  RE G        +     +  G G  EY  +E  
Sbjct: 11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGD-------VCYADVQKDGMGMVEYLRKEDM 63

Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRG 98
            A R L   +    +    +       +R+     G
Sbjct: 64 EYALRKLDDTKFRSHEGETSYIRVYP--ERSSGPSSG 98

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.3 bits (145), Expect = 4e-12
 Identities = 16/92 (17%), Positives = 28/92 (30%), Gaps = 8/92 (8%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          +R V V  +P   + + L +  R           +        G G  E+  +E    A 
Sbjct: 1  NR-VVVSGLPPSGSWQDLKDHMR-------EAGDVCYADVYRDGTGVVEFVRKEDMTYAV 52

Query: 66 RNLQGYEINGRQLRVDFAENDKGADRNREQGR 97
          R L   +    +    +        R+   GR
Sbjct: 53 RKLDNTKFRSHEGETAYIRVKVDGPRSPSYGR 84

>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 = 57.3 bits (138), Expect = 3e-11
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 2  ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
          A  +   ++V     D T   L            F  +ID     P+   F  Y+  E+A
Sbjct: 1  APRKGNTLYVYG--EDMTPTLLRGAFSP------FGNIIDLSMDPPRNCAFVTYEKMESA 52

Query: 62 LSARRNLQGYEINGRQLRVDFA 83
            A   L G ++   QL+V+ A
Sbjct: 53 DQAVAELNGTQVESVQLKVNIA 74

>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 = 57.8 bits (139), Expect = 4e-11
 Identities = 16/95 (16%), Positives = 42/95 (44%), Gaps = 7/95 (7%)

Query: 6  HRCVFVGNI-PYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
          +  + V N+ P   T + L  +    G V   +++ +++          +  D   A  A
Sbjct: 2  NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLA 56

Query: 65 RRNLQGYEINGRQLRVDFAE-NDKGADRNREQGRG 98
            +L G++++G+ +R+  ++  +    R  ++ +G
Sbjct: 57 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 91

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.0 bits (134), Expect = 2e-10
 Identities = 11/83 (13%), Positives = 29/83 (34%), Gaps = 8/83 (9%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            V V  +     E  L+E   + G +    ++  +           E+++ ++A     
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVT 69

Query: 67 --NLQGYEINGRQLRVDFAENDK 87
                  I G+Q   +++ + +
Sbjct: 70 FAADVPVYIAGQQAFFNYSTSKR 92

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.9 bits (131), Expect = 4e-10
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 3  SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
               CV++  +P++A  + +I+  +++  V     +     GK  G GF E+++E    
Sbjct: 15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 74

Query: 63 SARRNLQGYEINGRQLRVDFAENDK 87
          +A        +  R ++V       
Sbjct: 75 AA-LCRHKQYMGNRFIQVHPITKKG 98

>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 = 54.4 bits (130), Expect = 5e-10
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          +++ N+P    E++L  + +  G V+S R ++   +G  +G GF   +  E   +   + 
Sbjct: 21 LYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 69 QGYEINGRQLRVDFAE 84
           G  I          E
Sbjct: 80 NGKFIKTPPGVSAPTE 95

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.2 bits (129), Expect = 9e-10
 Identities = 11/89 (12%), Positives = 28/89 (31%), Gaps = 6/89 (6%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
            +   N+P      ++ E     G +            +       E+ +   A  A R
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKAFR 64

Query: 67 NLQGYEINGRQLRVDFAENDKGADRNREQ 95
          +L   + +   L +++A         +++
Sbjct: 65 HLAYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>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 = 52.9 bits (126), Expect = 1e-09
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 6  HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          ++ +F+ N+P +  E  L  +  +       RLV +R         F E+  E  + +A+
Sbjct: 8  NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFTTELQSNAAK 62

Query: 66 RNLQGYEI-NGRQLRVDFA 83
            LQG++I     +++ FA
Sbjct: 63 EALQGFKITPTHAMKITFA 81

>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 = 52.0 bits (124), Expect = 3e-09
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 9/84 (10%)

Query: 7  RCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
          R V + +         QL+++    G + +  ++            F E    E A +A 
Sbjct: 9  RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQAAV 62

Query: 66 R--NLQGYEINGRQLRVDFAENDK 87
                   + G+ +RV  ++  K
Sbjct: 63 DYYTTTPALVFGKPVRVHLSQKYK 86

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 4e-09
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 7/80 (8%)

Query: 4  SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
          +Q   V  G +    +  QL+ +  +        LV        K Y F  Y+  E +  
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEK------CGLVDALLMPPNKPYSFARYRTTEESKR 71

Query: 64 ARRNLQGYEI-NGRQLRVDF 82
          A   L G E+ +    ++  
Sbjct: 72 AYVTLNGKEVVDDLGQKITL 91

>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 = 51.4 bits (122), Expect = 5e-09
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 1  MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
          M  +  R + +  +P + TE ++I +         F  V +    K K   F E   EE 
Sbjct: 3  MDGAPSRVLHIRKLPGEVTETEVIALGLP------FGKVTNILMLKGKNQAFLELATEEA 56

Query: 61 ALSARR--NLQGYEINGRQLRVDFA 83
          A++     +     +  + + + ++
Sbjct: 57 AITMVNYYSAVTPHLRNQPIYIQYS 81

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.2 bits (117), Expect = 2e-08
 Identities = 8/70 (11%), Positives = 19/70 (27%), Gaps = 8/70 (11%)

Query: 9  VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
          V V   P  +    L++          +  ++         +    Y+ +  A  A  + 
Sbjct: 7  VTVFGFPQASASYILLQFA-------QYGNILKHVMSNTGNWMHIRYQSKLQARKA-LSK 58

Query: 69 QGYEINGRQL 78
           G       +
Sbjct: 59 DGRIFGESIM 68

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 7e-08
 Identities = 15/105 (14%), Positives = 31/105 (29%), Gaps = 21/105 (20%)

Query: 9   VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE-ETALSARRN 67
            F G++      E L  +    G +     V           G   +K++ + AL   ++
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKD 67

Query: 68  LQGYEINGRQLRVDFA--------------ENDKGADRNREQGRG 98
                +  R   V +                 D+    N+ + +G
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKG 112

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.2 bits (103), Expect = 2e-06
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 3/81 (3%)

Query: 7  RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
          R + + N+P+    +       ++               K + +   E +++  A+    
Sbjct: 19 RVIHLSNLPHSGYSD---SAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHC 75

