Citrus Sinensis ID: 019811

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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-----
Protein Sequence
MQHQRLKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccccEEEEEccccccEEEEEcccHHHHHHHHHHHcccccccccEEEEEcccccccccccccccEEEccccccccHHHHHHHHcccccccccEEEEEccccccccEEEEEcccHHHHHHHHHHccccccccccEEEEcccccccccccccccHHHHHHHHccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccccEEEEEEcccccEEEEEcccHHHHHHHHHHHccccccccccEEEEc
Secondary Structure Prediction (SSPRO)
cccccHEEcccccccHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHccccEEEEEEEEcccccEEEEEEccHHHHHHHHHHHcccEccccEEEEEEEccccccccccccEEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcHHcccEccccEEEEEEcccccccHHHHcccHHHccccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccEEEEEEccHHHHHHHHHHHcccEEEEEccEEEEc
Coil and Loop (DISEMBL)
MQHQRLKQQQQQQQQALMQQALLQQqslyhpgllaapqiepipsgnlppgfdpstcrsvyvgnihtqvtepllqevfsstgpvegcklirkdkssygfihYFDRRSAAMAILSLNgrhlfgqpikvnwayasgqredtsghfnifvgdlspevtdaTLFACFsvypscsdarvmwdqktgrsrgfgfvsfrnQQDAQSAINDLTgkwlgsrqircnwatkgagnnedkqssdAKSVVELtngssedgkettnteapennpqyttvyvgnlapevtqldlHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
Flexible Loop (DISEMBL)
MQHQRLKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATkgagnnedkqssdaKSVVELtngssedgkettnteapennpqYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQmgnttqssylfgkqmkv
Low Complexity Region (SEG)
MqhqrlkqqqqqqqqalmqqallqqqslYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
Disordered region (IsUnstruct)
*******************************GLL*****************DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT******************************************YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT*************
Disordered Region (DISOPRED)
*********************************************************SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV*****************IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN****************************************ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
Disordered Region (DISEMBL)
******************QQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG**********************************PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
Disordered Region (DISPRO)
*****LKQ****QQQALMQQALLQQQ**YHPGLLAAPQ***************STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK*************************************NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQHQRxxxxxxxxxxxxxxxxxxxxxSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV
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	335	2.2.26 [Sep-21-2011]
Q01085	375	Nucleolysin TIAR OS=Homo	yes	no	0.752	0.672	0.414	7e-51
P70318	392	Nucleolysin TIAR OS=Mus m	no	no	0.752	0.642	0.397	5e-49
P31483	386	Nucleolysin TIA-1 isoform	no	no	0.752	0.652	0.398	5e-47
P52912	386	Nucleolysin TIA-1 OS=Mus	yes	no	0.752	0.652	0.398	8e-47
P32588	453	Nuclear and cytoplasmic p	yes	no	0.495	0.366	0.4	2e-32
Q9LEB3	428	Polyadenylate-binding pro	N/A	no	0.794	0.621	0.326	7e-32
Q8VXZ9	425	Polyadenylate-binding pro	no	no	0.776	0.611	0.324	2e-31
Q0WW84	435	Polyadenylate-binding pro	no	no	0.782	0.602	0.322	4e-31
F4I3B3	445	Polyadenylate-binding pro	no	no	0.761	0.573	0.327	8e-30
Q9LEB4	409	Polyadenylate-binding pro	N/A	no	0.835	0.684	0.310	3e-29

>sp|Q01085|TIAR_HUMAN Nucleolysin TIAR OS=Homo sapiens GN=TIAL1 PE=1 SV=1

 Score =  201 bits (511), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 112/270 (41%), Positives = 167/270 (61%), Gaps = 18/270 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           R++YVGN+   VTE L+ ++FS  GP + CK+I +  S+  Y F+ +++ R AA A+ ++
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 115 NGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV 173
           NGR + G+ +KVNWA   S Q++DTS HF++FVGDLSPE+T   + + F+ +   SDARV
Sbjct: 69  NGRKILGKEVKVNWATTPSSQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARV 128

Query: 174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDA 233
           + D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+     +  Q ++ 
Sbjct: 129 VKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPKSTQENNT 188

Query: 234 KSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE 293
           K +           ++  N  +P+N     TVY G +A  +T   + + F   G   I E
Sbjct: 189 KQL---------RFEDVVNQSSPKN----CTVYCGGIASGLTDQLMRQTFSPFGQ--IME 233

Query: 294 VRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           +RV  +KG+ FVR+STH  AA AI   N T
Sbjct: 234 IRVFPEKGYSFVRFSTHESAAHAIVSVNGT 263

RNA-binding protein. Possesses nucleolytic activity against cytotoxic lymphocyte target cells. May be involved in apoptosis.
Homo sapiens (taxid: 9606)

>sp|P70318|TIAR_MOUSE Nucleolysin TIAR OS=Mus musculus GN=Tial1 PE=2 SV=1

 Score =  194 bits (494), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 114/287 (39%), Positives = 168/287 (58%), Gaps = 35/287 (12%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI------RKDKSS-------------YG 97
           R++YVGN+   VTE L+ ++FS  GP + CK+I      R+  SS             Y 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEQPDSRRVNSSVGFSVLQHTSNDPYC 68

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVTDA 156
           F+ +++ R AA A+ ++NGR + G+ +KVNWA   S Q++DTS HF++FVGDLSPE+T  
Sbjct: 69  FVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKKDTSNHFHVFVGDLSPEITTE 128

Query: 157 TLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN 216
            + + F+ +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR N
Sbjct: 129 DIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTN 188

Query: 217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQ 276
           WAT+     +  Q ++ K +           ++  N  +P+N     TVY G +A  +T 
Sbjct: 189 WATRKPPAPKSTQETNTKQL---------RFEDVVNQSSPKN----CTVYCGGIASGLTD 235

Query: 277 LDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
             + + F   G   I E+RV  +KG+ FVR+STH  AA AI   N T
Sbjct: 236 QLMRQTFSPFGQ--IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 280

RNA-binding protein. Possesses nucleolytic activity against cytotoxic lymphocyte target cells. May be involved in apoptosis.

Mus musculus (taxid: 10090)

>sp|P31483|TIA1_HUMAN Nucleolysin TIA-1 isoform p40 OS=Homo sapiens GN=TIA1 PE=1 SV=3

 Score =  188 bits (478), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 112/281 (39%), Positives = 163/281 (58%), Gaps = 29/281 (10%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           +++YVGN+   VTE L+ ++FS  GP + CK+I     +  Y F+ + + R AA A+ ++
Sbjct: 7   KTLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAGNDPYCFVEFHEHRHAAAALAAM 66

Query: 115 NGRHLFGQPIKVNWAYA-SGQREDTSG-----------HFNIFVGDLSPEVTDATLFACF 162
           NGR + G+ +KVNWA   S Q++DTS            HF++FVGDLSPE+T   + A F
Sbjct: 67  NGRKIMGKEVKVNWATTPSSQKKDTSSSTVVSTQRSQDHFHVFVGDLSPEITTEDIKAAF 126

Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
           + +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+  
Sbjct: 127 APFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 186

Query: 223 GNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRH 282
              +    S+ K +       S D  E  N  +P N     TVY G +   +T+  + + 
Sbjct: 187 PAPKSTYESNTKQL-------SYD--EVVNQSSPSN----CTVYCGGVTSGLTEQLMRQT 233

Query: 283 FHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           F   G   I E+RV  DKG+ FVR+++H  AA AI   N T
Sbjct: 234 FSPFGQ--IMEIRVFPDKGYSFVRFNSHESAAHAIVSVNGT 272

Involved in alternative pre-RNA splicing and regulation of mRNA translation by binding to AU-rich elements (AREs) located in mRNA 3' untranslated regions (3' UTRs). Possesses nucleolytic activity against cytotoxic lymphocyte target cells. May be involved in apoptosis.

Homo sapiens (taxid: 9606)

>sp|P52912|TIA1_MOUSE Nucleolysin TIA-1 OS=Mus musculus GN=Tia1 PE=1 SV=1

 Score =  187 bits (476), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 112/281 (39%), Positives = 163/281 (58%), Gaps = 29/281 (10%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           +++YVGN+   VTE L+ ++FS  GP + CK+I     +  Y F+ + + R AA A+ ++
Sbjct: 7   KTLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAGNDPYCFVEFHEHRHAAAALAAM 66

Query: 115 NGRHLFGQPIKVNWAYA-SGQREDTSG-----------HFNIFVGDLSPEVTDATLFACF 162
           NGR + G+ +KVNWA   S Q++DTS            HF++FVGDLSPE+T   + A F
Sbjct: 67  NGRKIMGKEVKVNWATTPSSQKKDTSSSTVVSTQRSQDHFHVFVGDLSPEITTEDIKAAF 126

Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
           + +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+  
Sbjct: 127 APFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 186

Query: 223 GNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRH 282
              +    S+ K +       S D  E  +  +P N     TVY G +   +T+  + + 
Sbjct: 187 PAPKSTYESNTKQL-------SYD--EVVSQSSPNN----CTVYCGGVTSGLTEQLMRQT 233

Query: 283 FHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           F   G   I E+RV  DKG+ FVR+S+H  AA AI   N T
Sbjct: 234 FSPFGQ--IMEIRVFPDKGYSFVRFSSHESAAHAIVSVNGT 272

Involved in alternative pre-RNA splicing and regulation of mRNA translation by binding to AU-rich elements (AREs) located in mRNA 3' untranslated regions (3' UTRs). Possesses nucleolytic activity against cytotoxic lymphocyte target cells. May be involved in apoptosis.

Mus musculus (taxid: 10090)

>sp|P32588|PUB1_YEAST Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUB1 PE=1 SV=4

 Score =  139 bits (351), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/170 (40%), Positives = 106/170 (62%), Gaps = 4/170 (2%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKS-SYGFIHYFDRRSAAMA 110
           ++ R +YVGN+   +TE +L++ F   GP+   K++  + +K+ +Y F+ Y     A +A
Sbjct: 72  TSDRVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIA 131

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
           + +LNG+ +    +K+NWA+ S Q+  +   FN+FVGDL+  V D TL   F  +PS   
Sbjct: 132 LQTLNGKQIENNIVKINWAFQS-QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLS 190

Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
             VMWD +TG SRG+GFVSF +Q DAQ+A++ + G+ L  R +R NWA K
Sbjct: 191 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 240

May be associated with hnRNA within the nucleus and remains associated during nucleocytoplasmic mRNA transport, once the proteins are in the cytoplasm, disassembly of PUB1-RNA complexes may occur prior to PAB1 binding and formation of a translationally competent RNP complex. Binds to polyadenylated RNA; prefers to bind poly(rU); binds to T-rich single-stranded DNA.

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

>sp|Q9LEB3|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1

 Score =  138 bits (347), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 93/285 (32%), Positives = 154/285 (54%), Gaps = 19/285 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
           +++++G++   + E  L   FS  G V   K+IR  ++     YGF+ +    +A   + 
Sbjct: 84  KTIWIGDLQQWMDESYLHSCFSQAGEVISVKIIRNKQTGQSERYGFVEFNTHAAAEKVLQ 143

Query: 113 SLNGRHL--FGQPIKVNWA-YASGQ-REDTSGHFNIFVGDLSPEVTDATLFACF-SVYPS 167
           S NG  +    QP ++NWA +++G+ R +T   F+IFVGDL+ +VTD  L   F S YPS
Sbjct: 144 SYNGTMMPNTEQPFRLNWAGFSTGEKRAETGSDFSIFVGDLASDVTDTMLRDTFASRYPS 203

Query: 168 CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNED 227
              A+V+ D  TG S+G+GFV F ++ +   A+ ++ G +  SR +R   AT    +  +
Sbjct: 204 LKGAKVVVDANTGHSKGYGFVRFGDESERSRAMTEMNGVYCSSRAMRIGVATPKKPSAHE 263

Query: 228 KQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG 287
           + SS A   V L+ G + +G  T  +++ + +   TT++VG L  EVT  +L + F+  G
Sbjct: 264 QYSSQA---VILSGGYASNGAATHGSQS-DGDSSNTTIFVGGLDSEVTDEELRQSFNQFG 319

Query: 288 AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ 332
              +  V++   KG GFV++S  + A  AIQ      S  + GKQ
Sbjct: 320 E--VVSVKIPAGKGCGFVQFSDRSSAQEAIQ----KLSGAIIGKQ 358

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q8VXZ9|R47BP_ARATH Polyadenylate-binding protein RBP47B' OS=Arabidopsis thaliana GN=RBP47B' PE=2 SV=1

 Score =  136 bits (342), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 141/271 (52%), Gaps = 11/271 (4%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAI 111
            R++++G++   V E  L   FS TG +   K+IR   +     YGFI +    +A   +
Sbjct: 23  VRTLWIGDLQYWVDENYLTSCFSQTGELVSVKVIRNKITGQPEGYGFIEFISHAAAERTL 82

Query: 112 LSLNGRHLFGQPI--KVNWA-YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSV-YPS 167
            + NG  + G  +  ++NWA + SGQ+ D     +IFVGDL+P+VTD  L   F V Y S
Sbjct: 83  QTYNGTQMPGTELTFRLNWASFGSGQKVDAGPDHSIFVGDLAPDVTDYLLQETFRVHYSS 142

Query: 168 CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNED 227
              A+V+ D  TGRS+G+GFV F  + +   A+ ++ G +  +R +R + AT    N   
Sbjct: 143 VRGAKVVTDPSTGRSKGYGFVKFAEESERNRAMAEMNGLYCSTRPMRISAATPKK-NVGV 201

Query: 228 KQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG 287
           +Q    K+V  +T  S+           PE++   TT+ V NL   VT+ +L + F  LG
Sbjct: 202 QQQYVTKAVYPVTVPSAVAAPVQAYVAPPESDVTCTTISVANLDQNVTEEELKKAFSQLG 261

Query: 288 AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
             +   V++   KG+G+V++ T   A  A+Q
Sbjct: 262 EVIY--VKIPATKGYGYVQFKTRPSAEEAVQ 290

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WW84|RB47B_ARATH Polyadenylate-binding protein RBP47B OS=Arabidopsis thaliana GN=RBP47B PE=2 SV=1

 Score =  135 bits (341), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 90/279 (32%), Positives = 149/279 (53%), Gaps = 17/279 (6%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAI 111
            ++++VG++   + E  L   FS TG V   K+IR   +S    YGF+ +  R +A   +
Sbjct: 107 VKTLWVGDLLHWMDETYLHSCFSHTGEVSSVKVIRNKLTSQSEGYGFVEFLSRAAAEEVL 166

Query: 112 LSLNGRHL--FGQPIKVNWA-YASGQRE--DTSGHFNIFVGDLSPEVTDATLFACFS-VY 165
            + +G  +    QP ++NWA +++G++   +     ++FVGDLSP+VTD  L   FS  Y
Sbjct: 167 QNYSGSVMPNSDQPFRINWASFSTGEKRAVENGPDLSVFVGDLSPDVTDVLLHETFSDRY 226

Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT-KGAGN 224
           PS   A+V+ D  TGRS+G+GFV F ++ +   A+ ++ G +  +RQ+R   AT K A  
Sbjct: 227 PSVKSAKVVIDSNTGRSKGYGFVRFGDENERSRALTEMNGAYCSNRQMRVGIATPKRAIA 286

Query: 225 NEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFH 284
           N+ + SS A   V L  G   +G     +++ +      T++VG + P+V   DL + F 
Sbjct: 287 NQQQHSSQA---VILAGGHGSNGSMGYGSQS-DGESTNATIFVGGIDPDVIDEDLRQPFS 342

Query: 285 SLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
             G   +  V++   KG GFV+++    A  AI+  N T
Sbjct: 343 QFGE--VVSVKIPVGKGCGFVQFADRKSAEDAIESLNGT 379

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|F4I3B3|RB47A_ARATH Polyadenylate-binding protein RBP47A OS=Arabidopsis thaliana GN=RBP47A PE=2 SV=1

 Score =  131 bits (329), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 92/281 (32%), Positives = 149/281 (53%), Gaps = 26/281 (9%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAI 111
            ++++VG++   + E  L   FS T  V   K+IR  ++     YGF+ +  R +A  A+
Sbjct: 118 VKTLWVGDLLHWMDETYLHTCFSHTNEVSSVKVIRNKQTCQSEGYGFVEFLSRSAAEEAL 177

Query: 112 LSLNGRHLFG--QPIKVNWA-YASGQRE--DTSGHFNIFVGDLSPEVTDATLFACFS-VY 165
            S +G  +    QP ++NWA +++G++   +     +IFVGDL+P+V+DA L   F+  Y
Sbjct: 178 QSFSGVTMPNAEQPFRLNWASFSTGEKRASENGPDLSIFVGDLAPDVSDAVLLETFAGRY 237

Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT-KGAGN 224
           PS   A+V+ D  TGRS+G+GFV F ++ +   A+ ++ G +  SRQ+R   AT K A  
Sbjct: 238 PSVKGAKVVIDSNTGRSKGYGFVRFGDENERSRAMTEMNGAFCSSRQMRVGIATPKRAAA 297

Query: 225 NEDKQSSDAKSVV--ELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRH 282
              +  S A ++      NGS  DG E+ N          +T++VG L  +VT+ DL + 
Sbjct: 298 YGQQNGSQALTLAGGHGGNGSMSDG-ESNN----------STIFVGGLDADVTEEDLMQP 346

Query: 283 FHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           F   G   +  V++   KG GFV+++    A  AI   N T
Sbjct: 347 FSDFGE--VVSVKIPVGKGCGFVQFANRQSAEEAIGNLNGT 385

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LEB4|RBP45_NICPL Polyadenylate-binding protein RBP45 OS=Nicotiana plumbaginifolia GN=RBP45 PE=1 SV=1

 Score =  129 bits (324), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 97/312 (31%), Positives = 151/312 (48%), Gaps = 32/312 (10%)

Query: 21  ALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSST 80
           A  QQ S    G +A     P P+GN      P+  RS+++G++   + E  L   F  T
Sbjct: 54  AWAQQPSQQQYGAMATTNPNPSPTGN------PNEVRSLWIGDLQYWMDENYLSTCFYHT 107

Query: 81  GPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSLNGRHL--FGQPIKVNWA-YASG 133
           G +   K+IR  ++     YGF+ +    +A   + + NG  +    Q  ++NWA   +G
Sbjct: 108 GELVSAKVIRNKQTGQSEGYGFLEFRSHAAAETILQTYNGTLMPNVEQNFRMNWASLGAG 167

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           +R D S    IFVGDL+ +VTD  L   F SVY S   A+V+ D+ TGRS+G+GFV F +
Sbjct: 168 ERRDDSAEHTIFVGDLAADVTDYILQETFKSVYSSVRGAKVVTDRITGRSKGYGFVKFAD 227

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTN 252
           + +   A+ ++ G    +R +R      G   N+    +  K+  +  N  +  G     
Sbjct: 228 ESEQLRAMTEMNGVLCSTRPMRI-----GPAANKKPVGTPQKATYQ--NPQATQG----- 275

Query: 253 TEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAE 312
               E++P  TT++VG L P V +  L + F   G  V   V++   K  GFV++ T A 
Sbjct: 276 ----ESDPNNTTIFVGGLDPTVAEEHLRQVFSPYGELV--HVKIVAGKRCGFVQFGTRAS 329

Query: 313 AALAIQMGNTTQ 324
           A  A+   N TQ
Sbjct: 330 AEQALSSLNGTQ 341

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

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	335
356519889	422	PREDICTED: nucleolysin TIAR-like [Glycin	0.994	0.789	0.925	1e-172
255576617	422	nucleolysin tia-1, putative [Ricinus com	0.913	0.725	0.931	1e-171
225442061	420	PREDICTED: nucleolysin TIAR [Vitis vinif	0.916	0.730	0.915	1e-169
147797981	420	hypothetical protein VITISV_027348 [Viti	0.916	0.730	0.912	1e-168
297742974	407	unnamed protein product [Vitis vinifera]	0.910	0.749	0.915	1e-168
224119532	426	predicted protein [Populus trichocarpa]	0.904	0.711	0.918	1e-168
356559021	416	PREDICTED: nucleolysin TIAR-like [Glycin	0.979	0.788	0.880	1e-167
449447926	422	PREDICTED: nucleolysin TIAR-like [Cucumi	0.910	0.722	0.902	1e-167
224073594	421	predicted protein [Populus trichocarpa]	0.913	0.726	0.905	1e-166
217074564	407	unknown [Medicago truncatula] gi|3885213	0.928	0.764	0.884	1e-165

>gi|356519889|ref|XP_003528601.1| PREDICTED: nucleolysin TIAR-like [Glycine max]

 Score =  611 bits (1575), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 310/335 (92%), Positives = 322/335 (96%), Gaps = 2/335 (0%)

Query: 1   MQHQRLKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVY 60
           MQ+ RLKQQQQQQQQALMQQALLQQQSLYHPGLLA PQIEP PSGNLPPGFDPSTCRSVY
Sbjct: 1   MQNHRLKQQQQQQQQALMQQALLQQQSLYHPGLLAPPQIEPYPSGNLPPGFDPSTCRSVY 60

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF 120
           VGNIHTQVTEPLLQEVFS TGPVEGCKLIRKDKSSYGFIHYFDRRSAA+AILSLNGRHLF
Sbjct: 61  VGNIHTQVTEPLLQEVFSGTGPVEGCKLIRKDKSSYGFIHYFDRRSAALAILSLNGRHLF 120

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180
           GQPIKVNWAYASGQREDTSGH+NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG
Sbjct: 121 GQPIKVNWAYASGQREDTSGHYNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELT 240
           RSRGFGFVSFRNQQDAQS+INDLTGKWLGSRQIRCNWATKGAG NE+KQ+SDAKSVVELT
Sbjct: 181 RSRGFGFVSFRNQQDAQSSINDLTGKWLGSRQIRCNWATKGAGGNEEKQNSDAKSVVELT 240

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK 300
           NGSSEDGKET+N++APENNPQYTTVYVGNLAPEVTQLDLHRHFH+LGAGV+EEVRVQRDK
Sbjct: 241 NGSSEDGKETSNSDAPENNPQYTTVYVGNLAPEVTQLDLHRHFHALGAGVMEEVRVQRDK 300

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           GFGFVRYSTHAEAALAIQMGN    S L GK +K 
Sbjct: 301 GFGFVRYSTHAEAALAIQMGNA--QSLLCGKPIKC 333

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576617|ref|XP_002529199.1| nucleolysin tia-1, putative [Ricinus communis] gi|223531377|gb|EEF33213.1| nucleolysin tia-1, putative [Ricinus communis]

 Score =  606 bits (1562), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 287/308 (93%), Positives = 298/308 (96%), Gaps = 2/308 (0%)