Query: 67 NLQGYEINGRQLRVDFAENDK 87
            +     GR ++VD +E  K
Sbjct: 76 LKKALWFQGRCVKVDLSEKYK 96

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	551
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.82
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.76
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.74
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.74
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.74
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.7
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.7
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.69
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.66
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.66
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.64
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.63
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.61
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.6
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.56
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.48
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	99.46
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.41
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.29
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.29
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.24
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.21
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.83
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.53
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.39
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	84.81

>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=99.84  E-value=9.2e-21  Score=169.58  Aligned_cols=83  Identities=33%  Similarity=0.586  Sum_probs=79.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++||++|+++|+.||.|++|+++.|+.||+++|||||+|.+.++|.+|++.||++.|+||+|+|++|.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus       121 ~~~  123 (139)
T d1u6fa1         121 SGH  123 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.83  E-value=1.2e-20  Score=154.18  Aligned_cols=80  Identities=28%  Similarity=0.572  Sum_probs=77.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +++|||+|||+++||++|+++|++||.|+++++++|+.+|+++|||||+|.+.++|++|++.||+..|+|+.|+|+||++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.82  E-value=1.2e-20  Score=157.22  Aligned_cols=83  Identities=27%  Similarity=0.490  Sum_probs=79.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||.|++|++++|+.||+++|||||+|.+.++|++|++.||+..|+|+.|+|++|+
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            56899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      +.+
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.82  E-value=3.3e-20  Score=157.22  Aligned_cols=85  Identities=33%  Similarity=0.484  Sum_probs=81.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +..+++|||+|||++++|++|+++|++||.|++|++++|+.||+++|||||+|.+.++|.+|++.||+..|+||.|+|++
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +..+.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98754

>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=99.82  E-value=5.1e-20  Score=154.85  Aligned_cols=83  Identities=25%  Similarity=0.464  Sum_probs=79.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++|||+|||+++||++|+++|+.||.|.+|+++.|+.+|+++|||||+|.+.++|..|++.||+..|+|+.|+|+|+
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            36789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            753

>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=99.82  E-value=1.9e-20  Score=157.49  Aligned_cols=85  Identities=33%  Similarity=0.522  Sum_probs=80.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+..++|||+|||+++|+++|+++|++||.|++|++++|+.||+++|||||+|.+.++|++|++.||+..|+|+.|+|+|
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      |+++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98654

>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=99.81  E-value=5e-20  Score=150.22  Aligned_cols=80  Identities=29%  Similarity=0.548  Sum_probs=77.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||++++|++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|++|++.|||..|+|+.|+|+||++
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            35799999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.81  E-value=3.5e-20  Score=158.38  Aligned_cols=86  Identities=23%  Similarity=0.512  Sum_probs=81.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+++++|||+|||++++|++|+++|+.||.|+++++++|+.+|++||||||+|.+.++|..|++.||++.|+|+.|+|+|
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            35678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      |+++..
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            987543

>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=99.81  E-value=5.9e-20  Score=152.83  Aligned_cols=83  Identities=33%  Similarity=0.539  Sum_probs=79.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .++++|||+|||+++|+++|+++|+.||.|++|++++|+.||+++|||||+|.+.++|++|++.|||..|+|+.|+|+||
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            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            763

>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=99.81  E-value=5.9e-20  Score=150.08  Aligned_cols=78  Identities=26%  Similarity=0.466  Sum_probs=76.0

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +|||||||+++||++|+++|+.||+|.+|+|++|+.||+++|||||+|.+.++|..|++.|+|..++||.|+|+||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999864

>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=99.80  E-value=8e-20  Score=152.44  Aligned_cols=83  Identities=27%  Similarity=0.466  Sum_probs=79.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||++++|++|+++|+.||.|.+|++++|+.||+++|||||+|.+.++|.+|++.|++..|+|+.|+|+||
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            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      +++
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            864

>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=99.79  E-value=1.8e-20  Score=160.03  Aligned_cols=83  Identities=75%  Similarity=1.157  Sum_probs=79.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||++++|++|+++|+.||.|.+|++++|+.||+++|||||+|.+.++|.+|++.|++..|+|+.|+|++|..
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            46899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCC
Q 008851           86 DKG   88 (551)
Q Consensus        86 ~~~   88 (551)
                      ...
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            543

>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=99.79  E-value=8.4e-20  Score=151.76  Aligned_cols=83  Identities=30%  Similarity=0.597  Sum_probs=79.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +.++|||||||++++|++|+++|+.||.|..+.+++++.+|+++|||||+|.+.++|++|++.|+++.|+|+.|+|++|.
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            56779999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      +..
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=2.5e-19  Score=153.31  Aligned_cols=82  Identities=30%  Similarity=0.531  Sum_probs=76.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||.|++|++++|+.||+++|||||+|.+.++|++|++.+++ .|+||.|+|++|.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            346799999999999999999999999999999999999999999999999999999999998875 7999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            643

>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=99.79  E-value=1.9e-19  Score=148.79  Aligned_cols=81  Identities=23%  Similarity=0.427  Sum_probs=76.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||||||+++||++|+++|+.||.|.++++++|+.||+++|||||+|.+.++|++|++ ++++.|+||.|+|+.
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4456899999999999999999999999999999999999999999999999999999999996 689999999999998


Q ss_pred             ec
Q 008851           83 AE   84 (551)
Q Consensus        83 A~   84 (551)
                      |.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            85

>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=99.79  E-value=1.6e-19  Score=148.07  Aligned_cols=77  Identities=26%  Similarity=0.562  Sum_probs=74.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      .++++|||+|||+++||++|+++|++||.|.+|++++|+.||+++|||||+|.+.++|.+|++.||+..|+||+|+|
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            35789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.79  E-value=6.4e-20  Score=151.82  Aligned_cols=80  Identities=34%  Similarity=0.602  Sum_probs=77.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      .+|||+|||+++||++|+++|+.||+|++|++++|+.||+++|||||+|.+.++|..|++.||++.|+|+.|+|++|...
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            46999999999999999999999999999999999999999999999999999999999999999999999999999864

>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=99.79  E-value=1.9e-19  Score=148.44  Aligned_cols=80  Identities=30%  Similarity=0.489  Sum_probs=76.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~   81 (551)
                      ...++|||+|||++++|++|+++|++||.|.++++++|+.+|+++|||||+|.+.++|.+|++.||+..+.|  ++|+|+
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            456789999999999999999999999999999999999999999999999999999999999999999976  889999