Query: 27  SLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC 86
           SLYHPGLLA PQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVF+STGPVE C
Sbjct: 23  SLYHPGLLAPPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFASTGPVESC 82

Query: 87  KLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 146
           KLIRK+KSSYGFIHYFDRRSAA+AILSLNGRHLFGQPIKVNWAYASGQREDTSGH+NIFV
Sbjct: 83  KLIRKEKSSYGFIHYFDRRSAALAILSLNGRHLFGQPIKVNWAYASGQREDTSGHYNIFV 142

Query: 147 GDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 206
           GDLSPEVTDATLFACFSVY SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK
Sbjct: 143 GDLSPEVTDATLFACFSVYHSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 202

Query: 207 WLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVY 266
           WLGSRQIRCNWATKGA +N+DKQSSDAKSVVELTNGSSE+GKET N +APENNPQYTTVY
Sbjct: 203 WLGSRQIRCNWATKGATSNDDKQSSDAKSVVELTNGSSEEGKETANNDAPENNPQYTTVY 262

Query: 267 VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSS 326
           VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVR+STHAEAALAIQMGNT   S
Sbjct: 263 VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRFSTHAEAALAIQMGNT--QS 320

Query: 327 YLFGKQMK 334
            L+GKQ+K
Sbjct: 321 ILYGKQIK 328

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442061|ref|XP_002270823.1| PREDICTED: nucleolysin TIAR [Vitis vinifera]

 Score =  600 bits (1548), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 283/309 (91%), Positives = 296/309 (95%), Gaps = 2/309 (0%)

Query: 27  SLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC 86
           SLYHPGLLA PQIEPIPSGNLPPGFD STCRSVYVGNIHTQV+EPLLQEVF+STGPVEGC
Sbjct: 23  SLYHPGLLAPPQIEPIPSGNLPPGFDSSTCRSVYVGNIHTQVSEPLLQEVFASTGPVEGC 82

Query: 87  KLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 146
           KL+RK+KSSYGFIHYFDRRSAA+AILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV
Sbjct: 83  KLVRKEKSSYGFIHYFDRRSAALAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 142

Query: 147 GDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 206
           GDLSPEVTDATLFACFSV+PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND+TGK
Sbjct: 143 GDLSPEVTDATLFACFSVFPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDITGK 202

Query: 207 WLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVY 266
           WLGSRQIRCNWATKGAG+N+DKQSSDAKSVVELTNGSSEDGKET   EAP+NNPQYTTVY
Sbjct: 203 WLGSRQIRCNWATKGAGSNDDKQSSDAKSVVELTNGSSEDGKETATNEAPDNNPQYTTVY 262

Query: 267 VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSS 326
           VGNLAPEVTQLDLHRHFH+ GAGVIEEVRVQRDKGFGFVRY+THAEAALAIQMGNT   S
Sbjct: 263 VGNLAPEVTQLDLHRHFHTFGAGVIEEVRVQRDKGFGFVRYNTHAEAALAIQMGNT--QS 320

Query: 327 YLFGKQMKV 335
            L GK +K 
Sbjct: 321 ILCGKPIKC 329

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147797981|emb|CAN65009.1| hypothetical protein VITISV_027348 [Vitis vinifera]

 Score =  597 bits (1540), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 282/309 (91%), Positives = 295/309 (95%), Gaps = 2/309 (0%)

Query: 27  SLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC 86
           SLYHPGLLA PQIEPIPSGNLPPGFD STCRSVYVGNIHTQV+EPLLQEVF+STGPVEGC
Sbjct: 23  SLYHPGLLAPPQIEPIPSGNLPPGFDSSTCRSVYVGNIHTQVSEPLLQEVFASTGPVEGC 82

Query: 87  KLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 146
           KL+RK+KSSYGFIHYFDRRSAA+AILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV
Sbjct: 83  KLVRKEKSSYGFIHYFDRRSAALAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 142

Query: 147 GDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 206
           GDLSPEVTDATLFACFSV+PSCSDARVMWDQKTGRSRGFGFVSFRNQQ AQSAIND+TGK
Sbjct: 143 GDLSPEVTDATLFACFSVFPSCSDARVMWDQKTGRSRGFGFVSFRNQQVAQSAINDITGK 202

Query: 207 WLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVY 266
           WLGSRQIRCNWATKGAG+N+DKQSSDAKSVVELTNGSSEDGKET   EAP+NNPQYTTVY
Sbjct: 203 WLGSRQIRCNWATKGAGSNDDKQSSDAKSVVELTNGSSEDGKETATNEAPDNNPQYTTVY 262

Query: 267 VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSS 326
           VGNLAPEVTQLDLHRHFH+ GAGVIEEVRVQRDKGFGFVRY+THAEAALAIQMGNT   S
Sbjct: 263 VGNLAPEVTQLDLHRHFHTFGAGVIEEVRVQRDKGFGFVRYNTHAEAALAIQMGNT--QS 320

Query: 327 YLFGKQMKV 335
            L GK +K 
Sbjct: 321 ILCGKPIKC 329

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742974|emb|CBI35841.3| unnamed protein product [Vitis vinifera]

 Score =  597 bits (1539), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 281/307 (91%), Positives = 294/307 (95%), Gaps = 2/307 (0%)

Query: 29  YHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL 88
           YHPGLLA PQIEPIPSGNLPPGFD STCRSVYVGNIHTQV+EPLLQEVF+STGPVEGCKL
Sbjct: 12  YHPGLLAPPQIEPIPSGNLPPGFDSSTCRSVYVGNIHTQVSEPLLQEVFASTGPVEGCKL 71

Query: 89  IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 148
           +RK+KSSYGFIHYFDRRSAA+AILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD
Sbjct: 72  VRKEKSSYGFIHYFDRRSAALAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 131

Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LSPEVTDATLFACFSV+PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND+TGKWL
Sbjct: 132 LSPEVTDATLFACFSVFPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDITGKWL 191

Query: 209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVG 268
           GSRQIRCNWATKGAG+N+DKQSSDAKSVVELTNGSSEDGKET   EAP+NNPQYTTVYVG
Sbjct: 192 GSRQIRCNWATKGAGSNDDKQSSDAKSVVELTNGSSEDGKETATNEAPDNNPQYTTVYVG 251

Query: 269 NLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL 328
           NLAPEVTQLDLHRHFH+ GAGVIEEVRVQRDKGFGFVRY+THAEAALAIQMGNT   S L
Sbjct: 252 NLAPEVTQLDLHRHFHTFGAGVIEEVRVQRDKGFGFVRYNTHAEAALAIQMGNT--QSIL 309

Query: 329 FGKQMKV 335
            GK +K 
Sbjct: 310 CGKPIKC 316

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119532|ref|XP_002331184.1| predicted protein [Populus trichocarpa] gi|222873305|gb|EEF10436.1| predicted protein [Populus trichocarpa]

 Score =  596 bits (1537), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 282/307 (91%), Positives = 293/307 (95%), Gaps = 4/307 (1%)

Query: 29  YHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL 88
           YHPGLLA PQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVF+STGPVEGCKL
Sbjct: 31  YHPGLLA-PQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFASTGPVEGCKL 89

Query: 89  IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 148
           IRK+KSSYGFIHYFDRR+AA+AILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD
Sbjct: 90  IRKEKSSYGFIHYFDRRAAALAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 149

Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LSPEVTDATL+ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL
Sbjct: 150 LSPEVTDATLYACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 209

Query: 209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVG 268
           GSRQIRCNWA KGA +N+DKQSSD+KSVVELTNG+SED KE TN EAPENNPQYTTVYVG
Sbjct: 210 GSRQIRCNWAAKGASSNDDKQSSDSKSVVELTNGTSEDCKEATNNEAPENNPQYTTVYVG 269

Query: 269 NLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL 328
           NLAPEV Q DLHRHFH+LGAGVIEEVRVQRDKGFGFVR+STHAEAALAIQMGNT     L
Sbjct: 270 NLAPEVAQPDLHRHFHALGAGVIEEVRVQRDKGFGFVRFSTHAEAALAIQMGNTQS---L 326

Query: 329 FGKQMKV 335
           FGKQMK 
Sbjct: 327 FGKQMKC 333

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559021|ref|XP_003547800.1| PREDICTED: nucleolysin TIAR-like [Glycine max]

 Score =  595 bits (1533), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 295/335 (88%), Positives = 307/335 (91%), Gaps = 7/335 (2%)

Query: 1   MQHQRLKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVY 60
           MQ+ RLKQQQQ   Q  + Q     QSLYHPGLLA PQIEPIPSGNLPPGFDPSTCRSVY
Sbjct: 1   MQNHRLKQQQQALMQQALLQQ----QSLYHPGLLAPPQIEPIPSGNLPPGFDPSTCRSVY 56

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF 120
           VGNIHTQVTEPLLQEVF+ TGPVE CKLIRKDKSSYGFIHYFDRRSAA+AILSLNGRHLF
Sbjct: 57  VGNIHTQVTEPLLQEVFAGTGPVEACKLIRKDKSSYGFIHYFDRRSAALAILSLNGRHLF 116

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180
           GQPIKVNWAYASGQREDTSGH+NIFVGDLSPEVTDATLFACFSVYP+CSDARVMWDQKTG
Sbjct: 117 GQPIKVNWAYASGQREDTSGHYNIFVGDLSPEVTDATLFACFSVYPTCSDARVMWDQKTG 176

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELT 240
           RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAG  E+KQ+SDAKSVVELT
Sbjct: 177 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGGTEEKQNSDAKSVVELT 236

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK 300
            GSS DGKET+N++APENNPQYTTVYVGNLAPE TQLDLH HFHSLGAGVIEEVRVQRDK
Sbjct: 237 YGSS-DGKETSNSDAPENNPQYTTVYVGNLAPEATQLDLHHHFHSLGAGVIEEVRVQRDK 295

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           GFGFVRYSTHAEAALAIQMGN    S L GKQ+K 
Sbjct: 296 GFGFVRYSTHAEAALAIQMGNA--QSLLCGKQIKC 328

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447926|ref|XP_004141717.1| PREDICTED: nucleolysin TIAR-like [Cucumis sativus] gi|449480481|ref|XP_004155906.1| PREDICTED: nucleolysin TIAR-like [Cucumis sativus]

 Score =  593 bits (1530), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 277/307 (90%), Positives = 293/307 (95%), Gaps = 2/307 (0%)

Query: 29  YHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL 88
           YHPGLLA PQ+EPIPSGNLPPGFDPSTCRSVYVGN+HTQVTEPLLQEVF STG VE CKL
Sbjct: 26  YHPGLLAHPQLEPIPSGNLPPGFDPSTCRSVYVGNVHTQVTEPLLQEVFGSTGLVESCKL 85

Query: 89  IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 148
           +RK+KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD
Sbjct: 86  VRKEKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 145

Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LSPEVTD+TLFACFSV+ SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL
Sbjct: 146 LSPEVTDSTLFACFSVFSSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 205

Query: 209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVG 268
           GSRQIRCNWATKGAG+N+DKQSSD KS+ ELTNGSSEDGKET +++APENNPQYTTVYVG
Sbjct: 206 GSRQIRCNWATKGAGSNDDKQSSDVKSIAELTNGSSEDGKETVSSDAPENNPQYTTVYVG 265

Query: 269 NLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL 328
           NLAPE TQ+DLHRHFHSLGAGVIEEVR+QRDKGFGFVRYSTHAEAALAIQMGNT   S+L
Sbjct: 266 NLAPEATQVDLHRHFHSLGAGVIEEVRIQRDKGFGFVRYSTHAEAALAIQMGNT--QSFL 323

Query: 329 FGKQMKV 335
            GKQ+K 
Sbjct: 324 CGKQIKC 330

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073594|ref|XP_002304117.1| predicted protein [Populus trichocarpa] gi|222841549|gb|EEE79096.1| predicted protein [Populus trichocarpa]

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 279/308 (90%), Positives = 293/308 (95%), Gaps = 2/308 (0%)

Query: 27  SLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC 86
           S+YHPGLLA PQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVF+STGPVEGC
Sbjct: 23  SIYHPGLLAPPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFASTGPVEGC 82

Query: 87  KLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 146
           KLIRK+KSSYGFIHYFDRR+AA+AILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV
Sbjct: 83  KLIRKEKSSYGFIHYFDRRAAALAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFV 142

Query: 147 GDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 206
           GDLSPEVTDATL+ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK
Sbjct: 143 GDLSPEVTDATLYACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 202

Query: 207 WLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVY 266
           WLGSRQIRCNWA+KGAG+NEDKQSSD+KSVVELT G+SEDG E  N EAPENNPQYTTVY
Sbjct: 203 WLGSRQIRCNWASKGAGSNEDKQSSDSKSVVELTIGTSEDGMEAPNNEAPENNPQYTTVY 262

Query: 267 VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSS 326
           VGNL+PEVTQ  LHRHFH LGAGVIEEVRVQRDKGFGFVR+STHAEAA+AIQMGN    S
Sbjct: 263 VGNLSPEVTQPVLHRHFHVLGAGVIEEVRVQRDKGFGFVRFSTHAEAAVAIQMGNA--QS 320

Query: 327 YLFGKQMK 334
            L GKQ+K
Sbjct: 321 LLCGKQIK 328

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074564|gb|ACJ85642.1| unknown [Medicago truncatula] gi|388521359|gb|AFK48741.1| unknown [Medicago truncatula]

 Score =  587 bits (1513), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 277/313 (88%), Positives = 292/313 (93%), Gaps = 2/313 (0%)

Query: 22  LLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTG 81
           + QQQSLYHPGLLA PQIEPIPSGNLPPGFDPSTCRSVYVGN+HTQVTEPLLQEVF+ TG
Sbjct: 7   MKQQQSLYHPGLLAPPQIEPIPSGNLPPGFDPSTCRSVYVGNVHTQVTEPLLQEVFAGTG 66

Query: 82  PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
           PVEGCKL RK+KSSYGFIHYFDRRSAA+AIL+LNGRHLFGQPIKVNWAYASGQREDTSGH
Sbjct: 67  PVEGCKLFRKEKSSYGFIHYFDRRSAALAILTLNGRHLFGQPIKVNWAYASGQREDTSGH 126

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           +NIFVGDLSPEVTDATLFACFSVY SCSDARVMWDQKTGRSRGFGFVSFR+QQDAQSAIN
Sbjct: 127 YNIFVGDLSPEVTDATLFACFSVYQSCSDARVMWDQKTGRSRGFGFVSFRSQQDAQSAIN 186

Query: 202 DLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQ 261
           DLTGKWLGSRQIRCNWATK AG  E+KQ+SD+KSVVELTNGSSEDGKE +  + PENNPQ
Sbjct: 187 DLTGKWLGSRQIRCNWATKVAGGIEEKQNSDSKSVVELTNGSSEDGKEISGNDVPENNPQ 246

Query: 262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN 321
           YTTVYVGNL  E TQLDLHRHFH+LGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN
Sbjct: 247 YTTVYVGNLGSEATQLDLHRHFHALGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN 306

Query: 322 TTQSSYLFGKQMK 334
               SYL GK +K
Sbjct: 307 A--QSYLCGKIIK 317

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	335
TAIR|locus:2018794	419	UBP1B "oligouridylate binding	0.907	0.725	0.888	3.8e-149
TAIR|locus:2087457	427	AT3G14100 [Arabidopsis thalian	0.907	0.711	0.852	1.6e-143
TAIR|locus:2014340	430	UBP1A "oligouridylate-binding	0.907	0.706	0.793	5.2e-136
UNIPROTKB|G4N7J4	479	MGG_06400 "Nuclear and cytopla	0.770	0.538	0.454	6.3e-53
ASPGD|ASPL0000061196	477	AN10164 [Emericella nidulans (	0.770	0.540	0.445	8e-53
UNIPROTKB|F2Z4H8	380	TIAL1 "Uncharacterized protein	0.767	0.676	0.418	6.5e-51
UNIPROTKB|Q01085	375	TIAL1 "Nucleolysin TIAR" [Homo	0.767	0.685	0.418	6.5e-51
ZFIN|ZDB-GENE-040426-1547	389	tial1 "TIA1 cytotoxic granule-	0.635	0.547	0.423	7.7e-50
ZFIN|ZDB-GENE-030131-1506	386	tia1 "cytotoxic granule-associ	0.767	0.665	0.410	1.5e-49
UNIPROTKB|Q800W4	372	TIA1 "Uncharacterized protein"	0.752	0.677	0.411	1.5e-49

TAIR|locus:2018794 UBP1B "oligouridylate binding protein 1B" [Arabidopsis thaliana (taxid:3702)]

 Score = 1456 (517.6 bits), Expect = 3.8e-149, P = 3.8e-149
 Identities = 272/306 (88%), Positives = 288/306 (94%)

Query:    29 YHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL 88
             YHPGLLA PQIEPIPSGNLPPGFDPSTCRSVYVGNIH QVTEPLLQEVF+ TGPVE CKL
Sbjct:    26 YHPGLLAPPQIEPIPSGNLPPGFDPSTCRSVYVGNIHIQVTEPLLQEVFAGTGPVESCKL 85

Query:    89 IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 148
             IRK+KSSYGF+HYFDRRSA +AILSLNGRHLFGQPIKVNWAYASGQREDTS HFNIFVGD
Sbjct:    86 IRKEKSSYGFVHYFDRRSAGLAILSLNGRHLFGQPIKVNWAYASGQREDTSSHFNIFVGD 145

Query:   149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
             LSPEVTDA LF CFSVYP+CSDARVMWDQKTGRSRGFGFVSFRNQQDAQ+AI+++TGKWL
Sbjct:   146 LSPEVTDAMLFTCFSVYPTCSDARVMWDQKTGRSRGFGFVSFRNQQDAQTAIDEITGKWL 205

Query:   209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVG 268
             GSRQIRCNWATKGA + EDKQSSD+KSVVELT+G SEDGK+TTN EAPENN QYTTVYVG
Sbjct:   206 GSRQIRCNWATKGATSGEDKQSSDSKSVVELTSGVSEDGKDTTNGEAPENNAQYTTVYVG 265

Query:   269 NLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL 328
             NLAPEV+Q+DLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTH EAALAIQMGNT   SYL
Sbjct:   266 NLAPEVSQVDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHVEAALAIQMGNT--HSYL 323

Query:   329 FGKQMK 334
              G+QMK
Sbjct:   324 SGRQMK 329

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=ISS

GO:0005829 "cytosol" evidence=RCA

TAIR|locus:2087457 AT3G14100 [Arabidopsis thaliana (taxid:3702)]

 Score = 1403 (498.9 bits), Expect = 1.6e-143, P = 1.6e-143
 Identities = 261/306 (85%), Positives = 282/306 (92%)

Query:    29 YHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL 88
             YHPG+LA PQ+EP+PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQE+F+STGPVE  KL
Sbjct:    31 YHPGVLAPPQLEPVPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEIFTSTGPVESSKL 90

Query:    89 IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 148
             IRKDKSSYGF+HYFDRRSAA+AILSLNGRHLFGQPIKVNWAYA+GQREDTS HFNIFVGD
Sbjct:    91 IRKDKSSYGFVHYFDRRSAALAILSLNGRHLFGQPIKVNWAYATGQREDTSSHFNIFVGD 150

Query:   149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
             LSPEVTDATL+  FSV+ SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ+AIN++ GKWL
Sbjct:   151 LSPEVTDATLYQSFSVFSSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQTAINEMNGKWL 210

Query:   209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVG 268
              SRQIRCNWATKGA + +DK SSD KSVVELT GSSEDGKET N E PENN Q+TTVYVG
Sbjct:   211 SSRQIRCNWATKGATSGDDKLSSDGKSVVELTTGSSEDGKETLNEETPENNSQFTTVYVG 270

Query:   269 NLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL 328
             NLAPEVTQLDLHR+FH+LGAGVIEEVRVQRDKGFGFVRY+TH EAALAIQMGNT    YL
Sbjct:   271 NLAPEVTQLDLHRYFHALGAGVIEEVRVQRDKGFGFVRYNTHPEAALAIQMGNT--QPYL 328

Query:   329 FGKQMK 334
             F +Q+K
Sbjct:   329 FNRQIK 334

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=ISS

GO:0005829 "cytosol" evidence=RCA

GO:0006007 "glucose catabolic process" evidence=RCA

TAIR|locus:2014340 UBP1A "oligouridylate-binding protein 1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 1332 (473.9 bits), Expect = 5.2e-136, P = 5.2e-136
 Identities = 246/310 (79%), Positives = 278/310 (89%)

Query:    29 YHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL 88
             YHPG++A PQ+EP+PSGNLPPGFDP+TCRSVY GNIHTQVTE LLQE+F+STGP+E CKL
Sbjct:    35 YHPGVMAPPQMEPLPSGNLPPGFDPTTCRSVYAGNIHTQVTEILLQEIFASTGPIESCKL 94

Query:    89 IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGD 148
             IRKDKSSYGF+HYFDRR A+MAI++LNGRH+FGQP+KVNWAYA+GQREDTS HFNIFVGD
Sbjct:    95 IRKDKSSYGFVHYFDRRCASMAIMTLNGRHIFGQPMKVNWAYATGQREDTSSHFNIFVGD 154

Query:   149 LSPEVTDATLFACFSVYPSCS----DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT 204
             LSPEVTDA LF  FS + SCS    DARVMWDQKTGRSRGFGFVSFRNQQDAQ+AIN++ 
Sbjct:   155 LSPEVTDAALFDSFSAFNSCSSYYRDARVMWDQKTGRSRGFGFVSFRNQQDAQTAINEMN 214

Query:   205 GKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTT 264
             GKW+ SRQIRCNWATKGA   EDK SSD KSVVELTNGSSEDG+E +N +APENNPQ+TT
Sbjct:   215 GKWVSSRQIRCNWATKGATFGEDKHSSDGKSVVELTNGSSEDGRELSNEDAPENNPQFTT 274

Query:   265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQ 324
             VYVGNL+PEVTQLDLHR F++LGAGVIEEVRVQRDKGFGFVRY+TH EAALAIQMGN   
Sbjct:   275 VYVGNLSPEVTQLDLHRLFYTLGAGVIEEVRVQRDKGFGFVRYNTHDEAALAIQMGNA-- 332

Query:   325 SSYLFGKQMK 334
               +LF +Q++
Sbjct:   333 QPFLFSRQIR 342

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0006007 "glucose catabolic process" evidence=RCA

UNIPROTKB|G4N7J4 MGG_06400 "Nuclear and cytoplasmic polyadenylated RNA-binding protein pub1" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 548 (198.0 bits), Expect = 6.3e-53, P = 6.3e-53
 Identities = 124/273 (45%), Positives = 168/273 (61%)

Query:    57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
             R++YVG +  +VTE +L+++F +TG V+  K+I  DK++    YGF+ Y D  +A  A+ 
Sbjct:    85 RALYVGGLDARVTEDVLRQIFETTGHVQNVKII-PDKNAKGYNYGFVEYDDPGAADRAMQ 143

Query:   113 SLNGRHLFGQPIKVNWAY---ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCS 169
             +LNGR +    I+VNWAY    S  +EDTS HF+IFVGDLS EV D  L   FSV+ S S
Sbjct:   144 TLNGRRVHQSEIRVNWAYQAATSATKEDTSNHFHIFVGDLSNEVNDEVLTQAFSVFGSVS 203

Query:   170 DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT-KGAGNNEDK 228
             +ARVMWD KTGRSRG+GFV+FR++ DA+ A++ + G+WLGSR IRCNWA  KG  +   +
Sbjct:   204 EARVMWDMKTGRSRGYGFVAFRDRSDAEKALSSMDGEWLGSRAIRCNWANQKGQPSIAQQ 263

Query:   229 QSSDAKSVVELTN-GSSEDGKETTNT-EAPENN-PQY-TTVYVGNLAPEVTQLDLHRHFH 284
             Q+  A  +   T  G          + E   N  P Y TT YVGNL P  T  D+   F 
Sbjct:   264 QAMSAVGMTPTTPFGHHHFPTHGMQSYEMVVNQTPAYQTTCYVGNLTPYTTANDVVPLFQ 323

Query:   285 SLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAI 317
             + G  V+E  R Q D+GF F++  +H  AA AI
Sbjct:   324 NFGY-VVES-RFQADRGFAFIKMDSHENAAQAI 354

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ASPGD|ASPL0000061196 AN10164 [Emericella nidulans (taxid:162425)]

 Score = 547 (197.6 bits), Expect = 8.0e-53, P = 8.0e-53
 Identities = 122/274 (44%), Positives = 166/274 (60%)

Query:    57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS------SYGFIHYFDRRSAAMA 110
             R++YVG +  +VTE +L+++F +TG V   K+I  DK+      +YGF+ + D  +A  A
Sbjct:    90 RALYVGGLDPRVTEDILKQIFETTGHVISVKII-PDKNFNSKGANYGFVEFDDPGAAERA 148

Query:   111 ILSLNGRHLFGQPIKVNWAYASG--QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
             + +LNGR +    I+VNWAY S    +EDTS HF+IFVGDLS EV D  L   FS + S 
Sbjct:   149 MQTLNGRRIHQSEIRVNWAYQSNTANKEDTSNHFHIFVGDLSNEVNDEVLLQAFSAFGSV 208

Query:   169 SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT-KGAGNNED 227
             S+ARVMWD KTGRSRG+GFV+FR + DA+ A+  + G+WLGSR IRCNWA  KG  +   
Sbjct:   209 SEARVMWDMKTGRSRGYGFVAFRERADAEKALTSMDGEWLGSRAIRCNWANQKGQPSISQ 268

Query:   228 KQSSDAKSVVELTN-GSSE---DGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHF 283
             +Q+  A  +   T  G       G ++ +    +     TT YVGNL P  TQ D+   F
Sbjct:   269 QQAMAAMGMTPTTPFGHHHFPTHGIQSYDMVVQQTPAWQTTCYVGNLTPYTTQNDIVPLF 328

Query:   284 HSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAI 317
              + G  VIE  R+Q D+GF F++  TH  AA AI
Sbjct:   329 QNFGY-VIE-TRMQADRGFAFIKMDTHENAASAI 360

GO:0034063 "stress granule assembly" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0043488 "regulation of mRNA stability" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

UNIPROTKB|F2Z4H8 TIAL1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 529 (191.3 bits), Expect = 6.5e-51, P = 6.5e-51
 Identities = 115/275 (41%), Positives = 168/275 (61%)

Query:    52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAM 109
             D    R++YVGN+   VTE L+ ++FS  GP + CK+I +  S+  Y F+ +++ R AA 
Sbjct:     4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query:   110 AILSLNGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
             A+ ++NGR + G+ +KVNWA   S Q++DTS HF++FVGDLSPE+T   + + F+ +   
Sbjct:    64 ALAAMNGRKILGKEVKVNWATTPSSQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKI 123

Query:   169 SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDK 228
             SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+     +  
Sbjct:   124 SDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPKST 183

Query:   229 QSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA 288
             Q ++ K +        ED     N  +P+N     TVY G +A  +T   + + F   G 
Sbjct:   184 QENNTKQL------RFED---VVNQSSPKN----CTVYCGGIASGLTDQLMRQTFSPFGQ 230

Query:   289 GVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
               I E+RV  +KG+ FVR+STH  AA AI   N T
Sbjct:   231 --IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 263

GO:0017145 "stem cell division" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0007281 "germ cell development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q01085 TIAL1 "Nucleolysin TIAR" [Homo sapiens (taxid:9606)]

 Score = 529 (191.3 bits), Expect = 6.5e-51, P = 6.5e-51
 Identities = 115/275 (41%), Positives = 168/275 (61%)

Query:    52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAM 109
             D    R++YVGN+   VTE L+ ++FS  GP + CK+I +  S+  Y F+ +++ R AA 
Sbjct:     4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query:   110 AILSLNGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
             A+ ++NGR + G+ +KVNWA   S Q++DTS HF++FVGDLSPE+T   + + F+ +   
Sbjct:    64 ALAAMNGRKILGKEVKVNWATTPSSQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKI 123

Query:   169 SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDK 228
             SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+     +  
Sbjct:   124 SDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPKST 183

Query:   229 QSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA 288
             Q ++ K +        ED     N  +P+N     TVY G +A  +T   + + F   G 
Sbjct:   184 QENNTKQL------RFED---VVNQSSPKN----CTVYCGGIASGLTDQLMRQTFSPFGQ 230

Query:   289 GVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
               I E+RV  +KG+ FVR+STH  AA AI   N T
Sbjct:   231 --IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 263

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0007281 "germ cell development" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0017145 "stem cell division" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:0003723 "RNA binding" evidence=TAS

GO:0006952 "defense response" evidence=TAS

GO:0005764 "lysosome" evidence=TAS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0006917 "induction of apoptosis" evidence=TAS

ZFIN|ZDB-GENE-040426-1547 tial1 "TIA1 cytotoxic granule-associated RNA binding protein-like 1" [Danio rerio (taxid:7955)]

 Score = 443 (161.0 bits), Expect = 7.7e-50, Sum P(2) = 7.7e-50
 Identities = 97/229 (42%), Positives = 140/229 (61%)

Query:    96 YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVT 154
             Y F+ +F+ R AA A+ ++NGR + G+ +KVNWA   S Q++DTS HF++FVGDLSPE+T
Sbjct:    68 YCFVEFFEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKKDTSNHFHVFVGDLSPEIT 127

Query:   155 DATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR 214
                + A F+ +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR
Sbjct:   128 TDDIRAAFAPFGKISDARVVKDMTTGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIR 187

Query:   215 CNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEV 274
              NWAT+     +  Q + AK +         D  E  N  +P+N     TVY G +   +
Sbjct:   188 TNWATRKPPAPKSVQDNSAKQL-------RFD--EVVNQSSPQN----CTVYCGGIQSGL 234

Query:   275 TQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
             T+  + + F   G   I E+RV  +KG+ F+R+S+H  AA AI   N T
Sbjct:   235 TEHLMRQTFSPFGQ--IMEIRVFPEKGYSFIRFSSHESAAHAIVSVNGT 281

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-030131-1506 tia1 "cytotoxic granule-associated RNA binding protein 1" [Danio rerio (taxid:7955)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 113/275 (41%), Positives = 163/275 (59%)

Query:    52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSSYGFIHYFDRRSAAM 109
             D    +++YVGN+   VTE L+ ++F   GP + CK+I        Y F+ +F+ R AA 
Sbjct:     3 DDEQPKTLYVGNLSRDVTEALIMQLFGQIGPCKSCKMIVDTAGNDPYCFVEFFEHRHAAA 62

Query:   110 AILSLNGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
             ++ ++NGR + G+ +KVNWA + S Q++DTS HF++FVGDLSPE+T   + A F+ +   
Sbjct:    63 SLAAMNGRKIMGKEVKVNWATSPSSQKKDTSNHFHVFVGDLSPEITTDDIRAAFAPFGRI 122

Query:   169 SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDK 228
             SDARV+ D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+        
Sbjct:   123 SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR-------- 174

Query:   229 QSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA 288
             +    K+  E TN       E  N  +P N     TVY G +   +T+  + + F   G 
Sbjct:   175 KPPAPKATYE-TNTKHLSFDEVVNQSSPSN----CTVYCGGVTTGLTEQLMRQTFSPFGQ 229

Query:   289 GVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
               I EVRV  DKG+ FVR+++H  AA AI   N T
Sbjct:   230 --IMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGT 262

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q800W4 TIA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 111/270 (41%), Positives = 164/270 (60%)

Query:    57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
             +++YVGN+   VTE L+ ++FS  GP + CK+I     +  Y F+ +++ R AA A+ ++
Sbjct:     7 KTLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAGNDPYCFVEFYEHRHAASALAAM 66

Query:   115 NGRHLFGQPIKVNWAYA-SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV 173
             NGR + G+ +KVNWA   S Q++DTS HF++FVGDLSPE+T   + A F+ +   SDARV
Sbjct:    67 NGRKIMGKEVKVNWATTPSSQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARV 126

Query:   174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDA 233
             + D  TG+S+G+GFVSF N+ DA++AI  + G+WLG RQIR NWAT+     +    S+ 
Sbjct:   127 VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 186

Query:   234 KSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE 293
             K +       S D  +  N  +P N     TVY G +   +T+  + + F   G   I E
Sbjct:   187 KQL-------SYD--DVVNQSSPSN----CTVYCGGVTSGLTEQLMRQTFSPFGQ--IME 231

Query:   294 VRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
             +RV  DKG+ FVR+++H  AA AI   N T
Sbjct:   232 IRVFPDKGYSFVRFNSHESAAHAIVSVNGT 261

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0042036 "negative regulation of cytokine biosynthetic process" evidence=IEA

GO:0048024 "regulation of mRNA splicing, via spliceosome" 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: GSVIVG00034047001 SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (420 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	335
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-50
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	9e-37
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-32
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-32
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-28
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	8e-28
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-27
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	9e-26
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-25
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	8e-24
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-23
smart00360	73	smart00360, RRM, RNA recognition motif	3e-22
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	6e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	7e-19
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-18
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-18
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	9e-18
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-18
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-17
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-17
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-17
smart00360	73	smart00360, RRM, RNA recognition motif	2e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-16
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-16
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-16
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-15
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-15
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-15
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-15
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-15
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-15
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-15
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	9e-15
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-14
smart00360	73	smart00360, RRM, RNA recognition motif	2e-14
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-14
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-14
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-14
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-14
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-13
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-13
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-13
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-13
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-13
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-13
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-13
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-13
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	9e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-12
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-12
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	9e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-11
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-11
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-11
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-11
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	7e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-10
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-10
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-10
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-10
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-10
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-10
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	6e-10
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-10
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	8e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-09
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-09
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-09
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-09
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-09
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	3e-09
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-09
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-09
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	4e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	5e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	5e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-09
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	8e-09
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	9e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-08
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	4e-08
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-08
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-08
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	4e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-08
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	5e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	6e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-08
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	6e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-08
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	7e-08
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	8e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	9e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	1e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-07
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-07
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-07
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-07
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-07
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-07
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	5e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-07
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-07
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	7e-07
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	7e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	8e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	8e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	9e-07
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	9e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	9e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-06
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	1e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	1e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-06
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-06
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-06
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	2e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-06
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	2e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-06
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-06
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	3e-06
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	3e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-06
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	4e-06
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	4e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	4e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	4e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	5e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	5e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	6e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	6e-06
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	6e-06
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	7e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	7e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-06
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	7e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	8e-06
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	8e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	9e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	9e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	1e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	1e-05
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	1e-05
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	1e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	1e-05
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	1e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	1e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	2e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-05
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	3e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	4e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	5e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	5e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	6e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	7e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	7e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	7e-05
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	7e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	8e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	8e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	8e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	8e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	9e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	9e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	9e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	9e-05
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	9e-05
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	9e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	1e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	1e-04
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	1e-04
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-04
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	1e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-04
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	2e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	2e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-04
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	3e-04
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	3e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	3e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-04
cd12624	91	cd12624, RRM_PRC, RNA recognition motif in peroxis	4e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	4e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	4e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	5e-04
cd12623	91	cd12623, RRM_PPARGC1A, RNA recognition motif in pe	5e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	5e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	5e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	6e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	6e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	6e-04
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	6e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	6e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	6e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	7e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	7e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	7e-04
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	7e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-04
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	8e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	8e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	9e-04
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	9e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	9e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	9e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.001
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.001
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.001
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.001
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.001
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.001
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	0.001
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.001
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.001
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.001
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.001
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.001
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.001
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.001
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.001
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.001
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.001
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.001
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.001
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.001
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12627	77	cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in	0.001
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.001
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.001
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.001
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.001
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	0.001
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.001
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	0.001
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.001
cd12520	74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	0.001
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	0.002
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.002
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.002
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.002
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	0.002
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.002
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.002
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.002
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	0.002
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.002
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.002
cd12538	104	cd12538, RRM_U2AF35, RNA recognition motif in U2 s	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	0.002
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.003
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.003
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.003
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.003
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.003
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.003
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.003
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	0.003
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	0.003
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.003
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.003
cd12752	87	cd12752, RRM1_RBM5, RNA recognition motif 1 in ver	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.003
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.003
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	0.004
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.004
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.004
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.004
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	0.004
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.004
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.004
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.004
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.004
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.004
cd12623	91	cd12623, RRM_PPARGC1A, RNA recognition motif in pe	0.004
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.004
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.004
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.004
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.004
cd12677	156	cd12677, RRM4_Nop4p, RNA recognition motif 4 in ye	0.004

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score =  161 bits (409), Expect = 3e-50
 Identities = 62/75 (82%), Positives = 70/75 (93%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           NIFVGDLSPEVTDATLFA FS +PSCSDARVMWD K+GRSRG+GFVSFR+QQDA++AIN+
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 203 LTGKWLGSRQIRCNW 217
           + GKWLGSR IRCNW
Sbjct: 61  MNGKWLGSRPIRCNW 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score =  126 bits (319), Expect = 9e-37
 Identities = 39/72 (54%), Positives = 51/72 (70%), Gaps = 1/72 (1%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-SSYGFIHYFDRRSAAMAILSLNGR 117
           +YVGN+   VTE LL E+FS  GP++ CKLIR+     Y F+ Y+D RSAA A+ ++NGR
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 118 HLFGQPIKVNWA 129
            + GQ IKVNWA
Sbjct: 61  LILGQEIKVNWA 72

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

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

 Score =  115 bits (291), Expect = 1e-32
 Identities = 41/75 (54%), Positives = 56/75 (74%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +IFVGDLSPE+   TL A F+ +   SDARV+ D +TG+S+G+GFVSF  ++DA++AI  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 203 LTGKWLGSRQIRCNW 217
           + G+WLG R IR NW
Sbjct: 61  MNGQWLGGRAIRTNW 75

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

 Score =  124 bits (314), Expect = 6e-32
 Identities = 77/281 (27%), Positives = 126/281 (44%), Gaps = 49/281 (17%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEG---CKLIRKDKS-SYGFIHYFDRRSAAMAILS 113
           S+YVG++   VTE  L ++F   GPV     C+     +S  YG++++ +   A  A+ +
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 114 LNGRHLFGQPIKVNWAYASGQREDT---SGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
           +N + L G+PI++ W+    QR+ +   SG  NIFV +L   V +  LF  FS + +   
Sbjct: 62  MNFKRLGGKPIRIMWS----QRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILS 117

Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
            +V  D+  G+SRG+GFV F  ++ A++AI  + G  L  +++                 
Sbjct: 118 CKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY---------------- 160

Query: 231 SDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGV 290
                 V       E               ++T +YV NL P V +  L   F     G 
Sbjct: 161 ------VGRFIKKHE--------REAAPLKKFTNLYVKNLDPSVNEDKLRELFAKF--GE 204

Query: 291 IEEVRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSS 326
           I    V +D     +GF FV +  H +AA A++  N  +  
Sbjct: 205 ITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG 245

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|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 =  103 bits (259), Expect = 5e-28
 Identities = 35/73 (47%), Positives = 44/73 (60%), Gaps = 5/73 (6%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           TTVYVGNL   +T+ +L R F     G IEEVRV +DKG+ FVR+ TH  AA AI   N 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSP--FGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNG 58

Query: 323 TQSSYLFGKQMKV 335
           T    + G+ +K 
Sbjct: 59  TS---INGQTVKC 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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score =  103 bits (258), Expect = 8e-28
 Identities = 45/80 (56%), Positives = 61/80 (76%)

Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           HF++FVGDLSPE+T   + A F+ +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI
Sbjct: 1   HFHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

Query: 201 NDLTGKWLGSRQIRCNWATK 220
             + G+WLG RQIR NWAT+
Sbjct: 61  QQMGGQWLGGRQIRTNWATR 80

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score =  101 bits (253), Expect = 4e-27
 Identities = 44/80 (55%), Positives = 61/80 (76%)

Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           HF++FVGDLSPE+T   + + F+ +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI
Sbjct: 1   HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60

Query: 201 NDLTGKWLGSRQIRCNWATK 220
             + G+WLG RQIR NWAT+
Sbjct: 61  VHMGGQWLGGRQIRTNWATR 80

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

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

 Score = 98.1 bits (245), Expect = 9e-26
 Identities = 34/79 (43%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 142 FNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
            +IFVGDL+P+VTD  L   F + YPS   A+V+ D  TGRS+G+GFV F ++ +   A+
Sbjct: 2   HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61

Query: 201 NDLTGKWLGSRQIRCNWAT 219
            ++ G +  SR +R + AT
Sbjct: 62  TEMNGVYCSSRPMRVSPAT 80

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

 Score =  105 bits (264), Expect = 3e-25
 Identities = 82/281 (29%), Positives = 118/281 (41%), Gaps = 30/281 (10%)

Query: 52  DPSTCRS----VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KS-SYGFIHYFDR 104
           DPS  RS    ++V N+   V    L + FS  G +  CK+   +  KS  YGF+H+   
Sbjct: 80  DPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKE 139

Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQREDT--SGHFNIFVGDLSPEVTDATLFACF 162
            SA  AI  +NG  L  + + V       +RE        N++V +L P V +  L   F
Sbjct: 140 ESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELF 199

Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
           + +   + A VM D   GRSRGF FV+F   +DA  A+ ++ GK +G            A
Sbjct: 200 AKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKKIG-----------LA 247

Query: 223 GNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRH 282
              +      A+   E         +E    +  +   Q   +YV NL   VT   L   
Sbjct: 248 KEGKKLYVGRAQKRAEREAELRRKFEEL--QQERKMKAQGVNLYVKNLDDTVTDEKLREL 305

Query: 283 FHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
           F   G   I   +V  D     +GFGFV +S   EA  A+ 
Sbjct: 306 FSECGE--ITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344

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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 92.7 bits (231), Expect = 8e-24
 Identities = 36/74 (48%), Positives = 51/74 (68%)

Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
            F IFVGDL  EVTD  L   FS YPS   A+V+ D++TG+S+G+GFVSF +  D   A+
Sbjct: 6   DFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAM 65

Query: 201 NDLTGKWLGSRQIR 214
            ++ GK++G+R I+
Sbjct: 66  KEMNGKYVGNRPIK 79

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 92.6 bits (230), Expect = 1e-23
 Identities = 37/79 (46%), Positives = 54/79 (68%), Gaps = 1/79 (1%)

Query: 142 FNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           ++IFVGDLSPEV ++ L + F S +PSC  A++M D  TG SRG+GFV F ++ D Q A+
Sbjct: 2   YSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRAL 61

Query: 201 NDLTGKWLGSRQIRCNWAT 219
            ++ G + G R +R + AT
Sbjct: 62  IEMQGVYCGGRPMRISTAT 80

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|214636 smart00360, RRM, RNA recognition motif

 Score = 88.4 bits (220), Expect = 3e-22
 Identities = 27/73 (36%), Positives = 45/73 (61%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FVG+L P+ T+  L   FS +      R++ D++TG+S+GF FV F +++DA+ A+  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 203 LTGKWLGSRQIRC 215
           L GK L  R ++ 
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 85.1 bits (211), Expect = 6e-21
 Identities = 35/80 (43%), Positives = 52/80 (65%), Gaps = 3/80 (3%)

Query: 142 FNIFVGDLSPEVTDATLFACFS-VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           F++FVGDL+P+V D  L+  FS  YPSC  A+V+ DQ  G SRG+GFV F ++ + + A+
Sbjct: 2   FSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRAL 60

Query: 201 NDLTG-KWLGSRQIRCNWAT 219
            ++ G   LG + IR + A 
Sbjct: 61  TEMQGASGLGGKPIRVSLAI 80

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 79.2 bits (196), Expect = 7e-19
 Identities = 30/71 (42%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L P+ T+  L   FS +      R++ D+ TGRS+GF FV F +++DA+ A+  L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 204 TGKWLGSRQIR 214
            GK LG R++R
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 86.0 bits (213), Expect = 1e-18
 Identities = 53/185 (28%), Positives = 87/185 (47%), Gaps = 25/185 (13%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           +YV N+   V E  L+E+F+  G +     + KD S     + F+++     AA A+  +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAA-VMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 115 NGRHL----FGQPIKVNWAYASGQRE---------------DTSGHFNIFVGDLSPEVTD 155
           NG+ +     G+ + V  A    +RE                 +   N++V +L   VTD
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 156 ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC 215
             L   FS     + A+VM D+K G SRGFGFV F N ++A  A+ ++ G+ LG + +  
Sbjct: 300 EKLRELFSECGEITSAKVMLDEK-GVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

Query: 216 NWATK 220
             A +
Sbjct: 359 ALAQR 363

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

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

 Score = 83.8 bits (206), Expect = 2e-18
 Identities = 55/252 (21%), Positives = 95/252 (37%), Gaps = 15/252 (5%)

Query: 74  QEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
            EV S     E     +K   S       +R               F + +  +      
Sbjct: 48  LEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKS 107

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +++    +  +FVG+L  +VT+  L   F  +      R++ D++TG+SRGF FV F ++
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESE 167

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNT 253
           + A+ AI +L GK L  R +R   A   +    +  ++   S             +  + 
Sbjct: 168 ESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASF-----------AKKLSR 216

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYST 309
                  +   +YVGNL  +  + +L   F S G  V   +   +D    K   FV    
Sbjct: 217 GKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEA 276