Q ss_pred             ee
Q 008851           82 FA   83 (551)
Q Consensus        82 ~A   83 (551)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>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=99.78  E-value=4.3e-19  Score=148.84  Aligned_cols=82  Identities=24%  Similarity=0.435  Sum_probs=76.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++||++|+++|+.||.|.+|+|++|+.||++||||||+|.+.++|++|++.  .+.|+||.|+|++|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3578899999999999999999999999999999999999999999999999999999999985  45899999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            8754

>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=99.78  E-value=1.8e-19  Score=148.91  Aligned_cols=80  Identities=25%  Similarity=0.515  Sum_probs=75.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~   81 (551)
                      -.+++|||+|||+++||++|+++|++||.|+++++++|+.+|+++|||||+|.+.++|.+|++.|||..++|  ++|+|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            356889999999999999999999999999999999999999999999999999999999999999999988  559999


Q ss_pred             ee
Q 008851           82 FA   83 (551)
Q Consensus        82 ~A   83 (551)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.78  E-value=2e-19  Score=146.63  Aligned_cols=80  Identities=14%  Similarity=0.250  Sum_probs=70.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +++|||+|||+++||++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|++.||+..++|++|+|+++++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            47999999999999999999999999999999988989999999999999999999999999999999999999999975

>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=99.78  E-value=6.3e-19  Score=146.94  Aligned_cols=84  Identities=25%  Similarity=0.547  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ++.+.++|||+|||+++||++|+++|+.||.|++|+++.|+.++  +|||||+|.+.++|.+|++.|++..|+|+.|+|+
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44578999999999999999999999999999999999987654  7999999999999999999999999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      ||++..
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            998643

>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=99.78  E-value=3.4e-19  Score=150.05  Aligned_cols=84  Identities=25%  Similarity=0.509  Sum_probs=78.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCEEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR-ETGKPKGYGFCEYKDEETALSARRNL-QGYEINGRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr-~TGksKGyAFVEF~d~e~A~sAi~~L-ng~~I~GR~LrV~   81 (551)
                      ..+++|||+|||++++|++|+++|+.||.|.+|+|+.|+ .+|+++|||||+|.+.++|.+|++.| |+..|+||+|+|+
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            367889999999999999999999999999999999885 48999999999999999999999998 8999999999999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      ||+.+.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998754

>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=99.78  E-value=2.8e-19  Score=146.45  Aligned_cols=79  Identities=23%  Similarity=0.476  Sum_probs=74.8

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCCC
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAENDK   87 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~v-rLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~~   87 (551)
                      |||+|||+++||++|+++|++||.|.++ ++++|+.||+++|||||+|.+.++|++|++.|++..++|++|+|++|.++.
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            7999999999999999999999999765 789999999999999999999999999999999999999999999998643

>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=99.77  E-value=6.2e-19  Score=143.43  Aligned_cols=77  Identities=19%  Similarity=0.447  Sum_probs=74.2

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +|||+|||++++|++|+++|++||.|.+|++.+|+ +|+++|||||+|.+.++|.+|++.|||..++|+.|+|++|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999996 799999999999999999999999999999999999999863

>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=99.77  E-value=1.1e-19  Score=148.16  Aligned_cols=76  Identities=21%  Similarity=0.381  Sum_probs=73.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      |+|||+|||+++||++|+++|++||.|+++++++|+.||++||||||+|.+.++|++|++ ++++.|+||.|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999996 6999999999999987

>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=99.77  E-value=8.8e-19  Score=144.05  Aligned_cols=77  Identities=32%  Similarity=0.596  Sum_probs=73.1

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETG---KPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TG---ksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      |||+|||+++|+++|+++|+.||.|.+|++++|+.++   ++||||||+|.+.++|.+|++.||+..|+|+.|+|+||+.
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            7999999999999999999999999999999998776   4689999999999999999999999999999999999864

>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=99.76  E-value=9.8e-19  Score=146.60  Aligned_cols=84  Identities=30%  Similarity=0.557  Sum_probs=78.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCCE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ------GYEINGR   76 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln------g~~I~GR   76 (551)
                      ..+.++|||||||+++||++|+++|+.||.|.+++++.++.+++++|||||+|.+.++|.+|++.|+      +..|+||
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3467899999999999999999999999999999999999999999999999999999999999886      6788999


Q ss_pred             EEEEEeecCC
Q 008851           77 QLRVDFAEND   86 (551)
Q Consensus        77 ~LrV~~A~~~   86 (551)
                      .|+|++|.++
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999999864

>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=99.76  E-value=1.3e-18  Score=140.88  Aligned_cols=77  Identities=25%  Similarity=0.439  Sum_probs=73.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      -++|||||||+++||++|+++|++||.|..+.+..|+.+++++|||||+|.+.+++.+|++ ++++.|+||.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4789999999999999999999999999999999999999999999999999999999985 8999999999999987

>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=99.76  E-value=3.9e-19  Score=143.75  Aligned_cols=75  Identities=27%  Similarity=0.525  Sum_probs=71.8

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +|||||||++++|++|+++|++||.|.++++++|+.||+++|||||+|.+.++|++|++ ++++.|+|+.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            59999999999999999999999999999999999999999999999999999999996 7999999999999765

>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=99.76  E-value=2.8e-19  Score=152.97  Aligned_cols=80  Identities=23%  Similarity=0.373  Sum_probs=76.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||+|||++++|++|+++|+.||.|.+|+|++|+.||++||||||+|.+.++|.+|++ |||..|+|+.|+|+++..
T Consensus        18 ~~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          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            5789999999999999999999999999999999999999999999999999999999995 999999999999999864


Q ss_pred             C
Q 008851           86 D   86 (551)
Q Consensus        86 ~   86 (551)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.76  E-value=1.4e-18  Score=146.63  Aligned_cols=85  Identities=28%  Similarity=0.498  Sum_probs=78.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVV--------SFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEIN   74 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~--------~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~   74 (551)
                      +...++|||+|||+++||++|+++|+.||.|.        .+.+..|+.+|+++|||||+|.+.++|.+|++.|||+.|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            45678999999999999999999999999874        5777888999999999999999999999999999999999


Q ss_pred             CEEEEEEeecCCC
Q 008851           75 GRQLRVDFAENDK   87 (551)
Q Consensus        75 GR~LrV~~A~~~~   87 (551)
                      ||.|+|++|+.+.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998643

>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=99.75  E-value=1.4e-18  Score=149.22  Aligned_cols=81  Identities=21%  Similarity=0.401  Sum_probs=76.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      .++|||||||++++|++|+++|++||.|.++.|.+|+.|++++|||||+|.+.++|.+|++ ++++.|+|+.|+|++|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            4789999999999999999999999999999999999999999999999999999999995 799999999999999986