Query: 310 HAEAALAIQMGN 321
             +A  +   GN
Sbjct: 277 SKDALESNSRGN 288

Length = 306

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

 Score = 76.5 bits (189), Expect = 9e-18
 Identities = 31/76 (40%), Positives = 44/76 (57%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++VG+L   VT+  L   F  +   + ARV+ D++TGRSRGFGFV     ++A +AI  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 203 LTGKWLGSRQIRCNWA 218
           L G   G R +  N A
Sbjct: 61  LNGTDFGGRTLTVNEA 76

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

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

 Score = 82.7 bits (204), Expect = 9e-18
 Identities = 49/143 (34%), Positives = 77/143 (53%), Gaps = 9/143 (6%)

Query: 68  VTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQ 122
           +T+  ++ +F+S G +E CKL+R DK +     YGF++Y     A  A+ SLNG  L  +
Sbjct: 15  MTQEEIRSLFTSIGEIESCKLVR-DKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNK 73

Query: 123 PIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRS 182
            IKV++A  S    D+    N++V  L   +T   L + FS +     +R++ D  TG S
Sbjct: 74  TIKVSYARPS---SDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLS 130

Query: 183 RGFGFVSFRNQQDAQSAINDLTG 205
           +G GF+ F  + +A  AI  L G
Sbjct: 131 KGVGFIRFDKRDEADRAIKTLNG 153

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

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

 Score = 75.7 bits (187), Expect = 1e-17
 Identities = 33/78 (42%), Positives = 45/78 (57%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FV  LS   T+  L A FS +    +  +M D +TG SRGFGFV+F + +DA +AI D
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 203 LTGKWLGSRQIRCNWATK 220
           L GK L  R I+   A +
Sbjct: 63  LNGKELEGRVIKVEKAKR 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 75.9 bits (187), Expect = 1e-17
 Identities = 33/76 (43%), Positives = 48/76 (63%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FVG+LS  V D  L A F  + +   ARV+ D++TGRSRGFG+V F + +DA+ AI  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 203 LTGKWLGSRQIRCNWA 218
           + GK L  R I  +++
Sbjct: 61  MDGKELDGRPINVDFS 76

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

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 75.5 bits (185), Expect = 2e-17
 Identities = 30/74 (40%), Positives = 49/74 (66%), Gaps = 2/74 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSLN 115
           ++YVGN+   VTE L+ ++FS  GP + CK+I     +  Y F+ +F+ R AA ++ ++N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 116 GRHLFGQPIKVNWA 129
           GR + G+ +KVNWA
Sbjct: 61  GRKIMGKEVKVNWA 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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 73.7 bits (181), Expect = 8e-17
 Identities = 31/75 (41%), Positives = 48/75 (64%), Gaps = 5/75 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           +YVGN+  +VTE +L+++F   GPV+  K+I  DK+    +YGF+ Y     A +A+ +L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKII-PDKNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 115 NGRHLFGQPIKVNWA 129
           NGR +    I+VNWA
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|214636 smart00360, RRM, RNA recognition motif

 Score = 72.2 bits (178), Expect = 2e-16
 Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           +++VGN+    TE  L+E+FS  G VE  +L+R  ++     + F+ +     A  A+ +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 114 LNGRHLFGQPIKV 126
           LNG+ L G+P+KV
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 72.3 bits (178), Expect = 2e-16
 Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L P+ T+  L   FS +      R++ D K G+S+GF FV F + +DA+ A+  L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 204 TGKWLGSRQIRCN 216
            GK L  R+++ +
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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 72.8 bits (178), Expect = 2e-16
 Identities = 31/74 (41%), Positives = 51/74 (68%), Gaps = 2/74 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSLN 115
           ++YVGN+   VTE L+ ++FS  GP + CK+I +  S+  Y F+ +++ R AA A+ ++N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 116 GRHLFGQPIKVNWA 129
           GR + G+ +KVNWA
Sbjct: 61  GRKILGKEVKVNWA 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 78.4 bits (193), Expect = 4e-16
 Identities = 51/178 (28%), Positives = 86/178 (48%), Gaps = 16/178 (8%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
           R+V+V  +  +  E  L E FS  G V   + I KD++S       ++ ++D  S   A+
Sbjct: 90  RTVFVLQLALKARERDLYEFFSKVGKVRDVQCI-KDRNSRRSKGVAYVEFYDVESVIKAL 148

Query: 112 LSLNGRHLFGQPIKVNWAYASGQRE-----DTSGH----FNIFVGDLSPEVTDATLFACF 162
            +L G+ L G+PI V  + A   R         G       ++VG+L   +T+  L   F
Sbjct: 149 -ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIF 207

Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
             +    D ++  D +TGRS+GFGF+ F + ++A+ A+  + G  L  R I+  +A  
Sbjct: 208 EPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD 265

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|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 = 71.5 bits (176), Expect = 4e-16
 Identities = 24/75 (32%), Positives = 41/75 (54%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG++  + T+  L   FS        R++ D+ TG+ +G+GF  F + + A SAI +L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 204 TGKWLGSRQIRCNWA 218
            G     R +R ++A
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---YGFIHYFDRRSAAMAILSLN 115
           ++VGN+    TE  L+E+FS  G +E  +++R        + F+ +     A  A+ +LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 116 GRHLFGQPIKVN 127
           G+ L G+ +KV+
Sbjct: 61  GKELDGRKLKVS 72

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

>gnl|CDD|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 = 70.0 bits (172), Expect = 2e-15
 Identities = 25/71 (35%), Positives = 44/71 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+  L  E TD  L+  F+ + +   A+V  D+ TG+S+ FGFVS+ N + AQ+AI  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 204 TGKWLGSRQIR 214
            G  +G ++++
Sbjct: 61  NGFQVGGKRLK 71

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

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           + +YV N+    TE  L+E+FS  G VE  K I KD   Y F+H+ +R  A  A+  +NG
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKI-KD---YAFVHFEERDDAVKAMEEMNG 57

Query: 117 RHLFGQPIKVNWA 129
           + L G PI+V+ A
Sbjct: 58  KELEGSPIEVSLA 70

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

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

 Score = 71.2 bits (174), Expect = 3e-15
 Identities = 34/77 (44%), Positives = 50/77 (64%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS    DA+L   F+ +    DA+V+ D++TGRSRGFGFV+F ++  A +AI+++
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 204 TGKWLGSRQIRCNWATK 220
            GK L  R IR N A  
Sbjct: 97  DGKELNGRHIRVNPAND 113

Length = 144

>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 = 68.8 bits (169), Expect = 4e-15
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           V+VGNI    TE  L E+FS  GPV   +L+  D+ +     YGF  + D  +AA AI +
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLV-TDRDTGKPKGYGFCEFEDIETAASAIRN 59

Query: 114 LNGRHLFGQPIKVNWA 129
           LNG    G+ ++V++A
Sbjct: 60  LNGYEFNGRALRVDFA 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 68.4 bits (168), Expect = 7e-15
 Identities = 28/78 (35%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V +L  ++ D  L   F  Y   + A+VM D + G+S+GFGFV+F N + AQ A+ +
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEE 61

Query: 203 LTGKWLGSRQIRCNWATK 220
           L GK +  +++    A K
Sbjct: 62  LNGKEVNGKKLYVGRAQK 79

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|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 = 68.3 bits (167), Expect = 8e-15
 Identities = 33/77 (42%), Positives = 48/77 (62%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS +  + +L   FS Y   S+  V+ D++T RSRGFGFV+F N  DA+ A+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 204 TGKWLGSRQIRCNWATK 220
            GK +  RQIR + A K
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

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

 Score = 68.1 bits (167), Expect = 9e-15
 Identities = 29/74 (39%), Positives = 45/74 (60%), Gaps = 5/74 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAIL 112
           R+++VGN+  +VTE +L E+F   GP+EG K I KD +    S+ F+ +    S   AI 
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVK-IPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 113 SLNGRHLFGQPIKV 126
            LNG  LFG+ +++
Sbjct: 61  LLNGIRLFGRELRI 74

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

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

 Score = 67.9 bits (167), Expect = 1e-14
 Identities = 28/73 (38%), Positives = 41/73 (56%)

Query: 145 FVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT 204
           +VGDL P+VT+A L+  FS        RV  D  T RS G+ +V+F+N  DA+ A++ L 
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 205 GKWLGSRQIRCNW 217
              +  + IR  W
Sbjct: 63  FDVIKGKPIRIMW 75

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|214636 smart00360, RRM, RNA recognition motif

 Score = 66.8 bits (164), Expect = 2e-14
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 11/78 (14%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           T++VGNL P+ T+ +L   F   G   +E VR+ RD      KGF FV + +  +A  A+
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGK--VESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58

Query: 318 QMGNTTQSSYLFGKQMKV 335
           +  N  +   L G+ +KV
Sbjct: 59  EALNGKE---LDGRPLKV 73

Length = 73

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

 Score = 66.8 bits (164), Expect = 2e-14
 Identities = 23/59 (38%), Positives = 32/59 (54%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +F+G LS + T+ +L   FS Y    D  +M D  TGRSRGFGFV+F +       +  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

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|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 = 2e-14
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG L    TD +L   FS +    +A V+ D++TG+SRG+GFV+F++++ A+ A  D 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 204 TGKWLGSRQIRCNWA 218
               +  R+   N A
Sbjct: 63  N-PIIDGRKANVNLA 76

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

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

 Score = 66.6 bits (163), Expect = 3e-14
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 10/76 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQM 319
           ++VGNL P+ T+ DL   F     G IE VR+ RD     KGF FV + +  +A  A++ 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSK--FGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEA 58

Query: 320 GNTTQSSYLFGKQMKV 335
            N  +   L G+++KV
Sbjct: 59  LNGKE---LDGRKLKV 71

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

>gnl|CDD|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 = 3e-14
 Identities = 30/70 (42%), Positives = 42/70 (60%)

Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LS   T+  L   FS Y      +V++DQKTGRSRGFGFV F + +DA+ A   L G  +
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 209 GSRQIRCNWA 218
             R+IR +++
Sbjct: 67  DGRRIRVDYS 76

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

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

 Score = 71.6 bits (175), Expect = 9e-14
 Identities = 53/223 (23%), Positives = 87/223 (39%), Gaps = 46/223 (20%)

Query: 6   LKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIH 65
           LKQ +  QQQ   Q    Q+Q      L                      CR VYVG+I 
Sbjct: 80  LKQTKAHQQQ---QLENQQRQQQRQQALAI-------------------MCR-VYVGSIS 116

Query: 66  TQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG 121
            ++ E  ++  F   GP++   +           + F+ Y    +A +A+  +NG+ L G
Sbjct: 117 FELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG 176

Query: 122 QPIKVNWAYASGQ--------REDTSGHFNIFVGDLSPEVTD---ATLFACFSVYPSCSD 170
           + IKV       Q        +E+      I+V  + P++++    ++F  F     C  
Sbjct: 177 RNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQL 236

Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN-----DLTGKWL 208
           AR          +G+GF+ + N Q    AI      DL G++L
Sbjct: 237 AR---APTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYL 276

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 31/74 (41%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-----SSYGFIHYFDRRSAAMAILS 113
           VYVGN+  +VTE LL E+F   GPV     I KD+       YGF+ +     A  AI  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVH-IPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59

Query: 114 LNGRHLFGQPIKVN 127
           +N   L+G+PI+VN
Sbjct: 60  MNMIKLYGKPIRVN 73

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|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 = 64.6 bits (158), Expect = 2e-13
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +VYVGN+   +TE  LQ  FS  G +E  + + KDK  Y F+ +    +AA AI+++NG 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVR-VFKDKG-YAFVRFDTHEAAATAIVAVNGT 59

Query: 118 HLFGQPIKVNW 128
            + GQ +K +W
Sbjct: 60  SINGQTVKCSW 70

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

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

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 4/72 (5%)

Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSLN 115
           YVGN+H  +TE  L+ +F   G +E  +L R  ++     YGFI + D   A  A+  LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 116 GRHLFGQPIKVN 127
           G  L G+PIKV 
Sbjct: 62  GFELAGRPIKVG 73

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

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

 Score = 69.3 bits (169), Expect = 3e-13
 Identities = 42/141 (29%), Positives = 73/141 (51%), Gaps = 9/141 (6%)

Query: 68  VTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSLNGRHLFGQP 123
           +T+  L  +F + GP+  C+++R  K+ Y     F+ +     +  AI +LNG  +  + 
Sbjct: 119 MTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178

Query: 124 IKVNWAYASGQR-EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRS 182
           +KV++A   G+  +DT    N++V +L   +TD  L   F  Y       ++ D+ TG  
Sbjct: 179 LKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTP 234

Query: 183 RGFGFVSFRNQQDAQSAINDL 203
           RG  FV F  +++AQ AI+ L
Sbjct: 235 RGVAFVRFNKREEAQEAISAL 255

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

 Score = 68.4 bits (166), Expect = 5e-13
 Identities = 41/180 (22%), Positives = 73/180 (40%), Gaps = 25/180 (13%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
            +++VGN+   VTE  L+E+F   GPV+  +L+R  ++     + F+ +    SA  AI 
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 113 SLNGRHLFGQPIKVNWA---------------------YASGQREDTSGHFNIFVGDLSP 151
            LNG+ L G+P++V  A                      + G+        N++VG+L  
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPL 235

Query: 152 EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSR 211
           +  +  L   F        A +   +     +   FV     +DA  + +    K +  R
Sbjct: 236 KTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGR 295

Length = 306

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

 Score = 63.5 bits (155), Expect = 5e-13
 Identities = 25/70 (35%), Positives = 43/70 (61%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           + IFV +L P+  ++ L+  FS + + ++ +V+ D  T + +G+GFV+  N ++A SAI 
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 202 DLTGKWLGSR 211
            L G  LG R
Sbjct: 62  SLNGYRLGGR 71

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

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

 Score = 63.5 bits (155), Expect = 5e-13
 Identities = 27/79 (34%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPS-CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           N+F+G+L PEV +  L+  FS +       ++M D  TG S+GF F+S+ + + + +AI 
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 202 DLTGKWLGSRQIRCNWATK 220
            + G++L +R I  ++A K
Sbjct: 63  AMNGQYLCNRPITVSYAFK 81

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

 Score = 63.1 bits (154), Expect = 6e-13
 Identities = 25/80 (31%), Positives = 48/80 (60%), Gaps = 2/80 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++GDL P + +A +++ F+     +  +++ +++TG+S G+GFV F   + A+ A+  L
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 204 TGKWLGSRQI--RCNWATKG 221
            GK + + Q   R NWA  G
Sbjct: 62  NGKPIPNTQQRFRLNWANFG 81

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

 Score = 63.0 bits (154), Expect = 7e-13
 Identities = 25/69 (36%), Positives = 44/69 (63%), Gaps = 1/69 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V +L   + D  L   FS + + + A+VM D+K GRS+GFGFV F + ++A  A+ +
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTE 61

Query: 203 LTGKWLGSR 211
           + G+ +G +
Sbjct: 62  MNGRIIGGK 70

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

 Score = 62.4 bits (152), Expect = 9e-13
 Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN-- 201
           IFVG L P+VT+      FS +    DA++M D  TGRSRGFGFV+F ++   +   +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 202 --DLTGK 206
             +L GK
Sbjct: 62  MLELGGK 68

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

 Score = 62.0 bits (151), Expect = 1e-12
 Identities = 26/71 (36%), Positives = 43/71 (60%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+LS +  + +++  F  Y   S  R+  D  +GR +GFG+V F +Q+ AQ+A++ L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 204 TGKWLGSRQIR 214
            G  L  R +R
Sbjct: 61  GGTDLLGRPVR 71

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

 Score = 61.3 bits (149), Expect = 2e-12
 Identities = 29/55 (52%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAI 317
           TTVYVGN+ P  TQ DL   F + G   I E R Q D+GF FV+  TH +AA+AI
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFG--YILEFRHQPDRGFAFVKLDTHEQAAMAI 53

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 21/70 (30%), Positives = 41/70 (58%), Gaps = 3/70 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---YGFIHYFDRRSAAMAILSLN 115
           ++VGN+    TE  L+++FS  GP+E  +++R +      + F+ + D   A  A+ +LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 116 GRHLFGQPIK 125
           G+ L G+ ++
Sbjct: 61  GKELGGRELR 70

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

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

 Score = 60.7 bits (148), Expect = 4e-12
 Identities = 26/73 (35%), Positives = 40/73 (54%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV +  L A F  +    D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 204 TGKWLGSRQIRCN 216
               L  R IR N
Sbjct: 61  NESELFGRTIRVN 73

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

 Score = 60.2 bits (147), Expect = 6e-12
 Identities = 26/78 (33%), Positives = 46/78 (58%), Gaps = 6/78 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           S+YVG++H  VTE +L E+FS  GPV   ++ R D  +     Y ++++ +   A  A+ 
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCR-DLITRRSLGYAYVNFQNPADAERALD 59

Query: 113 SLNGRHLFGQPIKVNWAY 130
           +LN   + G+PI++ W+ 
Sbjct: 60  TLNFDVIKGKPIRIMWSQ 77

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

 Score = 59.9 bits (145), Expect = 9e-12
 Identities = 30/77 (38%), Positives = 42/77 (54%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV +L+  VT   L   FS       A V+ D +TG SRG+GFV+F   +DAQ A+  L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 204 TGKWLGSRQIRCNWATK 220
             K L  R +R + A +
Sbjct: 62  KNKKLHGRILRLDIAER 78

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

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

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 8/66 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           +V+VGNL  ++ + +L +HF     G +E VR+ RD      KGFG+V + T    ALA+
Sbjct: 1   SVFVGNLPFDIEEEELRKHF--EDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL 58

Query: 318 QMGNTT 323
           ++    
Sbjct: 59  KLNGIK 64

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 64.1 bits (156), Expect = 2e-11
 Identities = 54/198 (27%), Positives = 91/198 (45%), Gaps = 35/198 (17%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  L+ +  +  L+  FS      D + + D+ + RS+G  +V F + +    A+  L
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-L 150

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
           TG+ L  R I               QSS A+          ++      T  P + P + 
Sbjct: 151 TGQMLLGRPIIV-------------QSSQAE----------KNRAAKAATHQPGDIPNFL 187

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            +YVGNL   +T+ +L + F   G   IE+V++ RD      KGFGF+++    EA  A+
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGD--IEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245

Query: 318 QMGNTTQSSYLFGKQMKV 335
           ++ N  +   L G+ +KV
Sbjct: 246 EVMNGFE---LAGRPIKV 260

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

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

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +YV ++H  ++E  ++ VF + G ++ C L    ++     YGFI Y + +SA  AI S+
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 115 NGRHLFGQPIKVN 127
           N   L GQ ++V 
Sbjct: 63  NLFDLGGQQLRVG 75

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

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

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 25/79 (31%), Positives = 49/79 (62%), Gaps = 3/79 (3%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMW---DQKTGRSRGFGFVSFRNQQDAQSA 199
           N++VG+L+P+VT+  L   F  +   +  ++MW   +++  R+R  GFV+F N+ DA+ A
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 200 INDLTGKWLGSRQIRCNWA 218
           +++L GK +   +++  W 
Sbjct: 63  LDELDGKDVMGYELKLGWG 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 57.9 bits (141), Expect = 4e-11
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGF--IHYFDRRSAAMAIL 112
           +YVGN+    TE  + E+FS  G ++  ++I    R  K+  GF  + Y+ R  A  A+ 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 113 SLNGRHLFGQPIKVNW 128
            LNG  L  + I+V+W
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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 57.8 bits (140), Expect = 4e-11
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 4/67 (5%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN-- 201
           IFVG L P VT+  L   FS + + ++  VM+D +  R RGFGF++F ++      +N  
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 202 --DLTGK 206
             D+ GK
Sbjct: 65  FHDINGK 71

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

 Score = 57.4 bits (139), Expect = 7e-11
 Identities = 23/76 (30%), Positives = 44/76 (57%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L  ++T   L + F         +++ D+ TG+S G+GFV + ++ DAQ AIN 
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 203 LTGKWLGSRQIRCNWA 218
           L G  + +++++ ++A
Sbjct: 62  LNGFEIRNKRLKVSYA 77

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

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

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 10/75 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQM 319
           ++VGNL P+ T+ DL   F     G IE +R+ RD     KGF FV +    +A  A++ 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFS--KFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALE- 57

Query: 320 GNTTQSSYLFGKQMK 334
                   L G++++
Sbjct: 58  --ALNGKELGGRELR 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 51  FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAA 108
            D     S++VG +   VT+  L E FS  G +    LI++    +++ FI +   ++AA
Sbjct: 1   IDK---YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAA 57

Query: 109 MAILSLNGRHLFGQPIKV 126
            A+ S N   L  + + V
Sbjct: 58  RAVESENHSMLKNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 60.8 bits (147), Expect = 2e-10
 Identities = 53/199 (26%), Positives = 82/199 (41%), Gaps = 46/199 (23%)

Query: 132 SGQREDTSGH---FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
           SG  +D   +    N+ V  L  ++TD  L+A F      +  R+M D KTG S G+ FV
Sbjct: 95  SGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFV 154

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGK 248
            F ++ D+Q AI +L G  + +++++ ++A  G  + +D                     
Sbjct: 155 DFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKD--------------------- 193

Query: 249 ETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GF 302
                         T +YV NL   +T   L   F   G   I +  + RDK      G 
Sbjct: 194 --------------TNLYVTNLPRTITDDQLDTIFGKYGQ--IVQKNILRDKLTGTPRGV 237

Query: 303 GFVRYSTHAEAALAIQMGN 321
            FVR++   EA  AI   N
Sbjct: 238 AFVRFNKREEAQEAISALN 256

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

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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 24/77 (31%), Positives = 40/77 (51%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV +L  + TD  L   FS         V+ D+ + + RGFG+V+F  ++DA+ A+ + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 204 TGKWLGSRQIRCNWATK 220
                G R+I   +A K
Sbjct: 62  KKTKFGGRKIHVEFAKK 78

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

>gnl|CDD|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 = 56.0 bits (135), Expect = 2e-10
 Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 4/75 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           V+VGNI  + TE  L+++FS  GPV   +L+   ++     YGF  Y D+ +A  A+ +L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 115 NGRHLFGQPIKVNWA 129
           NG  L G+ ++V+ A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 26/59 (44%), Positives = 36/59 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +F+G LS E TD +L   FS +   +D  VM D  T RSRGFGFV+F +  +  +A+N 
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 55.6 bits (134), Expect = 3e-10
 Identities = 26/75 (34%), Positives = 46/75 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG++  E T+  L   FS        R+++D++TG+ +G+GF  +++Q+ A SA+ +L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 204 TGKWLGSRQIRCNWA 218
            G  L  RQ+R + 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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 30/75 (40%), Positives = 44/75 (58%), Gaps = 5/75 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAIL 112
           R+++VGN+  +V E +L E+F   GP+     I KDK     S+GF+ +    S   AI 
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVT-ICKDKEGKPKSFGFVCFKHSESVPYAIA 60

Query: 113 SLNGRHLFGQPIKVN 127
            LNG  L+G+PIKV+
Sbjct: 61  LLNGIRLYGRPIKVH 75

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

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           I V +L   VT+  L   F      +D +VM   + G+SR FGFV F++++DAQ A+   
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVM-RTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 204 TGKWLGSRQIRCNWA 218
              ++ + +I    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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)

Query: 56  CRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL 114
            R V+VGN++T +V++  L+E+FS  G + G  L +     YGF+ + +   A  A+   
Sbjct: 1   SR-VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK----GYGFVQFDNEEDARAAVAGE 55

Query: 115 NGRHLFGQPIKVN 127
           NGR + GQ + +N
Sbjct: 56  NGREIAGQKLDIN 68

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

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 6/74 (8%)

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLN 115
           V  +   +T+  L+ +F + GP+E CK++R D+ +     YGF+ Y D   A  AI +LN
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVR-DRITGQSLGYGFVDYVDENDAQKAINTLN 63

Query: 116 GRHLFGQPIKVNWA 129
           G  +  + +KV++A
Sbjct: 64  GFEIRNKRLKVSYA 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.9 bits (133), Expect = 4e-10
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++V +L P VT+  L   FS Y      R++ ++   R RGF FV F + +DA++A+  L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 204 TGKWLGSRQIR 214
            G  L  R +R
Sbjct: 59  NGLVLDGRTLR 69

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

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

 Score = 55.1 bits (133), Expect = 4e-10
 Identities = 29/66 (43%), Positives = 41/66 (62%), Gaps = 6/66 (9%)

Query: 69  TEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQP 123
           T+  ++ +FSS G +E CKLIR DK +     YGF++Y D   A  AI +LNG  L  + 
Sbjct: 14  TQDEIRSLFSSIGEIESCKLIR-DKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72

Query: 124 IKVNWA 129
           IKV++A
Sbjct: 73  IKVSYA 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 54.4 bits (132), Expect = 4e-10
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 73  LQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           L ++FS  G VE  K + K K  + F+ +    +A  A+  LNG    G+P++V+++
Sbjct: 1   LYKLFSPFGNVEKIK-LLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 55.1 bits (133), Expect = 4e-10
 Identities = 25/79 (31%), Positives = 44/79 (55%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ +  L   +TD    + F       + +++ D++TG S GFGFV +++ +DAQ AI  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 203 LTGKWLGSRQIRCNWATKG 221
           L G  L +++I+  +A  G
Sbjct: 62  LNGLQLQNKRIKVAYARPG 80

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|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 = 54.9 bits (133), Expect = 5e-10
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
             ++V  L+   T+ +L   F   G   +EEV + +D       GFGFV + +  +A  A
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGR--VEEVLLMKDPETGESRGFGFVTFESVEDADAA 59

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           I+  N      L G+ +KV
Sbjct: 60  IRDLN---GKELEGRVIKV 75

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

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

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+L   +T+  L   F  +      ++  D +TGRS+G+GF+ F + +DA+ A+  L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 204 TGKWLGSRQIRCN 216
            G  L  R I+  
Sbjct: 61  NGFELAGRPIKVG 73

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

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

 Score = 54.3 bits (131), Expect = 6e-10
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR---KDKS-SYGFIHYFDRRSAAMAILSL 114
           ++VG++  ++    L+  F+  G +   ++++     KS  YGF+ +  +  A  AI S+
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 115 NGRHLFGQPIKVNW 128
           NG+ L G+ I+ NW
Sbjct: 62  NGQWLGGRAIRTNW 75

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

 Score = 54.5 bits (132), Expect = 6e-10
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           SV+VGN+   + E  L++ F   G VE  +++R  K+     +G++ +  + S A+A L 
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA-LK 59

Query: 114 LNGRHLFGQPIKV 126
           LNG  L G+ I+V
Sbjct: 60  LNGIKLKGRKIRV 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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ---KTGRSRGFGFVSFRNQQDAQSA 199
            +++G+L   +T+  L   FS Y        ++ +     G+ RG+ FV+F  +++A+ A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 200 INDLTGKWLGSRQIRCNWA 218
           +  L GK    +++   WA
Sbjct: 61  LKSLNGKTALGKKLVVRWA 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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 54.7 bits (131), Expect = 7e-10
 Identities = 27/76 (35%), Positives = 45/76 (59%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV +LSPE  ++ L+  F  + + ++ +V+ D  T + +GFGFV+  N  +A  AI  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 204 TGKWLGSRQIRCNWAT 219
            G  LG R ++ ++ T
Sbjct: 64  NGYRLGDRVLQVSFKT 79

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

 Score = 54.1 bits (131), Expect = 8e-10
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYP---SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           NIF+ +L   + +  L+  FS +    SC   +V  D+  G S+G+GFV F  ++ A  A
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSC---KVATDEN-GGSKGYGFVHFETEEAAVRA 59

Query: 200 INDLTGKWLGSRQI 213
           I  + G  L  +++
Sbjct: 60  IEKVNGMLLNDKKV 73

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|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 = 53.7 bits (130), Expect = 1e-09
 Identities = 23/62 (37%), Positives = 36/62 (58%)

Query: 145 FVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT 204
           FVG L    T+  + A F  Y +  +  ++ D+ TG+S+G  FV F ++++AQ AI  L 
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 205 GK 206
           GK
Sbjct: 63  GK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 53.9 bits (129), Expect = 1e-09
 Identities = 26/79 (32%), Positives = 45/79 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV +LSP+  ++ L+  F  + + ++ +V+ D  T + +GFGFV+  N  +A  AI  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 204 TGKWLGSRQIRCNWATKGA 222
            G  LG R ++ ++ T   
Sbjct: 66  NGYRLGDRVLQVSFKTNKT 84

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 13/78 (16%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAI- 317
           +YVG LA EV +  LH  F   G   I+++++      Q+ +GF FV +    +AA AI 
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGD--IKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID 58

Query: 318 QMGNTTQSSYLFGKQMKV 335
            M      S LFG+ ++V
Sbjct: 59  NMNE----SELFGRTIRV 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 9/81 (11%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--------RKDKSSYGFIHYFDRRSAAMA 110
           +YVGN++ +VTE +L + F   GP+   K++        R++++  GF+ + +R  A  A
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC-GFVAFMNRADAERA 62

Query: 111 ILSLNGRHLFGQPIKVNWAYA 131
           +  L+G+ + G  +K+ W  A
Sbjct: 63  LDELDGKDVMGYELKLGWGKA 83

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

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 27/70 (38%), Positives = 39/70 (55%)

Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LS   T+  L   FS Y   +   V++DQ+TGRSRGF FV F    D++ A+    G  L
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 209 GSRQIRCNWA 218
             R+IR +++
Sbjct: 67  DGRRIRVDYS 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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 30/86 (34%), Positives = 45/86 (52%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G R +   +  + V  LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F N
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWA 218
             DA+ A     G  L  R+IR +++
Sbjct: 61  VDDAKEAKERANGMELDGRRIRVDFS 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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 25/71 (35%), Positives = 43/71 (60%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           I++G L  E+T+  +   FS Y    D  ++ D+KTG+S+GF F+++ +Q+    A+++L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 204 TGKWLGSRQIR 214
            G  L  R IR
Sbjct: 72  NGIKLLGRTIR 82

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 22/57 (38%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           IFVG + P+ T+  L   FS + S  D +++ D + G S+G+GFV+F  Q+DA+  +
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKIL 60

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 53.0 bits (127), Expect = 3e-09
 Identities = 22/49 (44%), Positives = 31/49 (63%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           +F+G L+ E TD +L   F  +   +D  VM D  TGRSRGFGF++F+ 
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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 28/76 (36%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+LS       L   F       D R+  D   GRS+GFG V F  ++ AQ A+   
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALE-K 59

Query: 204 TGKWLGSRQIRCNWAT 219
           +G+ L  R+IR + AT
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|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAM-AILSLNGR 117
           + V N+H  VTE  + E+FS+ G ++  +L+R   +   ++    R+  A+ AI   N R
Sbjct: 3   LVVSNLHPSVTEDDIVELFSAIGALKRARLVRPGVAEVVYV----RKDDALTAIDKYNNR 58

Query: 118 HLFGQPIKVN 127
            L GQP+K  
Sbjct: 59  ELDGQPMKCK 68

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

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 52.9 bits (127), Expect = 3e-09
 Identities = 25/49 (51%), Positives = 30/49 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           +FVG LS E T  TL   FS Y    D  +M D+ T RSRGFGFV F++
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           ++IFVG LSP+VT   L   FS +    +  ++       +  F F+ F  +Q A  A+ 
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVE 61

Query: 202 DLTGKWLGSRQIR 214
                 L ++ + 
Sbjct: 62  SENHSMLKNKTMH 74

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 52.5 bits (127), Expect = 4e-09
 Identities = 24/73 (32%), Positives = 38/73 (52%)

Query: 146 VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           V +LS +  +  L   F  +   S   +  D++TG+SRGF FV+F  ++DA+ AI  L G
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 206 KWLGSRQIRCNWA 218
               +  +   WA
Sbjct: 64  FGYDNLILSVEWA 76

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

 Score = 52.1 bits (125), Expect = 4e-09
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+LS E T+  L A F         R+M  + +G+ +GF FV F   + A +A   L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57

Query: 204 TGKWLGSRQIR 214
            GK L  R +R
Sbjct: 58  KGKHLNGRALR 68

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

 Score = 52.2 bits (125), Expect = 4e-09
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
           R+++VGN+  +VTE L+ E+F   GPV   K I KDK      + F+++    S   A+ 
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVK-IPKDKDGKPKQFAFVNFKHEVSVPYAMN 60

Query: 113 SLNGRHLFGQPIKV 126
            LNG  L+G+P+ +
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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 52.2 bits (126), Expect = 4e-09
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           VYVGN+  + T+  L++ F   GP+    + R     + F+ + D R A  A+ +L+GR 
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-PPGFAFVEFEDPRDAEDAVRALDGRR 60

Query: 119 LFGQPIKV 126
           + G  ++V
Sbjct: 61  ICGNRVRV 68

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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 52.4 bits (125), Expect = 4e-09
 Identities = 25/76 (32%), Positives = 45/76 (59%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV +L+P+  ++ L+  F  + + ++ +V+ D  T + +GFGFV+  N  +A  AI  L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 204 TGKWLGSRQIRCNWAT 219
            G  LG R ++ ++ T
Sbjct: 66  NGYRLGDRVLQVSFKT 81

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSLNG 116
           +YV N+   VTE  L+E FS  G VEG +L+R       + F+ +     A  A+  LNG
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 117 RHLFGQPIK 125
             L G+ ++
Sbjct: 61  LVLDGRTLR 69

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

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 52.1 bits (125), Expect = 5e-09
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           IFVG LS   T+  +   FS +    DA +M+D++T R RGFGFV+F ++   
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54

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|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 = 52.2 bits (125), Expect = 5e-09
 Identities = 26/72 (36%), Positives = 41/72 (56%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+F+  L  E  DA L   F  + +   A+V  D+ T +S+ FGFVSF N   AQ+AI  
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 203 LTGKWLGSRQIR 214
           + G  +G ++++
Sbjct: 66  MNGFQIGMKRLK 77

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

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 24/76 (31%), Positives = 42/76 (55%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + VG+L  E TD       S + +     +++ + TG S+G+GFV + ++  A  A N L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 204 TGKWLGSRQIRCNWAT 219
            GK +G R+++ +WA 
Sbjct: 62  DGKQIGGRKLQVDWAD 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|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 = 51.5 bits (124), Expect = 8e-09
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           ++V  + T+ TE  L+ +FS  G VE   L+ KD  +     +GF+ +     A  AI  
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLM-KDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 114 LNGRHLFGQPIKV 126
           LNG+ L G+ IKV
Sbjct: 63  LNGKELEGRVIKV 75

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

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

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
            +V+VGNI   V++  ++++    G V   K + KD S+     +GF  + D   A  A+
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRV-KDPSTGKLKAFGFCEFEDPEGALRAL 59

Query: 112 LSLNGRHLFGQPIKVN 127
             LNG  L G+ + V 
Sbjct: 60  RLLNGLELGGKKLLVK 75

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

 Score = 51.1 bits (123), Expect = 9e-09
 Identities = 22/73 (30%), Positives = 38/73 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+L  +VT+  L+  F       +  +  D+ T   +G+GFV F +++DA  AI  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 204 TGKWLGSRQIRCN 216
               L  + IR N
Sbjct: 61  NMIKLYGKPIRVN 73

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|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 = 50.7 bits (122), Expect = 1e-08
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            ++VG+L   +T+  L   FS + +  + RV  D+      G+ FV F   + A +AI  
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVA 55

Query: 203 LTGKWLGSRQIRCNW 217
           + G  +  + ++C+W
Sbjct: 56  VNGTSINGQTVKCSW 70

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 144 IFVGDLSPEVTDA---TLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           I+V  + P++++    ++F  F    SCS A    D +TG+ +G+GF+ + N Q AQ AI
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAP---DPETGKHKGYGFIEYENPQSAQDAI 59

Query: 201 NDLTGKWLGSRQIR 214
             +    LG +Q+R
Sbjct: 60  ASMNLFDLGGQQLR 73

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

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 24/69 (34%), Positives = 37/69 (53%)

Query: 146 VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           V +L+   T   L   F  Y    D  +  D+ T  SRGF FV F +++DA+ A++ + G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 206 KWLGSRQIR 214
           K L  R++R
Sbjct: 63  KELDGRELR 71

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

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 51.1 bits (122), Expect = 1e-08
 Identities = 24/63 (38%), Positives = 34/63 (53%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   +T   L   FS Y     +R++ DQ TG SRG GF+ F  + +A+ AI  
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 203 LTG 205
           L G
Sbjct: 62  LNG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+F+  L  E TD  L   F  + +   A+V  D++T  S+ FGFVS+ N   AQ+AI  
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 203 LTGKWLGSRQIR 214
           + G  +G+++++
Sbjct: 66  MNGFQIGTKRLK 77

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+L   VT+  L   FS        +++ +     +  + FV + + + A +A+  +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHG---NDPYAFVEYYDHRSAAAALQTM 57

Query: 204 TGKWLGSRQIRCNWA 218
            G+ +  ++I+ NWA
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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSL 114
           YVGN+   VTE  L+++F   G V   ++I  D+ +     +GF+       A  AI  L
Sbjct: 3   YVGNLPYNVTEEDLKDLFGQFGEVTSARVIT-DRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 115 NGRHLFGQPIKVNWA 129
           NG    G+ + VN A
Sbjct: 62  NGTDFGGRTLTVNEA 76

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

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           +YVG +  +V E +L   F   G ++  ++    ++     + F+ + +   AA AI ++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 115 NGRHLFGQPIKVN 127
           N   LFG+ I+VN
Sbjct: 61  NESELFGRTIRVN 73

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

 Score = 50.7 bits (121), Expect = 2e-08
 Identities = 20/63 (31%), Positives = 36/63 (57%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V +L  ++T+  L   F  Y +     ++ D+ TG  RG  FV +  +++AQ+AI+ 
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 203 LTG 205
           L G
Sbjct: 62  LNG 64

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 21/70 (30%), Positives = 40/70 (57%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  L+ + T++ L   F  Y      R++ D+KTG+ RG+ F+ F +++D ++A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 204 TGKWLGSRQI 213
            GK +  R++
Sbjct: 64  DGKKIDGRRV 73

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSL-----GAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           +++VG+LAP+VT   L   F +      GA V+ +    R KG+GFVR+    E   A+ 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL- 61

Query: 319 MGNTTQSSYLFGKQMKV 335
                   Y   + M+V
Sbjct: 62  --TEMNGVYCSSRPMRV 76

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

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 6/64 (9%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQMG 320
           +YV NL P VT+ DL   F     G +E VR+ R+K    GF FV +++  +A  A++  
Sbjct: 1   LYVRNLPPSVTEEDLREFFS--PYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 321 NTTQ 324
           N   
Sbjct: 59  NGLV 62

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

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           ++V  +H +  E  + + F+  G ++   L   D+ +     Y  I Y  ++ A  AI  
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHL-NLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 114 LNGRHLFGQPIKVNWAYASGQ 134
           LNG+ L GQ I V+WA+  G 
Sbjct: 68  LNGKELLGQTISVDWAFVKGP 88

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|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 = 4e-08
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG---FGFVRYSTHAEAALAIQMGN 321
           +YVGNL   VT+  L   F  +G   I+  ++ R+ G   + FV Y  H  AA A+Q  N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGP--IKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMN 58

Query: 322 TTQSSYLFGKQMKV 335
                 + G+++KV
Sbjct: 59  GRL---ILGQEIKV 69

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

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 12/78 (15%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAAL-AI 317
           T++VGNL   VT+  L+  F  L AG +E V++ +D     K F FV +  H  +   AI
Sbjct: 3   TLFVGNLDARVTEEILYELF--LQAGPLEGVKIPKDPNGKPKSFAFVTF-KHEVSVPYAI 59

Query: 318 QMGNTTQSSYLFGKQMKV 335
           Q+ N  +   LFG+++++
Sbjct: 60  QLLNGIR---LFGRELRI 74

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

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           +V+V  +  +V E  L E FS  G V   ++IR   S       ++ ++D  S  +A L 
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA-LG 59

Query: 114 LNGRHLFGQPIKV 126
           L G+ L GQPI V
Sbjct: 60  LTGQRLLGQPIMV 72

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

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

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 20/69 (28%), Positives = 35/69 (50%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +VY G   T      ++ +F + GPV    ++ +    + FI + +  +A +AI +LNG 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 118 HLFGQPIKV 126
            + G  IKV
Sbjct: 61  SVDGNCIKV 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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 49.7 bits (118), Expect = 4e-08
 Identities = 24/58 (41%), Positives = 38/58 (65%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++ + ++  +A+N
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 49.4 bits (118), Expect = 4e-08
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +FVG L+ + +D+ L   F+ Y   ++  VM D  T RSRGFGF++F +  +A  A+
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 49.7 bits (118), Expect = 4e-08
 Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 6/78 (7%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
           S+ + +YV N+    TE  +++ F+S  P  VE  K IR     Y F+H+ +R  A  A+
Sbjct: 6   SSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIR----DYAFVHFSNREDAVDAM 61

Query: 112 LSLNGRHLFGQPIKVNWA 129
            +LNG+ + G PI+V  A
Sbjct: 62  NALNGKVIDGSPIEVTLA 79

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

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

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 11/77 (14%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
           T++VGNL+    Q DL   F     G + +VR+ +D     KGFG V ++T   A  A++
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKE--CGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE 58

Query: 319 MGNTTQSSYLFGKQMKV 335
                    L G++++V
Sbjct: 59  KSGEE----LLGREIRV 71

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 49.3 bits (117), Expect = 5e-08
 Identities = 22/70 (31%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           + ++V N+ T VTE +L++ FS  G +E  K ++     Y F+H+ +R +A  A+  +NG
Sbjct: 2   KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLK----DYAFVHFEERDAAVRAMDEMNG 57

Query: 117 RHLFGQPIKV 126
           + + G+ I++
Sbjct: 58  KEIEGEEIEI 67

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 48.8 bits (117), Expect = 5e-08
 Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 4/52 (7%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYST--HAEAA 314
           ++VGNL  ++T+ +    F   G   + EV + ++KGFGF+R  T  +AE A
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGE--VSEVFLNKEKGFGFIRLDTRTNAEKA 53

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

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 11/76 (14%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           ++VG+L+PE+    L   F   G   I + RV +D      KG+GFV +    +A  AIQ
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGE--ISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ 59

Query: 319 MGNTTQSSYLFGKQMK 334
              +    +L G+ ++
Sbjct: 60  ---SMNGQWLGGRAIR 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|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 23/77 (29%), Positives = 46/77 (59%), Gaps = 5/77 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIRKDKS----SYGFIHYFDRRSAAMAILS 113
           +++GN+  +V E LL + FS+ G  ++  K++R   +     + FI Y    ++  AI +
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 114 LNGRHLFGQPIKVNWAY 130
           +NG++L  +PI V++A+
Sbjct: 64  MNGQYLCNRPITVSYAF 80

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

 Score = 49.1 bits (118), Expect = 6e-08
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSD---ARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +FVG+L  ++ +  L   F     C D    R++ D+KTG  +GFG+V F+ +     A+
Sbjct: 2   VFVGNLPFDIEEEELRKHFE---DCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL 58

Query: 201 NDLTGKWLGSRQIR 214
             L G  L  R+IR
Sbjct: 59  K-LNGIKLKGRKIR 71

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|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 = 49.3 bits (118), Expect = 6e-08
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
            ++++G++  +VTE  L+ +F   G ++   +I     +Y  +    R+ A  A+  L  
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAY--VCMETRQDAHRALQKLRN 60

Query: 117 RHLFGQPIKVNWAYASG 133
             L G+ IKV WA   G
Sbjct: 61  VKLAGKKIKVAWAPNKG 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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L  + T+A L   FS +    +   +  +  G+ +GF FV F ++ DA+ AI  +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEV-TIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 204 TGKWLGSRQIRCNWA 218
            GK +  R +  +WA
Sbjct: 61  NGKKIKGRPVAVDWA 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|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 = 48.9 bits (117), Expect = 7e-08
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 3/73 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           R+++VG I   ++E  L+E FS+ G V   +L    + S  + F+ + D  SA  A L+L
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSA-LNL 59

Query: 115 NGRHLFGQPIKVN 127
           +G  L G P++V+
Sbjct: 60  SGTLLGGHPLRVS 72

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 21/50 (42%), Positives = 28/50 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +F+G LS + T   L   FS +    +  VM D  T RSRGFGFV+F + 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP 50

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 52.6 bits (125), Expect = 8e-08
 Identities = 27/120 (22%), Positives = 49/120 (40%), Gaps = 11/120 (9%)

Query: 222 AGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHR 281
               E ++ +D +                +     ++  +  T++VGNL  +VT+ DL  
Sbjct: 75  ENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRE 134

Query: 282 HFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            F   G   ++ VR+ RD      +GF FV + +   A  AI+         L G+ ++V
Sbjct: 135 LFKKFGP--VKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE---LNGKELEGRPLRV 189

Length = 306

>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 = 48.4 bits (116), Expect = 8e-08
 Identities = 22/71 (30%), Positives = 35/71 (49%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV +L    T+  L   F  +   S+  +  D++T RS+GF FVSF   + A  A ++L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 204 TGKWLGSRQIR 214
            G     R + 
Sbjct: 62  DGSIFQGRLLH 72

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

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

 Score = 52.6 bits (126), Expect = 9e-08
 Identities = 46/174 (26%), Positives = 72/174 (41%), Gaps = 42/174 (24%)

Query: 157 TLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN 216
           +LF       SC   R   D+ TG+S G+GFV++   +DA+ A+N L G  L ++ I+ +
Sbjct: 22  SLFTSIGEIESCKLVR---DKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVS 78