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.6e-18  Score=143.28  Aligned_cols=82  Identities=24%  Similarity=0.519  Sum_probs=76.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++++++|+++|+.||.|++|++++|+  +.++|||||+|.+.++|.+|++.||+..|+|+.|+|++|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            357889999999999999999999999999999999886  447999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      +++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8753

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.2e-18  Score=143.36  Aligned_cols=81  Identities=25%  Similarity=0.438  Sum_probs=75.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...+|||+|||+++++++|+++|+.||.|.+|+++.|+.  .++|||||+|.+.++|.+|++.|||..|+|+.|+|++|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            456899999999999999999999999999999999864  478999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ++.
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            643

>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=99.74  E-value=3.5e-18  Score=145.42  Aligned_cols=83  Identities=33%  Similarity=0.614  Sum_probs=74.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR-ETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr-~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+.++|||+|||+++||++|+++|+.|| +++++++.++ .+|+++|||||+|.+.++|++|+ .||++.|+||.|+|++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3568999999999999999999999999 8888887765 57899999999999999998776 6999999999999999


Q ss_pred             ecCCCC
Q 008851           83 AENDKG   88 (551)
Q Consensus        83 A~~~~~   88 (551)
                      |.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            986543

>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=99.74  E-value=5.5e-19  Score=143.53  Aligned_cols=75  Identities=27%  Similarity=0.410  Sum_probs=71.4

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +|||||||+++||++|+++|++||.|++|+|++|+.||+++|||||+|.+.++|++|++ .+++.|+|+.|+|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            69999999999999999999999999999999999999999999999999999999996 4778999999999875

>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=99.74  E-value=2e-18  Score=142.81  Aligned_cols=82  Identities=16%  Similarity=0.289  Sum_probs=71.9

Q ss_pred             CCCcEEEEecCCCCCC-HHHHHHHHHcCCCeeEEEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            4 SQHRCVFVGNIPYDAT-EEQLIEICREVGPVVSFRLVI-DRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~T-EEeLre~Fs~~G~V~~vrLv~-Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      -+.++|||+|||++++ |++|+++|++||.|++|+|.. ++.+|+++|||||+|.+.++|.+|++ +|++.|+||.|+|+
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            3678999999999986 566999999999999999876 46799999999999999999999995 99999999999999


Q ss_pred             eecCC
Q 008851           82 FAEND   86 (551)
Q Consensus        82 ~A~~~   86 (551)
                      +|+++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99854

>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=99.74  E-value=1.5e-18  Score=138.95  Aligned_cols=75  Identities=24%  Similarity=0.436  Sum_probs=72.6

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +|||||||+++||++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|++ +|++.|+||.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999996 9999999999999986

>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=99.74  E-value=5.7e-18  Score=146.19  Aligned_cols=80  Identities=26%  Similarity=0.482  Sum_probs=74.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +..+++|||+|||+++++++|+++|+.||.|++|++..   +++++|||||+|.+.++|..|++.|||+.|+|+.|+|++
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999875   467799999999999999999999999999999999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +..
T Consensus        81 a~~   83 (114)
T d2f9da1          81 YNA   83 (114)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=99.73  E-value=9.6e-18  Score=140.98  Aligned_cols=80  Identities=24%  Similarity=0.467  Sum_probs=73.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+++|||+|||+++++++|+++|+.||.|+.+++..+   +..+|||||+|.+.++|+.|++.||++.|+|++|+|+||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            46789999999999999999999999999999987643   567899999999999999999999999999999999998


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=99.72  E-value=8.8e-19  Score=148.33  Aligned_cols=83  Identities=22%  Similarity=0.425  Sum_probs=79.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ++++|||+|||.++++++|+++|+.||.|+.+.++.++.+|+++|||||+|.+.++|..|++.|||..|+|+.|+|+||+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ++.
T Consensus        97 ~k~   99 (102)
T d2cpxa1          97 NKK   99 (102)
T ss_dssp             CCS
T ss_pred             Ccc
Confidence            643

>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=99.71  E-value=1.7e-18  Score=145.23  Aligned_cols=80  Identities=18%  Similarity=0.336  Sum_probs=74.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||++++|++|+++|+.||.|.+++++.+ .+|+++|||||+|.+.++|.+|++ ||+..|+|+.|+|++|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            35679999999999999999999999999999988755 589999999999999999999996 9999999999999999


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.71  E-value=2.2e-17  Score=139.63  Aligned_cols=78  Identities=22%  Similarity=0.454  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+..++|||+|||.+++|++|+++|+.||.|++|+++.|      ||||||+|.+.++|.+|++.||+..|+|+.|+|+|
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~   88 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   88 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999865      78999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      +++.
T Consensus        89 ak~~   92 (96)
T d1x4ga1          89 GKES   92 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>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=1.5e-17  Score=136.52  Aligned_cols=78  Identities=24%  Similarity=0.455  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCEEEEE
Q 008851            2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI-NGRQLRV   80 (551)
Q Consensus         2 a~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I-~GR~LrV   80 (551)
                      +++++++|||+|||+++++++|+++|+.||.|++|+++.++     +|||||+|.+.++|.+|++.|||+.| +|+.|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            46789999999999999999999999999999999998653     78999999999999999999999988 5789999


Q ss_pred             Eeec
Q 008851           81 DFAE   84 (551)
Q Consensus        81 ~~A~   84 (551)
                      +||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.70  E-value=2.9e-17  Score=140.26  Aligned_cols=76  Identities=18%  Similarity=0.380  Sum_probs=70.8

Q ss_pred             CcEEEEecCCC-CCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPY-DATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~-d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      +++|||+||++ .+||++|+++|+.||.|++|+|++|+     +|||||+|++.++|.+|++.||+..|+|+.|+|+|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            68999999965 59999999999999999999999875     7999999999999999999999999999999999987


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.70  E-value=1.4e-17  Score=137.11  Aligned_cols=80  Identities=15%  Similarity=0.294  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      +..++|||+|||++++|++|+++|+.||.|..+.++.+.++|+++|||||+|.+.++|.+|++.||+..|+||+|+|+++
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            45677999999999999999999999999987544555578999999999999999999999999999999999999975

>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=99.70  E-value=3.8e-17  Score=135.03  Aligned_cols=78  Identities=22%  Similarity=0.308  Sum_probs=73.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++|+++|+++|+.||.|.+|++..++ +|++||||||+|.+.++|.+|++ +++..++|+.|+|.+++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            46899999999999999999999999999999998875 89999999999999999999995 79999999999999865