Query: 217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQ 276
           +A         + SSD+        G++                    +YV  L   +TQ
Sbjct: 79  YA---------RPSSDS------IKGAN--------------------LYVSGLPKTMTQ 103

Query: 277 LDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAALAIQMGNTTQSS 326
            +L   F   G  +   +         KG GF+R+    EA  AI+  N T  S
Sbjct: 104 HELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS 157

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

 Score = 48.5 bits (116), Expect = 9e-08
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
           T++VGNL+  V    L   F   G    A VI +    R +GFG+V + +  +A  AI+ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 320 GNTTQSSYLFGKQMKV 335
            +  +   L G+ + V
Sbjct: 61  MDGKE---LDGRPINV 73

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

 Score = 48.3 bits (115), Expect = 9e-08
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+L P VT+  L   F V     + +++ D K  +   +GFV +    DA+ A+  L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 204 TGKWLGSRQIRCNWA 218
            G+ + + +IR NWA
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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI-------RKDKSSYGFIHYFDRRSAAMAI 111
           +++GN+ +++TE  L ++FS  G ++    +       +     Y F+ +  +  A  A+
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 112 LSLNGRHLFGQPIKVNWA 129
            SLNG+   G+ + V WA
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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  LS +V +  L+  FS      D R++ D+ + RS+G  +V F +++    A+  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-L 60

Query: 204 TGKWLGSRQI 213
           TG+ L  + I
Sbjct: 61  TGQRLLGQPI 70

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           + V N+H  VTE  L+E+F   G V+  K I  D+S        + +  R  A  AI   
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVK-INYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 115 NGRHLFGQPIKVN 127
           NG  L GQP++V 
Sbjct: 62  NGVLLDGQPMQVE 74

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 4/73 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           + ++V N+   VTE +L++ F   G +E  K ++     Y FIH+ +R  A  A+  +NG
Sbjct: 2   KVLFVRNLANTVTEEILEKAFGQFGKLERVKKLK----DYAFIHFDERDGAVKAMEEMNG 57

Query: 117 RHLFGQPIKVNWA 129
           + L G+ I++ +A
Sbjct: 58  KELEGENIEIVFA 70

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 28/67 (41%), Positives = 42/67 (62%), Gaps = 6/67 (8%)

Query: 68  VTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQ 122
           +T+  L+ +F S G +E CKL+R DK +     YGF++Y D + A  AI +LNG  L  +
Sbjct: 16  MTQEELKSLFGSIGEIESCKLVR-DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 74

Query: 123 PIKVNWA 129
            IKV++A
Sbjct: 75  TIKVSYA 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           ++VGN+    T   L+ +F   G V  C +++     YGF+H  +   A  AI +LNG  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN----YGFVHMEEEEDAEDAIKALNGYE 57

Query: 119 LFGQPIKV 126
             G+ I V
Sbjct: 58  FMGKRINV 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +F+ +L  + T+  L   FS +     AR++ D+ TG S+G  FV F+ ++ AQ  +
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 19/64 (29%), Positives = 32/64 (50%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+++  L P  TD  L      +      + + D+KT + +G+GFV F + + A  AI  
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 203 LTGK 206
           L G+
Sbjct: 62  LNGR 65

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

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

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  LS + T+ TL   F        AR++ D+ TG S+GFGFV F +++DA++A   +
Sbjct: 3   LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 204 TGKWLGSRQIRCNWA 218
               +   ++  ++A
Sbjct: 60  EDGEIDGNKVTLDFA 74

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|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 = 48.0 bits (115), Expect = 1e-07
 Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 144 IFVGDLSPEVTDATLFACFS-VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           + V +L   +T+A L   FS      +D +++  +  G+SR   F+ ++ +++AQ A + 
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAKDY 61

Query: 203 LTGKWLGSRQIRCNWA 218
               ++ + +I   +A
Sbjct: 62  FNNTYINTSKISVEFA 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KS-SYGFIHYFDRRSAAMAILSLN 115
           VYV N+   + +  L+E+F   G +   K+++ D  KS  +GF+++ +  +A  A+  LN
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 116 GRHLFGQPIKV 126
           G+ + G+ + V
Sbjct: 64  GKEVNGKKLYV 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 11/76 (14%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQM 319
           YVGNL   +T+ DL   F   G   IE V++QRD      KG+GF++++   +A  A++ 
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGE--IEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59

Query: 320 GNTTQSSYLFGKQMKV 335
            N  +   L G+ +KV
Sbjct: 60  LNGFE---LAGRPIKV 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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 7/72 (9%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA-IQMGNTT 323
           ++VGNL P++T+ ++ + F   G     E+ + +DKGFGF+R  T   A +A  ++ N  
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKA--GEIFIHKDKGFGFIRLETRTLAEIAKAELDNMP 61

Query: 324 QSSYLFGKQMKV 335
               L GKQ++V
Sbjct: 62  ----LRGKQLRV 69

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 34/64 (53%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   +T   L A FS Y     +R++ D  TG SRG GF+ F  + +A+ AI  
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 203 LTGK 206
           L G 
Sbjct: 62  LNGT 65

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

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 20/75 (26%), Positives = 33/75 (44%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++V +++       L   F  Y    D  +  D  T R RGF +V F + +DA+ A+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 204 TGKWLGSRQIRCNWA 218
                  R+I   +A
Sbjct: 63  DRTRFLGREIEIQFA 77

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

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

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           +YV       +E  ++E+FS  G V+  K+I    S++ F+ +    SA  A  S++G+ 
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI----SNFAFVEFESLESAIRAKDSVHGKV 57

Query: 119 LFGQPIKV 126
           L   P+ V
Sbjct: 58  LNNNPLYV 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 23/57 (40%), Positives = 32/57 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +FVG L  +V +  L   FS +     A V+ D++TG+ RGFGFV F+N   A  A 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

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

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           ++ V  +   +T+   + +F S G +E CKL+R   +     YGF++Y D + A  AI +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 114 LNGRHLFGQPIKVNWAYAS 132
           LNG  L  + IKV++A  S
Sbjct: 64  LNGLRLQTKTIKVSYARPS 82

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG L P VT+  L + F  +      ++         +G GFV F ++  A++AI  L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAIQQL 57

Query: 204 TGKWLGSRQIRCNW 217
            G  +G  +IR +W
Sbjct: 58  QGTIIGGSRIRLSW 71

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

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALA 316
           +T VYV NL  ++    L   F   G   I   +V +D     KGFGFV +  H  A  A
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGK--ITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58

Query: 317 IQ 318
           ++
Sbjct: 59  VE 60

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           +Y+G +  ++TE  +  VFS  G +    L+R DK +     + F+ Y D+RS  +A+ +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVR-DKKTGKSKGFAFLAYEDQRSTILAVDN 70

Query: 114 LNGRHLFGQPIKV 126
           LNG  L G+ I+V
Sbjct: 71  LNGIKLLGRTIRV 83

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

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           R+VYV +I  QVTE  L  +FS+ G V  C++     S   + FI + D   A  A LSL
Sbjct: 3   RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAA-LSL 61

Query: 115 NGRHLFGQPIKV 126
           +G  L   P++V
Sbjct: 62  SGTMLGFYPVRV 73

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

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           ++ V N+ + +++  L+ +FS  G V+  +      S   F+ ++D R+A  A+ +LNGR
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-FVEFYDIRAAEAALDALNGR 61

Query: 118 HLFGQPIKV 126
              G  +KV
Sbjct: 62  PFLGGRLKV 70

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 24/70 (34%), Positives = 37/70 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG LS + T+ TL   FS Y      R++ D  TG S+G+ FV + +++DA  A  D 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 204 TGKWLGSRQI 213
               +   +I
Sbjct: 66  HKLVIDGSEI 75

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

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

 Score = 47.0 bits (111), Expect = 3e-07
 Identities = 27/76 (35%), Positives = 43/76 (56%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T   L + FS       A+++ D+  G S G+GFV++ N +DA+ AIN 
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L S+ I+ ++A
Sbjct: 63  LNGLRLQSKTIKVSYA 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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 47.0 bits (111), Expect = 3e-07
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +F+G LS E TD +L   F  + + +D  VM D +T RSRGFGFV++   ++  +A+
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 51.5 bits (123), Expect = 3e-07
 Identities = 34/100 (34%), Positives = 45/100 (45%), Gaps = 19/100 (19%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRSV---YVGNIHTQVTEPLLQEVFSSTGP--VEGCKLI 89
           A P+ E           D      V   YV N+ T  TE ++++ FS   P  VE  K I
Sbjct: 219 AEPEEEV----------DEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI 268

Query: 90  RKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           R     Y F+H+ DR  A  A+  LNG+ L G  I+V  A
Sbjct: 269 R----DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA 304

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

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 24/70 (34%), Positives = 37/70 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV +L     +  L   FS +   S+  V  D+K+G+S+GF +V F + +DA  A  +L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 204 TGKWLGSRQI 213
            GK    R I
Sbjct: 65  DGKVFQGRLI 74

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

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

 Score = 50.7 bits (121), Expect = 4e-07
 Identities = 26/79 (32%), Positives = 45/79 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV +LSP+  +  L+  F  + +  + +++ D  T + +G+GFVS  N  +A  AI  L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 204 TGKWLGSRQIRCNWATKGA 222
            G  LG+R ++ ++ T  A
Sbjct: 332 NGYTLGNRVLQVSFKTNKA 350

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
             ++V NL P+  +  L + F   GA  +  V+V RD      KG+GFV  + + EA  A
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGA--VTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSA 59

Query: 317 IQMGNTTQ 324
           I   N  +
Sbjct: 60  IASLNGYR 67

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

 Score = 46.9 bits (111), Expect = 4e-07
 Identities = 25/76 (32%), Positives = 40/76 (52%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++FV +++ +     L   F  Y    D  V  D  T R RGF +V F + +DA+ A+++
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 203 LTGKWLGSRQIRCNWA 218
           L  KW+  RQI   +A
Sbjct: 62  LDRKWICGRQIEIQFA 77

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

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

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDAR--VM-WDQKTGRSRGFGFVSFRNQQDAQSAI 200
           ++VG+LS   T+  ++  FS    C D +  +M  D+ T    GF FV +  ++DA++A+
Sbjct: 1   LYVGNLSFYTTEEQIYELFS---RCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAV 57

Query: 201 NDLTGKWLGSRQIRCNW 217
             L G  L  R IR +W
Sbjct: 58  KYLNGTKLDDRIIRVDW 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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 149 LSPEVTDATLFACFSVYPS--CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK 206
           L    T+  +    S   S    D R++ D+ TG SRGF FV F + +DA   ++ L   
Sbjct: 10  LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69

Query: 207 W---LGSRQIRCNWA 218
               +  R +R ++A
Sbjct: 70  DPFVIDGRVVRVSYA 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 46.6 bits (110), Expect = 5e-07
 Identities = 22/76 (28%), Positives = 43/76 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IF+ +L  +  +  L+  F  + + ++ +V+ D  T + +GFGFV+  N ++A  AI  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 204 TGKWLGSRQIRCNWAT 219
            G  LG + ++ ++ T
Sbjct: 64  NGYRLGDKILQVSFKT 79

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

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGR 117
           V N+  + TE  L+++FS  G V    + RK    K  + F+ +  +  A  AI  +NG+
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGK 63

Query: 118 HLFGQPIKVNWA 129
            + G+P+ V+WA
Sbjct: 64  KIKGRPVAVDWA 75

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

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

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 30/70 (42%), Positives = 43/70 (61%), Gaps = 6/70 (8%)

Query: 68  VTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQ 122
           +T+  L+ +FSS G VE  KLIR DK +     YGF++Y + + A  AI +LNG  L  +
Sbjct: 13  MTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSK 71

Query: 123 PIKVNWAYAS 132
            IKV++A  S
Sbjct: 72  TIKVSYARPS 81

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

 Score = 46.0 bits (110), Expect = 7e-07
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 11/77 (14%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAIQ 318
           VYVGNL  +VT+  L   F  + AG +  V + +D+      G+GFV + +  +A  AI+
Sbjct: 1   VYVGNLDEKVTEELLWELF--IQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIK 58

Query: 319 MGNTTQSSYLFGKQMKV 335
           + N  +   L+GK ++V
Sbjct: 59  IMNMIK---LYGKPIRV 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|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 45.8 bits (109), Expect = 7e-07
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           TTV+VG L P VT+ +L   F   G   I  V++   KG GFV++   A A  AIQ
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGE--IVYVKIPPGKGCGFVQFVHRAAAEAAIQ 55

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

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 46.2 bits (109), Expect = 7e-07
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 59  VYVGNIHTQVTEPL-LQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           V++GN++T V +   ++ +FS  G V GC +       Y F+ Y + R A  A++  NGR
Sbjct: 4   VFIGNLNTAVVKKSDVETIFSKYGRVVGCSV----HKGYAFVQYSNERHARGAVIGENGR 59

Query: 118 HLFGQPIKVNWA 129
            L GQ + +N A
Sbjct: 60  VLAGQTLDINMA 71

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILS 113
           R+++VGN+   +TE  L+  F   G VE   + R  +   ++Y F+ + +   A  A ++
Sbjct: 3   RTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVA 62

Query: 114 LNGRHLFGQPIKVNW 128
           ++G+++    IK+ +
Sbjct: 63  MSGQYIGRNQIKIGY 77

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSLN 115
            VGN+  + T+   +E+ S  G VE C L+  + +     YGF+ Y  + SA  A   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 116 GRHLFGQPIKVNWA 129
           G+ + G+ ++V+WA
Sbjct: 63  GKQIGGRKLQVDWA 76

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

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

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 13/76 (17%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVE----GCKLIRKDKSSYGFI--HYFDRRSAAMA 110
           R+++V NI++ V +  L+ +F   G +      CK         GFI   Y+D R+A  A
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQFGDIRTLYTACK-------HRGFIMVSYYDIRAARRA 54

Query: 111 ILSLNGRHLFGQPIKV 126
             +L G  L G+ + +
Sbjct: 55  KRALQGTELGGRKLDI 70

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

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 28/78 (35%), Positives = 35/78 (44%), Gaps = 11/78 (14%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            +YVGNL   VT+ DL   F   G   +   RV  D      +GFGFV   T  EA  AI
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGE--VTSARVITDRETGRSRGFGFVEMETAEEANAAI 58

Query: 318 QMGNTTQSSYLFGKQMKV 335
           +  N T      G+ + V
Sbjct: 59  EKLNGTD---FGGRTLTV 73

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

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 45.8 bits (108), Expect = 9e-07
 Identities = 21/50 (42%), Positives = 29/50 (58%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           IFVG LS   T   +   F  +    DA +M+D+ T R RGFGFV+F ++
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

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

 Score = 45.8 bits (109), Expect = 9e-07
 Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYG--FIHYFDRRSAAMAIL 112
           +VYV N+   +T   L ++FS  G V     I KDK    S G  FI + DR  A   + 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKV-VKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 113 SLNGRHLFGQPIKVNWA 129
           +LN + LFG+ +K + A
Sbjct: 62  ALNNKELFGRTLKCSIA 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 11/76 (14%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAIQM 319
           YVG+L P+VT+  L+  F    AG +  +RV RD       G+ +V +   A+A  A+  
Sbjct: 3   YVGDLHPDVTEAMLYEIFSP--AGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 320 GNTTQSSYLFGKQMKV 335
            N      + GK +++
Sbjct: 61  LNFD---VIKGKPIRI 73

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

 Score = 49.7 bits (118), Expect = 1e-06
 Identities = 40/184 (21%), Positives = 78/184 (42%), Gaps = 32/184 (17%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG +S E+ + T+   F  +       + WD  TG+ +GF FV +   + AQ A+  +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
            G+ LG R I+                  A+ +++                  E   ++ 
Sbjct: 170 NGQMLGGRNIKV---------GRPSNMPQAQPIID---------------MVQEEAKKFN 205

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            +YV ++ P++++ D+   F + G   I + ++ R       KG+GF+ Y+     + AI
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGE--IVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI 263

Query: 318 QMGN 321
              N
Sbjct: 264 ASMN 267

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG++ P  T A L   F  +    + R   D      RGF FV     + A  AI  L
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56

Query: 204 TGKWLGSRQIRCNW 217
            G  +  R +RC W
Sbjct: 57  QGFPVHGRPLRCGW 70

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN 115
           CR ++VGN+   +TE   +E+FS  G V     + K+K  +GFI    R +A  A   L+
Sbjct: 2   CR-LFVGNLPNDITEEEFKELFSKYGEVSEV-FLNKEKG-FGFIRLDTRTNAEKAKAELD 58

Query: 116 GRHLFGQPIKV 126
           G    G+ ++V
Sbjct: 59  GIMRKGRQLRV 69

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L  +VT+  L   F         ++ +D ++GRS G   V F  ++DA+ AI   
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQF 61

Query: 204 TGKWLGSRQIRCN 216
            G  L  + ++  
Sbjct: 62  NGVLLDGQPMQVE 74

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

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 6/62 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
            T+ +  L    T+ D+ +   ++ +  I++VR+ RDK      GF FV + +  +A   
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62

Query: 317 IQ 318
           + 
Sbjct: 63  MD 64

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

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 19/71 (26%), Positives = 35/71 (49%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + VG L+  V    L   FS Y +  D  +  D++    RG+ +V F + +DA+ AI  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 204 TGKWLGSRQIR 214
            G  +  +++ 
Sbjct: 61  DGGQIDGQEVT 71

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

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           +FVG+L   V    L   FS +       V +D++TG S+G+GFVSF ++   ++A+ 
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ 59

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 19/47 (40%), Positives = 29/47 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +FVG L  +VT+  L   FS Y +     ++ D++TG+ RGF FV+F
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 60  YVGNIHTQVTEPLLQEVFS-STGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           Y+GN+ + V E  L+++F     PV    +    K  Y F+   D+  A  AI  LNG+ 
Sbjct: 2   YIGNLSSDVNESDLRQLFEEHKIPVSSVLVK---KGGYAFVDCPDQSWADKAIEKLNGKI 58

Query: 119 LFGQPIKV 126
           L G+ I+V
Sbjct: 59  LQGKVIEV 66

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           TT+YVG L   VT+ DL  HF+  G   I  + V   +   FV ++T   A  A
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGE--IRSITVVPRQQCAFVTFTTREAAEKA 53

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG---FGFVRYSTHAEAALAIQMG 320
           +++VG L+P+VT+ +L+  F   G  ++E   ++R      F F+++     AA A++  
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGK-ILEVNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 321 NTTQSSYLFGKQMKV 335
           N    S L  K M V
Sbjct: 64  N---HSMLKNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 3/61 (4%)

Query: 158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
           LF+      SC   R   D+ TG+S G+GFV++ + +DA+ AIN L G  L ++ I+ ++
Sbjct: 21  LFSSIGEIESCKLIR---DKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSY 77

Query: 218 A 218
           A
Sbjct: 78  A 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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 24/76 (31%), Positives = 43/76 (56%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T   L + F         +++ D+ TG+S G+GFV++ + +DA+ AIN 
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L ++ I+ ++A
Sbjct: 66  LNGLRLQTKTIKVSYA 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           ++VGN+  + TE  ++ +F   G V  C +I+    +YGF+H  D+ +A  AI +L+   
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIK----NYGFVHMDDKTAADEAIRNLHHYK 58

Query: 119 LFGQPIKV 126
           L G  I V
Sbjct: 59  LHGVAINV 66

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

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR---KDKSSYGFIHYFDRRSAAMAILSLN 115
           ++VG ++ Q TE  ++EVFS  G VE   ++R   K      F+ Y  +  A  AI +LN
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 116 GRHLF---GQPIKVNWA 129
           G +      QP+ V +A
Sbjct: 62  GVYTMRGCDQPLIVRFA 78

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK-DKSS--------YGFIHYFDRRSA 107
            +++V N++ + TE  L++ F   G V    + +K D           YGF+ +  + +A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 108 AMAILSLNGRHLFGQPI 124
             A+  L G  L G  +
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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 5/83 (6%)

Query: 144 IFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++GDL P + +  +   F S+  +    +++ ++ TG   G+ FV F ++  A+  ++ 
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 203 LTGKWL-GS---RQIRCNWATKG 221
           L GK + GS   ++ + N AT G
Sbjct: 62  LNGKPIPGSNPPKRFKLNRATYG 84

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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   +T   L   FS Y     +R++ DQ TG SRG GF+ F  + +A+ AI  
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 203 LTGK 206
           L G+
Sbjct: 64  LNGQ 67

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 59  VYVGNIHTQVTEPL-LQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           V++GN++T + +   ++ +F+  G + GC +       Y F+ Y   R A  A+   N R
Sbjct: 4   VFIGNLNTAIVKKADIEAIFAKYGKIVGCSV----HKGYAFVQYISERHARAAVAGENAR 59

Query: 118 HLFGQPIKVN 127
            + GQP+ +N
Sbjct: 60  IIAGQPLDIN 69

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           ++VGN+    ++  L+ +F + G V  C ++R+    + F+H     +A  AI  LNGR 
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ----FAFVHLRGEAAADRAIEELNGRE 58

Query: 119 LFGQPIKV 126
           L G+ + V
Sbjct: 59  LHGRKLVV 66

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

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+F+  L  E  D  L   F  + +   A+V  D++T  S+ FGFVS+ N   AQ+AI  
Sbjct: 9   NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68

Query: 203 LTGKWLGSRQIR 214
           + G  +G ++++
Sbjct: 69  MNGFQIGMKRLK 80

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 4/79 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           ++ V  +   +T+   + +F S G +E CKL+R   +     YGF++Y D   A  AI +
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 114 LNGRHLFGQPIKVNWAYAS 132
           LNG  L  + IKV++A  S
Sbjct: 65  LNGLKLQTKTIKVSYARPS 83

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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +VY G + + +TE L+++ FS  G +   ++   DK  Y F+ +    SAA AI+S+NG 
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVF-PDKG-YSFVRFNSHESAAHAIVSVNGT 59

Query: 118 HLFGQPIKVNWA 129
            + G  +K  W 
Sbjct: 60  TIEGHVVKCYWG 71

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 22/71 (30%), Positives = 37/71 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG +S E+ + T+   FS +       + WD  T + +GF FV +   + AQ A+  +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 204 TGKWLGSRQIR 214
            G  LG R I+
Sbjct: 63  NGVMLGGRNIK 73

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 18/51 (35%), Positives = 31/51 (60%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
           IFVG LSPE T+  +   F  + +  +  +  D+KT + RGF F++F +++
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 48.1 bits (114), Expect = 3e-06
 Identities = 44/182 (24%), Positives = 71/182 (39%), Gaps = 15/182 (8%)

Query: 90  RKDKSSYGFIHYFDRRSAAMAILSL-NGR-HLFGQPIKVNWAYASGQ-REDTSGHFNI-F 145
           +K    + F+ Y   R+AAMA   L  GR  L+G  I V+WA    +  ED      I +
Sbjct: 178 KKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILY 237

Query: 146 VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           V +L    T+  +   FS +      RV       + R + FV F +++DA  A+++L G
Sbjct: 238 VRNLMTTTTEEIIEKSFSEFKPGKVERVK------KIRDYAFVHFEDREDAVKAMDELNG 291

Query: 206 KWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTV 265
           K L   +I    A        DK+S    +      G        +  +  +   +    
Sbjct: 292 KELEGSEIEVTLAKP-----VDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAY 346

Query: 266 YV 267
             
Sbjct: 347 ED 348

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV +++  V D  L A F  +    D R ++     + RGF  VS+ + + A+ A   L
Sbjct: 4   LFVRNINSNVEDEELRALFEQF---GDIRTLYT--ACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 204 TGKWLGSRQI 213
            G  LG R++
Sbjct: 59  QGTELGGRKL 68

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGR 117
           VY+G +   V E  +Q  F   G     KL+  D K+ YGF+ + D R A  A+  LNG+
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYG-----KLLEIDLKNGYGFVEFEDSRDADDAVYELNGK 56

Query: 118 HLFGQPIKVNWA 129
            L G+ + V  A
Sbjct: 57  DLCGERVIVEHA 68

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

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 10/58 (17%)

Query: 161 CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
           CF VY             TG S+G+GFV +  +  A  A +DL GK LGSR +  +W 
Sbjct: 29  CFLVYSE----------TTGHSKGYGFVEYMKKDSAARAKSDLLGKQLGSRTLYVHWT 76

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|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 = 3e-06
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 155 DATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR 214
           D  L   F  +    D  ++++++   S+GFGFV+F N  DA  A   L G  +  R+I 
Sbjct: 14  DPDLRQMFGQFGPILDVEIIFNERG--SKGFGFVTFANSADADRAREKLHGTVVEGRKIE 71

Query: 215 CNWAT 219
            N AT
Sbjct: 72  VNNAT 76

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

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 20/59 (33%), Positives = 34/59 (57%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           F +FV +L  + T+ +L   FS + S   A  + D+ TGR++G GFV F++Q    + +
Sbjct: 2   FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           +++VG++  +VT+  L   FS+       +++   KS     YGF+ +  ++ A  AI  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 114 LNGRHLFGQPIKVNW 128
           +NG+ L  +PI+ NW
Sbjct: 61  MNGKWLGSRPIRCNW 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           T ++VG L    T   L ++F   G    A VI + +  + +G+GFV +     A  A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L   + +  L   F  + + +D ++ +  K G+ R FGFV ++ +++AQ A+   
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYT-KDGKFRKFGFVGYKTEEEAQKALKHF 61

Query: 204 TGKWLGSRQIR 214
              ++ + +I 
Sbjct: 62  NNSFIDTSKIT 72

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

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGF--IHYFDRRSAAMAILSL 114
           RS++V N+   VTE  L+ +F   G V G +  R    S G   +H++D R A  A+  L
Sbjct: 2   RSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERI---SEGIVTVHFYDIRDAKRAVREL 58

Query: 115 NGRHLFGQ 122
            GRH+  Q
Sbjct: 59  CGRHMQQQ 66

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

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 44.4 bits (104), Expect = 4e-06
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   +T   L   FS Y     +R++ DQ TG SRG GF+ F  + +A+ AI  
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 203 LTGK 206
           L G+
Sbjct: 67  LNGQ 70

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           ++VGN+    T   L+ +F   G V  C  + KD   Y F+H      A  AI +LNG+ 
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV-KD---YAFVHMEREEEALAAIEALNGKE 58

Query: 119 LFGQPIKV 126
           + G+ I V
Sbjct: 59  VKGRRINV 66

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

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           ++VGN+   V +  L+  F   G V G ++I   ++     +G++ +     A  AI ++
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 115 NGRHLFGQPIKVNWA 129
           +G+ L G+PI V+++
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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 44.0 bits (103), Expect = 5e-06
 Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+LS +VT+  +   FS    C   +++ +  +     + FV F   +DA +A+  +
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59

Query: 204 TGKWLGSRQIRCNWAT 219
            G+ +  ++++ NWAT
Sbjct: 60  NGRKILGKEVKVNWAT 75

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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 43.5 bits (102), Expect = 5e-06
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +VY G I + +TE L+++ FS  G +   ++    +  Y FI +    SAA AI+S+NG 
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVF--PEKGYSFIRFSTHESAAHAIVSVNGT 59

Query: 118 HLFGQPIKVNWA 129
            + G  +K  W 
Sbjct: 60  TIEGHVVKCYWG 71

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 43.5 bits (102), Expect = 6e-06
 Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSL 114
           V+VG++  ++T   ++  F+  G +   ++++         YGF+ ++++  A  AI+ +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 115 NGRHLFGQPIKVNWA 129
            G+ L G+ I+ NWA
Sbjct: 64  GGQWLGGRQIRTNWA 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 13/81 (16%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS--YGFIHYFDRRSAAMAIL 112
             ++VG +    T+  L++ FS  G +E   +I  R+   S  YGF+ + D+ SA  A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 113 SLN----GRHLFGQPIKVNWA 129
             N    GR        VN A
Sbjct: 61  DPNPIIDGRKA-----NVNLA 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 43.6 bits (102), Expect = 6e-06
 Identities = 23/76 (30%), Positives = 42/76 (55%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ + +DA+ AIN 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L ++ I+ ++A
Sbjct: 64  LNGLRLQTKTIKVSYA 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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 43.6 bits (102), Expect = 6e-06
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +F+G LS E T+ +L   +  +   +D  VM D  + RSRGFGFV+F    +  +A+
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 43.1 bits (101), Expect = 7e-06
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+LS +VT+A +   FS    C   +++ D  T  +  + FV F   + A +++  +
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 204 TGKWLGSRQIRCNWA 218
            G+ +  ++++ NWA
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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           ++V N+     E LL ++FS  G V   K+IR   ++    YGF+   +   A  AI SL
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 115 NGRHLFGQPIKV 126
           NG  L G+ ++V
Sbjct: 64  NGYRLGGRVLQV 75

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

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

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 18/79 (22%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPV--------EGCKLIRKDKSSYGFIHYFDRRSAAM 109
           +V+VG +   VTE  L+ +F   G +        +GC          GF+ +  R +A  
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGC----------GFVQFVHRAAAEA 52

Query: 110 AILSLNGRHLFGQPIKVNW 128
           AI  L G  + G  I+++W
Sbjct: 53  AIQQLQGTIIGGSRIRLSW 71

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

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 43.1 bits (101), Expect = 7e-06
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           +YV N+  + +E  +++ F    P  VE  K IR     Y F+H+  R  A  A+ +LNG
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIR----DYAFVHFTSREDAVHAMNNLNG 59

Query: 117 RHLFGQPIKVNWA 129
             L G  I+V  A
Sbjct: 60  TELEGSCIEVTLA 72

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 20/75 (26%), Positives = 39/75 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV  +  E  +  +   F+ +    +  +  D++TG  +G+  + +  +++AQ+AI  L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 204 TGKWLGSRQIRCNWA 218
            GK L  + I  +WA
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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 43.1 bits (101), Expect = 8e-06
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG LS       +   F  +    DA +M+D+ T R RGFGFV+F   +D    + ++
Sbjct: 6   IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE-NEDVVEKVCEI 64

Query: 204 TGKWLGSRQIRCNWA 218
               + ++ + C  A
Sbjct: 65  HFHEINNKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 69  TEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSLNGRHLFGQPI 124
           T+   + +F + GPV+ CK++R  ++ Y    GF+ Y     A  AI +LNG  L  + I
Sbjct: 13  TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72

Query: 125 KVNWAYASG 133
           KV +A   G
Sbjct: 73  KVAYARPGG 81

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

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 42.6 bits (100), Expect = 9e-06
 Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           ++VGNL  ++T+ D  + F   G     EV + RD+GFGF+R  +   A +A
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEP--SEVFINRDRGFGFIRLESRTLAEIA 53

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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSL 114
           V+VG++  ++T   ++  F+  G +   ++++         YGF+ +F++  A  AI  +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 115 NGRHLFGQPIKVNWA 129
            G+ L G+ I+ NWA
Sbjct: 64  GGQWLGGRQIRTNWA 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|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 = 42.5 bits (100), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALAIQ 318
           +++G L+ +  +  L + F   G   I EV V      QR +GFGFV +    +A  A+ 
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQ--ISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 319 MGNTTQSSYLFGKQMKV 335
             N      + G+Q++V
Sbjct: 61  AMNGKS---VDGRQIRV 74

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

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 10/77 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           +++GNL PEV +  L+  F + G  +++  ++ RD      KGF F+ Y +   +  AI+
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFG-VILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 319 MGNTTQSSYLFGKQMKV 335
             N     YL  + + V
Sbjct: 63  AMN---GQYLCNRPITV 76

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 14/82 (17%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLG--AGV-I------EEVRVQRDKGFGFVRYSTHAEA 313
           T +YVGNL P+VT+  L + F   G  A V I      EE R  R+   GFV +   A+A
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC--GFVAFMNRADA 59

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
             A+          + G ++K+
Sbjct: 60  ERALD---ELDGKDVMGYELKL 78

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

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           +++V N+    T+  L+E FS  GP++ C +++ DK S     +G++ +     A  A+ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVK-DKGSKKCRGFGYVTFALEEDAKRALE 59

Query: 113 SLNGRHLFGQPIKVNWA 129
                   G+ I V +A
Sbjct: 60  EKKKTKFGGRKIHVEFA 76

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 7/63 (11%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
            ++VG + P+ T+ +L   F   G+  +++V++  D     KG+GFV + T  +A   + 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGS--VKDVKIITDRAGVSKGYGFVTFETQEDAEKILA 61

Query: 319 MGN 321
           MGN
Sbjct: 62  MGN 64

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 10/80 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           TV++ NL  + T+ +L   F   G   ++  R+ +D      KG  FV++ T   A   +
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGE--VKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

Query: 318 QMGNTTQSSYLF--GKQMKV 335
           +  +  + S L   G+++ V
Sbjct: 60  EAADNAEDSGLSLDGRRLIV 79

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

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 21/77 (27%), Positives = 40/77 (51%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
             ++V +L   +T+  L   FS Y       ++ D++T +S+G  F+ F +++DA   + 
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 202 DLTGKWLGSRQIRCNWA 218
            L  K L  R ++C+ A
Sbjct: 62  ALNNKELFGRTLKCSIA 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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           TVY G +A  +T+  + + F   G   I E+RV  +KG+ F+R+STH  AA AI   N T
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQ--IMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGT 59

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 22/64 (34%), Positives = 35/64 (54%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   ++   +   FS Y     +R++ DQ TG SRG GF+ F  + +A+ AI  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 203 LTGK 206
           L G+
Sbjct: 63  LNGQ 66

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEV----RVQRDKGFGFVRYSTHAEAALAIQMG 320
           +YVG +  + T+ +L + F   G   IEE+    R   D  +GFV Y    +A  AI+ G
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGE--IEEITLHFRDDGDN-YGFVTYRYACDAFRAIEHG 61

Query: 321 NT 322
           N 
Sbjct: 62  ND 63

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|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL 114
           + +YV N+    TE  ++  F+   P  VE  K +R     Y F+H+F+R  A  A+  +
Sbjct: 2   KVLYVRNLMISTTEETIKAEFNKFKPGVVERVKKLR----DYAFVHFFNREDAVAAMSVM 57

Query: 115 NGRHLFGQPIKVNWA 129
           NG+ + G  I+V  A
Sbjct: 58  NGKCIDGASIEVTLA 72

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 59  VYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           V++GN++T  V +  ++ +FS  G + GC +       + F+ Y + R+A  A+   +GR
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV----HKGFAFVQYVNERNARAAVAGEDGR 59

Query: 118 HLFGQPIKVNWA 129
            + GQ + +N A
Sbjct: 60  MIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL 114
            R+VY+GN+    +E  L+E     GP++  K+++  + +  F+H+    +A   + +L
Sbjct: 3   SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVK--EKNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           IFVG +  +  +  L   FS Y +  + +++ D + G S+G+GFV+F  Q+DAQ  + +
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 22/49 (44%), Positives = 28/49 (57%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           +FVG LS + T   L   FS +    D  +  D  TGRSRGFGFV F++
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKD 49

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 153 VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQ 212
           VT+  L   F+ +    D  V+ D++T  S+G  +V F     A  A+ ++ GK LG   
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI--- 200
           +F+G LS + T   L   FS +    D  +  D  TGRSRGFGFV F+  +     +   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 201 -NDLTGK 206
            + L GK
Sbjct: 61  EHKLNGK 67

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV +L  +V    L   F +      A +  D K G+SRG G V F +  +A  AI+  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMF 59

Query: 204 TGKWLGSRQIRC 215
            G+ L  R +R 
Sbjct: 60  NGQMLFDRPMRV 71

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

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 33/63 (52%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+++  L   +T   +   FS +    ++RV+ DQ TG SRG  F+ F  + +A+ AI  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 203 LTG 205
             G
Sbjct: 62  FNG 64

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

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

 Score = 45.3 bits (107), Expect = 2e-05
 Identities = 36/121 (29%), Positives = 55/121 (45%), Gaps = 9/121 (7%)

Query: 10  QQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVT 69
            QQQQ A+ QQ   Q+ S          Q   + +G             ++V N+     
Sbjct: 228 HQQQQHAVAQQHAAQRASP----PATDGQTAGLAAGAQIAAS-DGAGYCIFVYNLSPDTD 282

Query: 70  EPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSLNGRHLFGQPIK 125
           E +L ++F   G V+  K+IR   ++    YGF+   +   AAMAILSLNG  L  + ++
Sbjct: 283 ETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQ 342

Query: 126 V 126
           V
Sbjct: 343 V 343

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILS 113
           ++++G++   + E  +   F+  G V   K+IR  ++     YGF+ +    +A  A+ S
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 114 LNGRHL--FGQPIKVNWA 129
           LNG+ +    Q  ++NWA
Sbjct: 61  LNGKPIPNTQQRFRLNWA 78

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 7/58 (12%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
           YV NL   +    L   F   G   I   +V  D     KGFGFV +S+  EA  A+ 
Sbjct: 5   YVKNLDDSIDDERLREEFSPFGT--ITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

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

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +VYVGNI    T+  L  +F + G +   +  + D+  + F+       AAMAI+ L G 
Sbjct: 2   TVYVGNIPPYTTQADLIPLFQNFGYILEFR-HQPDRG-FAFVKLDTHEQAAMAIVQLQGF 59

Query: 118 HLFGQPIKVNW 128
            + G+P++  W
Sbjct: 60  PVHGRPLRCGW 70

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR--KDKS-SYGFIHYFDRRSAAMAILSLN 115
           +++ N+   +    L + FS+ G +  CK+       S  YGF+H+    +A  AI  +N
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 116 GRHLFGQPIKVN 127
           G  L  + + V 
Sbjct: 65  GMLLNDKKVFVG 76

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

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

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L P+VT+  +F  F         ++  D K G+ + F FV+F+++     A+N L
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 204 TGKWLGSRQIR 214
            G  L  R + 
Sbjct: 63  NGIKLYGRPLN 73

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAIQMGNTT 323
           VYVGNL P  T+ +L   F     G +  V V R+  GF FV +    +A  A++  +  
Sbjct: 2   VYVGNLGPRATKRELEDEFEKY--GPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALD-- 57

Query: 324 QSSYLFGKQMKV 335
               + G +++V
Sbjct: 58  -GRRICGNRVRV 68

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

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 8/79 (10%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           ++YV N+  Q+TE  L+++F + G +  C L+R DKS+       F+ Y  R  A  AI 
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLR-DKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 113 SLNGRHLFG--QPIKVNWA 129
           SLNG    G   P+ V +A
Sbjct: 61  SLNGTIPPGSTMPLSVRYA 79

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

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR---KDKSS-YGFIHYFDRRSA 107
           DP    +++VG +  Q TE  L+EVFS  G +   +L+R      S  Y F+ Y   R A
Sbjct: 1   DPY--LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDA 58

Query: 108 AMA 110
             A
Sbjct: 59  LRA 61

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 46.1 bits (109), Expect = 2e-05
 Identities = 67/304 (22%), Positives = 105/304 (34%), Gaps = 78/304 (25%)

Query: 45  GNLPPGFD---PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK---DKSSYGF 98
           G  PPG+    P     V+VG I   + E  L  +F   GP+   +L+         Y F
Sbjct: 44  GGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAF 103

Query: 99  IHYFDRRSAAMAILSLN------GRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPE 152
           + +  +  A  A+  LN      GR L G  I V+             +  +FVG +   
Sbjct: 104 VTFCGKEEAKEAVKLLNNYEIRPGRLL-GVCISVD-------------NCRLFVGGIPKN 149

Query: 153 VTDATLFACFS----------VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
                +   FS          VY S +D +        ++RGF FV + + + A  A   
Sbjct: 150 KKREEILEEFSKVTEGVVDVIVYHSAADKK--------KNRGFAFVEYESHRAAAMARRK 201

Query: 203 L-TGK-WLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNP 260
           L  G+  L    I  +WA      +ED  +                              
Sbjct: 202 LMPGRIQLWGHVIAVDWAEPEEEVDEDVMAK----------------------------- 232

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG 320
               +YV NL    T+  + + F     G +E V+  RD  + FV +    +A  A+   
Sbjct: 233 -VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--YAFVHFEDREDAVKAMDEL 289

Query: 321 NTTQ 324
           N  +
Sbjct: 290 NGKE 293

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           ++VG +   V +  L+E+FS+ G V+   L    + +    Y ++ +     A  AI  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 115 NGRHLFGQPIKV 126
           +G  + GQ + 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ +  DA  AIN 
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L ++ I+ ++A
Sbjct: 65  LNGLKLQTKTIKVSYA 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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 25/60 (41%), Positives = 34/60 (56%), Gaps = 2/60 (3%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           TVY G +   +T+  + + F   G   I EVRV  DKG+ FVR+++H  AA AI   N T
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQ--IMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGT 59

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           + ++V NI  +  +P L+++F   GP+   ++I  ++ S  +GF+ + +   A  A   L
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 115 NGRHLFGQPIKVNWA 129
           +G  + G+ I+VN A
Sbjct: 61  HGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           S++VGN+    T   LQE F S G +     I  DK +     + +I + D+ S   A L
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINRIT-ILCDKFTGQPKGFAYIEFLDKSSVENA-L 58

Query: 113 SLNGRHLFGQPIKV 126
            LN     G+ IKV
Sbjct: 59  LLNESEFRGRQIKV 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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 19/49 (38%), Positives = 29/49 (59%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           +FVG LS + +   L   F+ +   +D  +  D  TGRSRGFGF+ F++
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKD 50

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           +FV  L+P  TD  L   FS +       V+ D+KTG S  + F+ F  ++D + A
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 21/50 (42%), Positives = 28/50 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +F+G LS + T   L   F  +    +  VM D  T RSRGFGFV+F +Q
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 24/76 (31%), Positives = 38/76 (50%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++FV +++       L   F  Y    D  V  D  T R RGF ++ F + +DA+ A+ +
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 203 LTGKWLGSRQIRCNWA 218
           L  KW+  RQI   +A
Sbjct: 62  LNRKWVCGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 7/58 (12%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
           +VG L+ + T+ D+ R F   G   IEE  + R      KG  FV++S+HAEA  AI 
Sbjct: 5   FVGMLSKQQTEDDVRRLFEPFGT--IEECTILRGPDGNSKGCAFVKFSSHAEAQAAIN 60

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           VY+G +  +  E  ++  F   G +    L    K+ +GF+ + D R A  A+  LNG+ 
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL----KNGFGFVEFEDPRDADDAVYELNGKE 57

Query: 119 LFGQPIKVNWA 129
           L G+ + V  A
Sbjct: 58  LCGERVIVEHA 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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSL 114
           R++YVGN+    T   L E FS  G V+  ++   +   + Y F+ + ++ S   A L L
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINA-LKL 63

Query: 115 NGRHLFGQPIKVN 127
           NG    G+P+KVN
Sbjct: 64  NGAMFGGRPLKVN 76

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-------YGFIHYFDRRSAAM 109
           R +YV N+  ++ E  L+ +FS  G VE  ++ +K           + F+ + D  S+A 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKD-ASSAE 59

Query: 110 AILSLNGRHLFGQPIKVN 127
             L LNG  L G+ I V+
Sbjct: 60  NALQLNGTELGGRKISVS 77

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

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 51  FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRR 105
           +  +  R ++VG++  +VT+ +L   FS     +  K++R DK +     YGF+ + D  
Sbjct: 2   WPENDFR-IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVR-DKRTGKSKGYGFVSFSDPN 59

Query: 106 SAAMAILSLNGRHLFGQPIKV 126
               A+  +NG+++  +PIK+
Sbjct: 60  DYLKAMKEMNGKYVGNRPIKL 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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-SSYGFIHY-FDRRSAAMAILSLN 115
           +++VGN+     +  L+E F   G V   ++ + D   S GF H  F     A   L  +
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 116 GRHLFGQPIKVNWA 129
           G  L G+ I+V+ A
Sbjct: 61  GEELLGREIRVDLA 74

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|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 7/77 (9%)

Query: 57  RSVYVGNI-----HTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
           R+VY+GN+        + E  L++     G +E  +++R+   +  FI++ +  +A  A+
Sbjct: 3   RNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACA--FINFMNIPNAIAAL 60

Query: 112 LSLNGRHLFGQPIKVNW 128
            +LNG+  +   +++N+
Sbjct: 61  QTLNGKKPYDTIVRINY 77

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>gnl|CDD|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 = 41.1 bits (97), Expect = 4e-05
 Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           +++ +L  E T  DL++ F   G  VI   +V  D      K FGFV Y     A  AI+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFG-NVIS-AKVFVDKNTGQSKCFGFVSYDNPESAQAAIK 58

Query: 319 MGNTTQSSYLFGKQMKV 335
             N  Q   + GK++KV
Sbjct: 59  AMNGFQ---VGGKRLKV 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 45.1 bits (106), Expect = 4e-05
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 4/72 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAILSL 114
           +YV ++H  ++E  ++ VF + G +  C+L R    +    YGFI Y + +S + AI S+
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 115 NGRHLFGQPIKV 126
           N   L GQ ++V
Sbjct: 267 NLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
           T++V NLA  VTQ DL   F  +     A V+ +      +G+GFV ++   +A  A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEAL-- 58

Query: 320 GNTTQSSYLFGKQMKV 335
               ++  L G+ +++
Sbjct: 59  -AKLKNKKLHGRILRL 73

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 4/48 (8%)