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.2e-17  Score=138.88  Aligned_cols=83  Identities=29%  Similarity=0.484  Sum_probs=74.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCC-eeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCEEEEEE
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGP-VVSFRLVIDR-ETGKPKGYGFCEYKDEETALSARRNLQG--YEINGRQLRVD   81 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~-V~~vrLv~Dr-~TGksKGyAFVEF~d~e~A~sAi~~Lng--~~I~GR~LrV~   81 (551)
                      +|+|||||||.+++|++|+++|+.||+ |.+++++.|. .+|+++|||||+|.+.++|.+|++.|++  ..++|+.|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 8999999885 5789999999999999999999999864  56689999999


Q ss_pred             eecCCCC
Q 008851           82 FAENDKG   88 (551)
Q Consensus        82 ~A~~~~~   88 (551)
                      ||++...
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9986543

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=9.9e-18  Score=142.55  Aligned_cols=82  Identities=21%  Similarity=0.368  Sum_probs=75.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ..+.++|||+|||++++|++|+++|+.||.|..+++..+. +++++|||||+|.+.++|.+|++.|||..|.||+++|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3456899999999999999999999999999999998885 799999999999999999999999999999999988877


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      +++
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.69  E-value=3.7e-17  Score=139.49  Aligned_cols=83  Identities=14%  Similarity=0.225  Sum_probs=76.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..+.+|||+||||++||++|+++|+.+|.|..+.++.+..+++++|||||+|.+.++|++|++ +|+..|+||.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            356789999999999999999999999999988777888899999999999999999999995 8999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      ....
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            8653

>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=99.69  E-value=3.6e-17  Score=135.23  Aligned_cols=78  Identities=23%  Similarity=0.316  Sum_probs=71.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCEEEEEEe
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI-NGRQLRVDF   82 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I-~GR~LrV~~   82 (551)
                      +++++|||+|||++++|++|+++|+.||.|+++++..    ++.+|||||+|.+.++|.+|+..|||+.| +|+.|+|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            5789999999999999999999999999999887764    44589999999999999999999999998 589999999


Q ss_pred             ecC
Q 008851           83 AEN   85 (551)
Q Consensus        83 A~~   85 (551)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=99.69  E-value=2.8e-17  Score=138.38  Aligned_cols=79  Identities=25%  Similarity=0.452  Sum_probs=72.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .+.++|||+|||+++||++|+++|+.||.|..++     .+|+++|||||+|.+.++|.+|++.||+..|+||.|+|+|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            3578999999999999999999999999887654     36889999999999999999999999999999999999999


Q ss_pred             cCCC
Q 008851           84 ENDK   87 (551)
Q Consensus        84 ~~~~   87 (551)
                      .++.
T Consensus        89 ~~k~   92 (96)
T d1fjca_          89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            8654

>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=99.68  E-value=4.9e-17  Score=138.02  Aligned_cols=74  Identities=26%  Similarity=0.453  Sum_probs=68.3

Q ss_pred             CCcEEEEecCC-CCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            5 QHRCVFVGNIP-YDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP-~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ..++|||+||+ +.+++++|+++|++||.|++|++.        ||||||+|.+.++|++|++.||++.|+|+.|+|+|+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            46789999996 678899999999999999999983        799999999999999999999999999999999999


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      +..
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            754

>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=99.68  E-value=2.3e-17  Score=136.90  Aligned_cols=78  Identities=27%  Similarity=0.368  Sum_probs=70.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +..+++|||+|||+++||++|+++|++||.|++|++.     ..++|||||+|.+.++|++|+.  +++.|+|+.|+|++
T Consensus         2 s~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~   74 (88)
T d1wf0a_           2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISN   74 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEe
Confidence            4578999999999999999999999999999999865     4468999999999999999985  77899999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      |+++.
T Consensus        75 a~~k~   79 (88)
T d1wf0a_          75 AEPKH   79 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97643

>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=99.68  E-value=3e-17  Score=136.79  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=71.3

Q ss_pred             CCcEEEEecCCCCCCHHHH---HHHHHcCCCeeEEEEeecCCCCCcc---eEEEEEeCCHHHHHHHHHHhCCceeCCEEE
Q 008851            5 QHRCVFVGNIPYDATEEQL---IEICREVGPVVSFRLVIDRETGKPK---GYGFCEYKDEETALSARRNLQGYEINGRQL   78 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeL---re~Fs~~G~V~~vrLv~Dr~TGksK---GyAFVEF~d~e~A~sAi~~Lng~~I~GR~L   78 (551)
                      +.++|||+|||+++++++|   +++|++||.|.+|.+.+|+.++..+   |||||+|.+.++|.+|++.|||..|+||.|
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            4678999999999999999   6789999999999999998777654   999999999999999999999999999999


Q ss_pred             EEE
Q 008851           79 RVD   81 (551)
Q Consensus        79 rV~   81 (551)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=4.1e-17  Score=138.93  Aligned_cols=82  Identities=20%  Similarity=0.338  Sum_probs=73.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      +...++|||+|||+++||++|+++|+.|| ++.++++++. +|+.+|||||+|.+.++|++|++ +|+..|+||.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34678999999999999999999999998 5678888876 58999999999999999999986 899999999999999


Q ss_pred             ecCCC
Q 008851           83 AENDK   87 (551)
Q Consensus        83 A~~~~   87 (551)
                      +....
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            88643

>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=99.67  E-value=1.2e-17  Score=133.03  Aligned_cols=71  Identities=24%  Similarity=0.568  Sum_probs=68.8

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEE
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLR   79 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~Lr   79 (551)
                      |||+|||+++||++|+++|+.||.|..+++..++.+++++|||||+|.+.++|.+|++.|||..|+||.|+
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            79999999999999999999999999999999999999999999999999999999999999999998764

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=6.5e-17  Score=138.26  Aligned_cols=77  Identities=16%  Similarity=0.162  Sum_probs=70.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      .+++|||+|||+++++++|+++|+.||.|++|.|.      +.+|||||+|.+.++|.+|++.|||..|.|+.|+|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            35789999999999999999999999999999874      347999999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.67  E-value=1.7e-17  Score=141.06  Aligned_cols=80  Identities=21%  Similarity=0.378  Sum_probs=72.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...+|||+|||+++|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++|++ +|+..|+||.|+|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            45789999999999999999999999999876555666789999999999999999999995 89999999999999986


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.66  E-value=2.2e-16  Score=129.96  Aligned_cols=77  Identities=22%  Similarity=0.403  Sum_probs=70.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||++++|++|+++|+.||.|..+++.      +++|||||+|.+.++|.+|+..||+..|+|+.|+|+||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45899999999999999999999999999887764      457999999999999999999999999999999999998


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      +..
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.66  E-value=6.1e-17  Score=134.62  Aligned_cols=77  Identities=21%  Similarity=0.350  Sum_probs=67.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      .+.+++|||+|||+++++++|+++|+.|| ++.+.+      ++.+|||||+|.+.++|++|++.||++.|+|++|+|++
T Consensus         2 ~s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~   74 (88)
T d1wg1a_           2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999 333332      45689999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      ++.+
T Consensus        75 a~~~   78 (88)
T d1wg1a_          75 QPTD   78 (88)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9654

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=6.2e-17  Score=134.01  Aligned_cols=76  Identities=34%  Similarity=0.540  Sum_probs=71.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|+.||.|.+|++..+      +|||||+|.+.++|.+|++.|||..|+|+.|+|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4578999999999999999999999999999999755      6899999999999999999999999999999999998


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>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=99.66  E-value=6.2e-17  Score=132.16  Aligned_cols=75  Identities=24%  Similarity=0.513  Sum_probs=68.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCEEEEEEeecC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY-EINGRQLRVDFAEN   85 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~-~I~GR~LrV~~A~~   85 (551)
                      ++|||||||+++||++|+++|++||.|.++++..+      +|||||+|.+.++|.+|++.|||. .|+|+.|+|+||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            36999999999999999999999999987776643      799999999999999999999985 79999999999987


Q ss_pred             CC
Q 008851           86 DK   87 (551)
Q Consensus        86 ~~   87 (551)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.66  E-value=1.8e-17  Score=137.27  Aligned_cols=74  Identities=20%  Similarity=0.263  Sum_probs=68.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      .+|||+|||+++++++|+++|++||.|.++++..       +|||||+|.+.++|++|++.||+..|+|+.|+|.+++..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            3699999999999999999999999999999864       389999999999999999999999999999999988654


Q ss_pred             C
Q 008851           87 K   87 (551)
Q Consensus        87 ~   87 (551)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=6.6e-17  Score=134.75  Aligned_cols=79  Identities=20%  Similarity=0.465  Sum_probs=72.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHH----HHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEE
Q 008851            5 QHRCVFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRV   80 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre----~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV   80 (551)
                      ++++|||+|||+++++++|++    +|++||.|.+|++..   +++++|||||+|.+.++|.+|++.+|+..++|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            679999999999999998864    589999999988753   5788999999999999999999999999999999999


Q ss_pred             EeecCC
Q 008851           81 DFAEND   86 (551)
Q Consensus        81 ~~A~~~   86 (551)
                      +||+.+
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            999864

>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=3.1e-16  Score=126.73  Aligned_cols=74  Identities=15%  Similarity=0.248  Sum_probs=68.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ++|||+|||+++++++|+++|+.||.|.++++..|+++  .+|||||+|.+.++|.+|+ .+++..|+|+.|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999998753  4589999999999999999 48999999999999875

>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=99.64  E-value=1.7e-16  Score=129.06  Aligned_cols=76  Identities=20%  Similarity=0.301  Sum_probs=69.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEe
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDF   82 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~   82 (551)
                      ....++|||+|++  +||++|+++|++||.|.+|++..+      +|||||+|.+.++|.+|++.||+..|+|+.|+|+|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4578999999985  899999999999999999998643      68999999999999999999999999999999999


Q ss_pred             ecCC
Q 008851           83 AEND   86 (551)
Q Consensus        83 A~~~   86 (551)
                      ++++
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9754

>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=99.64  E-value=2.9e-16  Score=132.41  Aligned_cols=78  Identities=22%  Similarity=0.459  Sum_probs=71.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--EEEEEE
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEING--RQLRVD   81 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~G--R~LrV~   81 (551)
                      .++++|||+|||++++|++|+++|++||.|..|++.++      ++||||+|.+.++|.+|++.||+..|+|  ++|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            46899999999999999999999999999999998754      6899999999999999999999999976  589999


Q ss_pred             eecCCC
Q 008851           82 FAENDK   87 (551)
Q Consensus        82 ~A~~~~   87 (551)
                      ||+.++
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998654

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=5.3e-16  Score=128.26  Aligned_cols=80  Identities=18%  Similarity=0.343  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCEEE
Q 008851            1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL--QGYEINGRQL   78 (551)
Q Consensus         1 ma~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L--ng~~I~GR~L   78 (551)
                      ++.+++++|||+|||+++++++|+++|+.||.|.++++..+      +|||||+|.+.++|.+|++.+  ++..++|+.|
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEE
Confidence            46779999999999999999999999999999999998754      589999999999999999865  6779999999


Q ss_pred             EEEeecCC
Q 008851           79 RVDFAEND   86 (551)
Q Consensus        79 rV~~A~~~   86 (551)
                      +|+|++.+
T Consensus        77 ~v~~sk~~   84 (88)
T d2cq1a1          77 YIQYSNHK   84 (88)
T ss_dssp             EEEECSCS
T ss_pred             EEEECCCC
Confidence            99999754

>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=3.3e-16  Score=132.80  Aligned_cols=76  Identities=21%  Similarity=0.260  Sum_probs=70.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++++++|+++|++||.|++|++..       +|||||+|.+.++|++|++.||+..|+|+.|+|.+++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            467899999999999999999999999999999863       5899999999999999999999999999999999997


Q ss_pred             CCC
Q 008851           85 NDK   87 (551)
Q Consensus        85 ~~~   87 (551)
                      .+.
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            643

>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=99.62  E-value=4.1e-16  Score=133.75  Aligned_cols=81  Identities=25%  Similarity=0.314  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI--NGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I--~GR~LrV   80 (551)
                      ..+..+|||+||++++||++|+++|++||.|++|.+..++    .+|||||+|.+.++|++|++.||+..|  .|++|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            3467789999999999999999999999999999998764    489999999999999999999999988  5788999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      .|++...
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9987643

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=1.4e-15  Score=129.74  Aligned_cols=79  Identities=16%  Similarity=0.201  Sum_probs=70.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCEEEEE
Q 008851            3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL--QGYEINGRQLRV   80 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L--ng~~I~GR~LrV   80 (551)
                      ..++++|||+|||++++|++|+++|+.||.|+++++.++      ||||||+|.+.++|.+|++.|  ++..++|++|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            457899999999999999999999999999999998643      789999999999999999977  566789999999


Q ss_pred             EeecCCC
Q 008851           81 DFAENDK   87 (551)
Q Consensus        81 ~~A~~~~   87 (551)
                      .|++..+
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9997543

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=1.1e-15  Score=123.35  Aligned_cols=71  Identities=20%  Similarity=0.329  Sum_probs=64.6

Q ss_pred             EEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecCC
Q 008851            9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEND   86 (551)
Q Consensus         9 VFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~~   86 (551)
                      |||+|||+++++++|+++|++|| +..+++      ++.+|||||+|.+.++|.+|++.||+..++|++|+|+|+..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555443      567899999999999999999999999999999999999754

>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=99.58  E-value=3e-15  Score=136.99  Aligned_cols=82  Identities=23%  Similarity=0.398  Sum_probs=77.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         4 ~~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      ...++|||+|||+++|+++|+++|+.||.|..+.++.|+.+|+++|||||+|.+.++|.+|++ +++..|+|+.|+|++|
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            356899999999999999999999999999999999999999999999999999999999996 7889999999999998


Q ss_pred             cCC
Q 008851           84 END   86 (551)
Q Consensus        84 ~~~   86 (551)
                      .++
T Consensus       174 ~~k  176 (183)
T d1u1qa_         174 LSK  176 (183)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            753

>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=99.58  E-value=4.5e-16  Score=134.65  Aligned_cols=80  Identities=20%  Similarity=0.377  Sum_probs=73.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||+|||+++|+++|+++|+.||.+..+.++.+..+|+++|||||+|.+.++|.+|++ +|+..|+||.|+|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            46799999999999999999999999999887777777899999999999999999999995 89999999999999986


Q ss_pred             C
Q 008851           85 N   85 (551)
Q Consensus        85 ~   85 (551)
                      .
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.56  E-value=1.9e-15  Score=128.13  Aligned_cols=77  Identities=19%  Similarity=0.354  Sum_probs=69.6

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH--HhCCceeCCEEEEE
Q 008851            4 SQHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR--NLQGYEINGRQLRV   80 (551)
Q Consensus         4 ~~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~--~Lng~~I~GR~LrV   80 (551)
                      ..+++|||+|||++ +||++|+++|+.||.|+++++..+      +|||||+|.+.++|.+|++  .+++..|+|+.|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            35789999999986 899999999999999999999754      6899999999999999998  57888999999999


Q ss_pred             EeecCC
Q 008851           81 DFAEND   86 (551)
Q Consensus        81 ~~A~~~   86 (551)
                      +||+..
T Consensus        90 ~~s~~~   95 (99)
T d1x4fa1          90 DLSEKY   95 (99)
T ss_dssp             EEECSC
T ss_pred             EEcCCc
Confidence            999754

>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=99.54  E-value=8.2e-15  Score=122.03  Aligned_cols=78  Identities=17%  Similarity=0.221  Sum_probs=70.3

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCEEEE
Q 008851            3 SSQHRCVFVGNIPYD-ATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL--QGYEINGRQLR   79 (551)
Q Consensus         3 ~~~srtVFVGNLP~d-~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~L--ng~~I~GR~Lr   79 (551)
                      ...+++|||+|||.. +|++||+++|+.||.|.+|++..+      ++||||+|++.++|.+|++.|  ++..++|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            457899999999986 889999999999999999999765      579999999999999999966  67889999999


Q ss_pred             EEeecCC
Q 008851           80 VDFAEND   86 (551)
Q Consensus        80 V~~A~~~   86 (551)
                      |+||+..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999754

>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=99.54  E-value=6.7e-17  Score=134.14  Aligned_cols=76  Identities=22%  Similarity=0.467  Sum_probs=68.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEE-----eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEE
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRL-----VIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVD   81 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrL-----v~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~   81 (551)
                      ++|||||||+++||++|+++|+.||.|..+.+     +.+..+++++|||||+|.+.++|++|++ |||+.++|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            78999999999999999999999998876654     3466789999999999999999999984 99999999999996


Q ss_pred             ee
Q 008851           82 FA   83 (551)
Q Consensus        82 ~A   83 (551)
                      ++
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=3.1e-14  Score=122.07  Aligned_cols=79  Identities=18%  Similarity=0.186  Sum_probs=70.2

Q ss_pred             CCCCcEEEEecCCCCC-CH----HHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE
Q 008851            3 SSQHRCVFVGNIPYDA-TE----EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ   77 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~-TE----EeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~   77 (551)
                      ++..++|||+||+.++ ++    ++|+++|+.||.|++|++.+      .+|||||+|.+.++|.+|++.|||..|+|+.
T Consensus         2 ~~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~   75 (104)
T d1weya_           2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKE   75 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEE
T ss_pred             CCCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCE
Confidence            4568899999999886 33    57999999999999999874      4789999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q 008851           78 LRVDFAENDK   87 (551)
Q Consensus        78 LrV~~A~~~~   87 (551)
                      |+|+||+...
T Consensus        76 l~v~~a~~~~   85 (104)
T d1weya_          76 MKLYFAQTLH   85 (104)
T ss_dssp             CEEECCCCSS
T ss_pred             eEEeecccCC
Confidence            9999997543

>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=99.46  E-value=7e-15  Score=126.11  Aligned_cols=75  Identities=19%  Similarity=0.202  Sum_probs=69.6

Q ss_pred             EEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEee
Q 008851            8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA   83 (551)
Q Consensus         8 tVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A   83 (551)
                      .++|+++..+++|++|+++|++||.|++|+|.++ .+|+++|||||+|.+.++|.+|++.|||..++||.|+|+|+
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 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3667778888999999999999999999999877 58999999999999999999999999999999999999985

>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=99.41  E-value=4.6e-13  Score=122.15  Aligned_cols=81  Identities=23%  Similarity=0.431  Sum_probs=73.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ..++|||||||+++||++|+++|++||.|.++.+++|..+|+++|||||+|.+.++|.+|++. ++..++++.+.+.+..
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            348999999999999999999999999999999999999999999999999999999999974 5568899988888765


Q ss_pred             CC
Q 008851           85 ND   86 (551)
Q Consensus        85 ~~   86 (551)
                      ..
T Consensus        84 ~~   85 (183)
T d1u1qa_          84 SR   85 (183)
T ss_dssp             CT
T ss_pred             hc
Confidence            44

>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=99.32  E-value=1.4e-12  Score=110.97  Aligned_cols=65  Identities=25%  Similarity=0.400  Sum_probs=59.0

Q ss_pred             CCCCcEEEEec--CCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            3 SSQHRCVFVGN--IPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         3 ~~~srtVFVGN--LP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      +.+.+++||+|  |++++||++|+++|++||.|++|++..+      +|||||+|.+.++|.+|++.|||..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            44678899955  9999999999999999999999988754      67999999999999999999999987

>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=99.29  E-value=4.6e-12  Score=107.18  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=68.7

Q ss_pred             CCCcEEEEecC--CCCCC---------HHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 008851            4 SQHRCVFVGNI--PYDAT---------EEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYE   72 (551)
Q Consensus         4 ~~srtVFVGNL--P~d~T---------EEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~   72 (551)
                      ..+++|+|.|+  +.++.         +++|++.|++||.|..|++..+    +.+|||||+|.+.++|.+|++.|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            46899999999  65432         3679999999999999988643    568999999999999999999999999


Q ss_pred             eCCEEEEEEeecCC
Q 008851           73 INGRQLRVDFAEND   86 (551)
Q Consensus        73 I~GR~LrV~~A~~~   86 (551)
                      ++||.|+|+++.+.
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999998754

>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=99.29  E-value=1.8e-12  Score=111.97  Aligned_cols=73  Identities=16%  Similarity=0.227  Sum_probs=63.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHhCCceeCCEEEEEEeec
Q 008851            6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE-ETALSARRNLQGYEINGRQLRVDFAE   84 (551)
Q Consensus         6 srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~-e~A~sAi~~Lng~~I~GR~LrV~~A~   84 (551)
                      ...+|||||++++||++|+++|+.||+|.+|+|+.+      +|||||+|.+. ++|..|+..+++..+.++.++|.++.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            345699999999999999999999999999999854      79999999985 78999999999998887777776654

>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=99.24  E-value=6.1e-12  Score=103.20  Aligned_cols=73  Identities=14%  Similarity=0.105  Sum_probs=62.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEE-EEEEee
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ-LRVDFA   83 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~-LrV~~A   83 (551)
                      +++.|||+++|++++++.| ++|++||.|+++++.      +.+|||||+|.+.++|++|++ +||..|+|+. |.|..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            4678999999999987655 579999999999864      447999999999999999995 9999999974 678877


Q ss_pred             cC
Q 008851           84 EN   85 (551)
Q Consensus        84 ~~   85 (551)
                      ..
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.21  E-value=6.1e-12  Score=107.10  Aligned_cols=82  Identities=17%  Similarity=0.232  Sum_probs=71.2

Q ss_pred             CCCcEEEEecC--CCCCC--------HHHHHHHHHcCCCeeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCc
Q 008851            4 SQHRCVFVGNI--PYDAT--------EEQLIEICREVGPVVSFRLVIDRETG--KPKGYGFCEYKDEETALSARRNLQGY   71 (551)
Q Consensus         4 ~~srtVFVGNL--P~d~T--------EEeLre~Fs~~G~V~~vrLv~Dr~TG--ksKGyAFVEF~d~e~A~sAi~~Lng~   71 (551)
                      .++++|+|.|+  +.+..        .++|++.|++||.|++|.|.++.++.  ..+|++||+|.+.++|.+|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            47899999999  55443        35789999999999999998876554  34689999999999999999999999


Q ss_pred             eeCCEEEEEEeecC
Q 008851           72 EINGRQLRVDFAEN   85 (551)
Q Consensus        72 ~I~GR~LrV~~A~~   85 (551)
                      .++||.|+|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.83  E-value=0.0014  Score=54.01  Aligned_cols=73  Identities=19%  Similarity=0.320  Sum_probs=57.5

Q ss_pred             CCCCcEEEEecCCCCCCH---------HHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 008851            3 SSQHRCVFVGNIPYDATE---------EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEI   73 (551)
Q Consensus         3 ~~~srtVFVGNLP~d~TE---------EeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I   73 (551)
                      .+++-+|.|.=...+..|         .+|.+.|..||+|.-+|++.|.        -+|+|.|-+.|.+|+ .+++.++
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al-~l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVL-DVDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHH-HGGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHh-ccCCeEE
Confidence            456677777544433322         3578889999999999999664        699999999999999 5899999


Q ss_pred             CCEEEEEEeec
Q 008851           74 NGRQLRVDFAE   84 (551)
Q Consensus        74 ~GR~LrV~~A~   84 (551)
                      .|+.|+|....
T Consensus        83 ~G~~l~It~~~   93 (95)
T d1ufwa_          83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             cceEEEEecCC
Confidence            99999997643

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.0074  Score=49.54  Aligned_cols=78  Identities=23%  Similarity=0.339  Sum_probs=63.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcc--eEEEEEeCCHHHHHHHHHHhCCceeC---C--EEEE
Q 008851            7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPK--GYGFCEYKDEETALSARRNLQGYEIN---G--RQLR   79 (551)
Q Consensus         7 rtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksK--GyAFVEF~d~e~A~sAi~~Lng~~I~---G--R~Lr   79 (551)
                      ++|.|++||...||+++.+.++..|.+..+..+..+.+-+..  .-|||.|.+.++.....+.++|+.+-   |  .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            578999999999999999999999999888777655444433  56899999999999999999998872   2  2346


Q ss_pred             EEeec
Q 008851           80 VDFAE   84 (551)
Q Consensus        80 V~~A~   84 (551)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            77764

>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=96.39  E-value=0.0088  Score=46.99  Aligned_cols=62  Identities=21%  Similarity=0.269  Sum_probs=51.7

Q ss_pred             HHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCEEEEEEeecC
Q 008851           21 EQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFAEN   85 (551)
Q Consensus        21 EeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Lng~~I~GR~LrV~~A~~   85 (551)
                      +.|.+.|+++|.|.++.+....+ |.  -.|-|...+.++|..|+..||.++|++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-Cc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            34667789999999998865432 33  3578999999999999999999999999999999864

>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=84.81  E-value=1.1  Score=36.75  Aligned_cols=57  Identities=14%  Similarity=0.195  Sum_probs=46.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHHHcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 008851            5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ   69 (551)
Q Consensus         5 ~srtVFVGNLP~d~TEEeLre~Fs~~G~V~~vrLv~Dr~TGksKGyAFVEF~d~e~A~sAi~~Ln   69 (551)
                      ....||.-.+|.+|...+|.++|+.||.|. |..+.|-       -|||...+.++++.++..++
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            345688889999999999999999999764 3334332       68999999999999987655