Query: 289 GVIEEVRVQRDK-GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           G +E++++ + K GF FV +ST   A  A+Q  N        G+ ++V
Sbjct: 9   GNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGV---LFGGRPLRV 53

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

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 153 VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND---LTGKWL 208
            T+  L   FS +      +V  D KTG+S+GFGFV F + +D    ++    + G+W 
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMIDGRWC 69

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 17/54 (31%), Positives = 29/54 (53%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +FVG LSP+ T+  +   F  +    +  +  D KT   RGF FV++ +++  Q
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQ 55

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +FVG LS +  +  +   F+ + S  +  V+ DQ  G+SRG  FV+F ++Q A +AI
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCALNAI 59

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 12/77 (15%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           ++VGN+    T  +L  HF S   G I  + +  D      KGF ++ +   +    A+ 
Sbjct: 2   IFVGNVDYGTTPEELQEHFKS--CGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL 59

Query: 319 MGNTTQSSYLFGKQMKV 335
           +  +       G+Q+KV
Sbjct: 60  LNESE----FRGRQIKV 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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 16/79 (20%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL--IR--KDKSS-----YGFIHYFDRRSAA 108
           +VY+GN+   +TE  ++E F       GC++  +R   DK +     +G + + D  S  
Sbjct: 1   TVYIGNLAWDITEDDVREFFK------GCEITSVRLATDKETGEFKGFGHVDFADEESLD 54

Query: 109 MAILSLNGRHLFGQPIKVN 127
            A L L+G  L G+PI++ 
Sbjct: 55  AA-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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRR 105
           P  D    R++++GN+   V+E  L+  F   G +E   + R  +    +Y F+ + +  
Sbjct: 1   PEDDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLD 60

Query: 106 SAAMAILSLNGRHLFGQPIKVNWA 129
            A  A ++++GR +   PIK+ + 
Sbjct: 61  MAHRAKVAMSGRVIGRNPIKIGYG 84

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
           P  C+ VYVGN+     +  L+  F   GP+    + R +   + F+ + D R AA A+ 
Sbjct: 2   PLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVR 59

Query: 113 SLNGRHLFGQPIKV 126
            L+GR L G  ++V
Sbjct: 60  ELDGRTLCGCRVRV 73

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

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
           T + V  L  ++TQ +L   F ++G   IE  ++ RD+      G+GFV Y    +A  A
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGP--IESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           I   N  +   +  K++KV
Sbjct: 59  INTLNGFE---IRNKRLKV 74

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

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

 Score = 39.9 bits (94), Expect = 6e-05
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 9/69 (13%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L    T   L A F  Y + ++  V+        + +GFV    ++DA+ AI  L
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKAL 53

Query: 204 TGK-WLGSR 211
            G  ++G R
Sbjct: 54  NGYEFMGKR 62

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 68  VTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAILSLNGRHLFG-- 121
           VTE  L+E F+  G ++   +++    K+     ++ +    SAA A+  +NG+ L G  
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

Query: 122 QPIKV 126
           +P+KV
Sbjct: 74  KPLKV 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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 13/27 (48%), Positives = 18/27 (66%)

Query: 170 DARVMWDQKTGRSRGFGFVSFRNQQDA 196
           D R+M  + TG SRGF FV F + ++A
Sbjct: 32  DVRLMRRKTTGASRGFAFVEFMSLEEA 58

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 144 IFVGDLSPEVTDATLFAC----FSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           +FV  L    +D  L A     FS Y +    +V+ D    R R + FV F N  DA++A
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDAKNA 61

Query: 200 INDLTGKWLGSRQIRC 215
           +    G  L  R IRC
Sbjct: 62  LAKGQGTILDGRHIRC 77

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 267 VGNLAPEVTQLDLHRHFHSLGAGVIEEV-----RVQRDKGFGFVRYSTHAEAALAIQMGN 321
           V NL  + T+ DL + F   G   + EV        + KGF FV++++ A+A  AI+  N
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGF--VWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 322 TT 323
             
Sbjct: 62  GK 63

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSR---GFGFVSFRNQQDAQSAI 200
           I+V +L  ++ +  L   FS +      R+   Q   + R   GF FV+F++   A++A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 201 NDLTGKWLGSRQI 213
             L G  LG R+I
Sbjct: 63  Q-LNGTELGGRKI 74

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 20/91 (21%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVE----------GCKLIRKDKSSYGFIH------ 100
           R+V+VGN+     +  L+++F   GP+E            KL +K  +     H      
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 101 --Y--FDRRSAAMAILSLNGRHLFGQPIKVN 127
             Y  F    +A   L LNG    G  I+V+
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIRVD 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|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           F++FVG+L+P      L    S + S  +  V  D + G S+ FG+V F + +D + A+ 
Sbjct: 1   FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQ-DVRIGSSKKFGYVDFESAEDLEKAL- 58

Query: 202 DLTGKWLGSRQIR 214
           +LTGK L   +I+
Sbjct: 59  ELTGKKLLGNEIK 71

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

>gnl|CDD|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 = 40.2 bits (95), Expect = 8e-05
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR--KDKSSYG--FIHYFDRRSAAMAILSL 114
           ++VG +    TE  ++ +F   G +E   +IR      S G  F+ +  R  A  AI +L
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 115 NGRHLF---GQPIKVN 127
           +G+       +P++V 
Sbjct: 62  HGKVTMPGASRPLQVK 77

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

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
           +TVYV NL   +T  DLH+ F   G  V  +V + +DK      G  F+ +    +A   
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVV--KVTIVKDKETRKSKGVAFILFLDREDAHKC 59

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           ++  N  +   LFG+ +K 
Sbjct: 60  VKALNNKE---LFGRTLKC 75

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 13/68 (19%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK-----------GFGFVRYSTHA 311
           TT++V NL  + T+  L +HF   G   +  V + + K           G+GFV + +  
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGG--VRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKE 58

Query: 312 EAALAIQM 319
            A  A++ 
Sbjct: 59  AAQKALKR 66

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

 Score = 40.2 bits (94), Expect = 8e-05
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAAMAILSLN 115
           ++ V N+   V+   L ++F + G +   K IR+  +K  + FI ++D RSA  A+ +LN
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEI---KEIRETPNKRHHKFIEFYDVRSAEAALKALN 59

Query: 116 GRHLFGQPIKV 126
              + G+ IK+
Sbjct: 60  RSEIAGKRIKL 70

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

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

 Score = 40.2 bits (95), Expect = 8e-05
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR-NQQDAQSAIND 202
           +FVG LSP VT++ L   FS + + SD  ++  +  G  RGF ++  R ++   +   + 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 203 LTG-KWLGSR 211
           L G KW GS 
Sbjct: 62  LNGTKWKGSV 71

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

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLN 115
           ++ + N+   V+   L+ +F   G V   K +R+   K    F+ +FD R AA A+ ++N
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDV---KELRETPCKREQRFVEFFDVRDAAKALRAMN 59

Query: 116 GRHLFGQPIKV 126
           G+ + G+P+ +
Sbjct: 60  GKEISGKPVVI 70

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 9/75 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAI-QM 319
           V+VG+L+PE+T  D+   F   G    A V++++   + KG+GFV +    +A  AI QM
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 320 GNTTQSSYLFGKQMK 334
           G      +L G+Q++
Sbjct: 64  G----GQWLGGRQIR 74

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

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 13/78 (16%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           TVY+GNLA ++T+ D+   F       I  VR+  D      KGFG V ++       A+
Sbjct: 1   TVYIGNLAWDITEDDVREFF---KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAAL 57

Query: 318 QMGNTTQSSYLFGKQMKV 335
           ++  T     L G+ +++
Sbjct: 58  KLDGT----VLCGRPIRI 71

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

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           ++VG L P  +  +L R F   GA  I  +     + + ++ Y +  EAA A
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGA--IRRIDYDPGRNYAYIEYES-IEAAQA 49

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 18/57 (31%), Positives = 26/57 (45%)

Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           +S  VT   L   F + P      +  D  TG+S+GF +V++ N   A  A   L G
Sbjct: 7   VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.6 bits (93), Expect = 9e-05
 Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 72  LLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV 126
           +L++VF   G +    L+   K+ YG+  Y DR SA  AI +L+G+ + G  +KV
Sbjct: 15  ILEDVFCRFGGLIDVYLVP-GKN-YGYAKYADRESAERAITTLHGKEVNGVKLKV 67

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 40.3 bits (94), Expect = 9e-05
 Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 3/84 (3%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAA 108
           D    R++++GN+   VTE  L+  F   G +    + R  +   S+YGF+ + +   A 
Sbjct: 3   DQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAH 62

Query: 109 MAILSLNGRHLFGQPIKVNWAYAS 132
            A L+++G+ L   PIK+ +  A+
Sbjct: 63  RAKLAMSGKVLRRNPIKIGYGKAT 86

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS---SYGFIHYFDRRSAAMAILSLN 115
           +YV N+   VT+  L+E+FS  G +   K++  +K     +GF+ + +   A  A+  ++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMH 347

Query: 116 GRHLFGQPIKVNWAYASGQR 135
           GR L G+P+ V  A    QR
Sbjct: 348 GRMLGGKPLYVALAQRKEQR 367

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAI-QM 319
           V+VG+L+PE+T  D+   F   G    A V++++   + KG+GFV +    +A  AI  M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 320 GNTTQSSYLFGKQMK 334
           G      +L G+Q++
Sbjct: 64  G----GQWLGGRQIR 74

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
           +  GF FV F  ++ A+ A+  L G   G R +R +++
Sbjct: 19  KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|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 = 39.8 bits (94), Expect = 1e-04
 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           ++VG L    T+ D+ R       G IEEV + RD      KG  FV++S+  EA  AI+
Sbjct: 2   LFVGQLPKTATEEDV-RALFEE-YGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIE 59

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 11/74 (14%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSD---ARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           ++VG+L P  T   L   F  Y        AR           GF FV F + +DA+ A+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR--------NPPGFAFVEFEDPRDAEDAV 53

Query: 201 NDLTGKWLGSRQIR 214
             L G+ +   ++R
Sbjct: 54  RALDGRRICGNRVR 67

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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG L+ + T+  +   FS Y    D  +M D+   +SRG  FV + +++ AQ+AI  L
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60

Query: 204 TG 205
            G
Sbjct: 61  NG 62

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYP---SCSDAR--VMWDQKTGRSRGFGFVSFRNQQDAQS 198
           +FV +L+ + T+ TL   F       S + A+           S G+GFV F++++ AQ 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 199 AINDLTGK 206
           A+  L G 
Sbjct: 63  ALKRLQGT 70

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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L  ++T+      F  Y   S+  +       R RGFGF+   ++  A+ A  +L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAEL 57

Query: 204 TGKWLGSRQIR 214
            G  L +R +R
Sbjct: 58  DGTILKNRPLR 68

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 144 IFVGDLSPEVTDATLFACFSVY-PSCSDARVMWD---QKTGRSRGFGFVSFRNQQDAQSA 199
           ++V +LS  VT+  L   F  +  S S+ + M+D      GR +G  FV+F +++ A  A
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKA 63

Query: 200 INDLTG 205
           +N + G
Sbjct: 64  LNLVNG 69

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +FVG +   + +  + + F+ Y S  + +++ D +TG S+G+GFVSF +  D Q  +
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIV 63

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G L+P   +  +   F  Y    D  +         RGFGFV F + +DA  A+ +L
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAVYEL 53

Query: 204 TGKWLGSRQI 213
            GK L + ++
Sbjct: 54  DGKELCNERV 63

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

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 12/78 (15%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLN 115
           R V+ GN      +  ++ +F   G V+     R D KS + F++  D R A  AI  L+
Sbjct: 1   RPVFCGNFEYDARQSEIERLFGKYGRVD-----RVDMKSGFAFVYMEDERDAEDAIRGLD 55

Query: 116 ----GRHLFGQPIKVNWA 129
               GR    + ++V WA
Sbjct: 56  NFEFGRQ--RRRLRVEWA 71

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           R+VY+GNI   +TE  L+  FS  G +E    +R+      F+++ +  +A  AI  +  
Sbjct: 4   RNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNC--AFVNFTNISNAIKAIDGVKS 61

Query: 117 RHLFGQPIKVNWA 129
             LF +  K+++ 
Sbjct: 62  HPLF-KKFKISYG 73

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGR 117
           VY+G +  Q  E  ++  F   G     K++  D K+ YGF+ + D R A  A+  LNG+
Sbjct: 2   VYIGRLSYQARERDVERFFKGYG-----KILEVDLKNGYGFVEFDDLRDADDAVYELNGK 56

Query: 118 HLFGQPIKVNWAYASGQRED 137
            L G+ + V   +A G R D
Sbjct: 57  DLCGERVIVE--HARGPRRD 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|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 264 TVYVGNLAPEVTQL-DLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           T++V N  P  T+  DL RHF   G    + V V+  + F FV+Y T  +A  A++   +
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYG----KLVNVRIRRNFAFVQYETQEDATKALE---S 53

Query: 323 TQSSYLFGKQMKV 335
           T  S +  + + V
Sbjct: 54  TNMSKVLDRVISV 66

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS---SYGFIHYFDRRSAAMAILSLNG 116
           YV N+   + +  L+E FS  G +   K++  +K     +GF+ +     A  A+  +NG
Sbjct: 5   YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64

Query: 117 RHLFGQPIKVNWAYASGQR 135
           R + G+P+ V  A    QR
Sbjct: 65  RIIGGKPLYVALA----QR 79

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

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 12/81 (14%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAA 314
           +   ++VG L P VT+ DL ++F     G + EV V      +R +GFGF+ + +     
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQF--GTVTEVVVMYDHEKKRPRGFGFITFESEDSVD 58

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
             +          + GK+++V
Sbjct: 59  QVVNEHFHD----INGKKVEV 75

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

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 6/82 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSA 107
           DP+ C  V+  +++T  TE  L+EVFS  GP+    ++   +S     + F+++ +   A
Sbjct: 7   DPNCCLGVFGLSLYT--TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
             A    NG  L G+ I+V+++
Sbjct: 65  KEAKERANGMELDGRRIRVDFS 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLN 115
           V N+  + T   L+ VF   G V G   I +D+ +     + F+ ++D+R A  A+ +++
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEV-GDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMD 61

Query: 116 GRHLFGQPIKV 126
           G+ L G+ ++V
Sbjct: 62  GKELDGRELRV 72

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

>gnl|CDD|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 = 39.3 bits (92), Expect = 2e-04
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 3/73 (4%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           I VG +   +++  L   FS     +  R+  D++   S  F FV F + + A SA+N L
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSALN-L 59

Query: 204 TGKWLGSRQIRCN 216
           +G  LG   +R +
Sbjct: 60  SGTLLGGHPLRVS 72

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 10/76 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK-----GFGFVRYSTHAEAALAIQM 319
           ++V NL  +V    L   F    AG +    ++ DK     G G V++    EA  AI M
Sbjct: 1   IFVANLDYKVGWKKLKEVFKL--AGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISM 58

Query: 320 GNTTQSSYLFGKQMKV 335
            N      LF + M+V
Sbjct: 59  FNG---QMLFDRPMRV 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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG LS + T+  +   F  + +  +  ++     G S+G  FV F +  +AQ+AIN L
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSHAEAQAAINAL 62

Query: 204 TG 205
            G
Sbjct: 63  HG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 11/68 (16%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK---------GFGFVRYSTHAEAAL 315
           +YV NL  ++ + DL   F     G +E +R+ + +         GF FV +   + A  
Sbjct: 3   IYVRNLDFKLDEDDLRGIFS--KFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 316 AIQMGNTT 323
           A+Q+  T 
Sbjct: 61  ALQLNGTE 68

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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           VYVGN+ T   +  L+  FS  GP+     I ++   + F+ + D R A  A+  L+G+ 
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTV-WIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60

Query: 119 LFGQPIKV 126
           + G  ++V
Sbjct: 61  ICGSRVRV 68

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG +  ++ +  L   F       D R+M D  +G++RG+ F++F  ++ AQ A+   
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 204 ------TGKWLG 209
                  GK LG
Sbjct: 64  DNYEIRPGKHLG 75

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +Y+G++     E  L++ FS  G V+  ++ R  K+     YGFI + +   AA+A  S+
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 115 NGRHLFGQPIKV 126
           N   L G+ ++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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 73  LQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           L+++F   G V    + RK       + F+    R++A +A+ + NG  + G+P+ V+WA
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           +F+G LS + +   L    S +    D  +  D  TGRSRGFGFV F+   DA S
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFK---DAAS 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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 20/47 (42%), Positives = 28/47 (59%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +F+G LS + +  +L   FS +    +  VM D  T RSRGFGFV+F
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 142 FNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           F +FVG+L  + T   L A F +     S  R++ D+KTG+S+G  FV F   +    A+
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPS-VRLLTDKKTGKSKGCAFVEFDTAEAMTKAL 59

Query: 201 NDLTGKWLGSRQI 213
             L    L  R+I
Sbjct: 60  K-LHHTLLKGRKI 71

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 15/84 (17%)

Query: 56  CRSVYVGNIH----TQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA---- 107
            R++YVG I      +  E +L+  F   G +E  +++        F+ Y  R SA    
Sbjct: 1   NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVL--PSKGIAFVRYKYRASAEFAK 58

Query: 108 -AMAILSLNGRHLFGQPIKVNWAY 130
            AMA  SL+G    G+ + V WA 
Sbjct: 59  EAMADQSLDG----GEVLNVRWAN 78

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           VY+G++     EP L++ FS  G V   +L R  K+     Y F+ +     A +   ++
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 115 NGRHLFGQPIKV 126
           N   LF + +K 
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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.1 bits (99), Expect = 3e-04
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 13/79 (16%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAI 317
           ++YVG+L P+VT+  L+  F   G   +  VRV RD       G+G+V +   A+A  A+
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGP--VLSVRVCRDSVTRRSLGYGYVNFQNPADAERAL 59

Query: 318 -QMGNTTQSSYLFGKQMKV 335
             M        L GK +++
Sbjct: 60  ETMNFKR----LGGKPIRI 74

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLI--RKDKSS--YGFIHYFDRRSAAMA 110
             S++VG++   VT+ +LQE F +  P V G K++       S  YGF+ + D      A
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 111 ILSLNGRHLFGQPIKVNWA 129
           +  +NG +   +P++V+ A
Sbjct: 61  LTEMNGVYCSSRPMRVSPA 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L   VT+  L+  F         ++  D   G+ + F FV+F+++     AI  L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKD-PNGKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 204 TGKWLGSRQIR 214
            G  L  R++R
Sbjct: 63  NGIRLFGRELR 73

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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 8/59 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           ++V NLAP+  +  L + F   GA  +  V+V RD      KGFGFV  + + EAA+AI
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGA--VTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKS----SYGFIHYFDRRSAAMAIL 112
           S+++G++   + E  ++  F+S G  V   K+IR   +     Y F+ + D  +A   + 
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 113 SLNGRHLFG-QPI---KVNWAYAS 132
            LNG+ + G  P    K+N A   
Sbjct: 61  KLNGKPIPGSNPPKRFKLNRATYG 84

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 7/77 (9%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-----IRKDKSSYGFIHYFDRRSAAMA 110
           CR VYVG+I  ++ E  +++ FS  GP++   +       K K  + F+ Y    +A +A
Sbjct: 1   CR-VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHK-GFAFVEYEVPEAAQLA 58

Query: 111 ILSLNGRHLFGQPIKVN 127
           +  +NG  L G+ IKV 
Sbjct: 59  LEQMNGVMLGGRNIKVG 75

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

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYGF--IHYFDRRSAAMAILSLN 115
           ++V N+  +V    L+EVF   G V    +   K+  S G   + +     A  AI   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 116 GRHLFGQPIKV 126
           G+ LF +P++V
Sbjct: 61  GQMLFDRPMRV 71

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

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 20/76 (26%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSR------GFGFVSFRNQQDAQ 197
           +++G L     +  +   F  Y              GR R      GFGFV F + +DA 
Sbjct: 2   VYIGRLPYRARERDVERFFKGY--------------GRIREINLKNGFGFVEFEDPRDAD 47

Query: 198 SAINDLTGKWLGSRQI 213
            A+ +L GK L   ++
Sbjct: 48  DAVYELNGKELCGERV 63

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA---QSAI 200
           I++G L     +  L   FS + +  + RV   +KTG S+ +GF+ F N + A     ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 201 ND--LTGKWL 208
           N+  L GK L
Sbjct: 62  NNYLLMGKVL 71

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS-YGFIHYFDRRSAAMAILSLN 115
           ++V  +   VT+  L+++F   G V+  +L+  R  K     ++ Y +  SA+ A+L ++
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 116 GRHLFGQPIKV 126
           G  +  + I V
Sbjct: 65  GTEIKEKTISV 75

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

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCK-LIRKDKSSYGFIHYFDRRSAAMAI 111
            R +Y+ N+ + ++   L++ F   G +E CK LI+     YGFI Y     AA+++
Sbjct: 2   GRVIYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEKYGFITYRHSEHAALSL 58

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFI--HYFDRRSAAMAILSL 114
           R++ +  +   + E  L+      G V     ++ D  + G +  H++D R A  A+  +
Sbjct: 2   RALLLSGVPPHIPETQLRRDLEQWGAVRA---VQMDAMAEGIVTVHFYDLRHAEDALRDI 58

Query: 115 NGRHLFGQ 122
             +HLF Q
Sbjct: 59  RAQHLFQQ 66

This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARV--MWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           I V +L  E T   +   FS Y      RV   +DQ     RGF FV F   ++A +A+N
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAMN 59

Query: 202 DLTGKWLGSRQIRCNWA 218
            L    L  R++   +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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
           IFVG LSP+  +  +   F  +       +  D KT + RGF F++F+ ++
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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 15/83 (18%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           ++V NL+PE  +  L + F   GA  +  V+V RD      KGFGFV  + + EAA+AI 
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGA--VTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIA 61

Query: 319 MGN-------TTQSSYLFGKQMK 334
             N         Q S+   KQ K
Sbjct: 62  SLNGYRLGDRVLQVSFKTSKQHK 84

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 20/84 (23%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSS-----YGFIHYFDRRSAA 108
           ++ V N+     E  L+E+F   GP+      R    KDK +     + F+ +  R  A 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPI-----SRVYLAKDKETGQSRGFAFVTFHTREDAE 55

Query: 109 MAILSLNGR---HLFGQPIKVNWA 129
            AI  LNG    +L    + V WA
Sbjct: 56  RAIEKLNGFGYDNLI---LSVEWA 76

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|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYGFIHYFDRRSAAMAI 111
           R VY+G I +++T   L++ FS  G +E C +  R +  +YGF+ Y     A  AI
Sbjct: 3   RVVYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYGFVTYRYTEEAFAAI 58

This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 91

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

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IF+G L  ++ +  L           + R+M D   G +RG+ FV+F N+Q+A++AI  L
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 204 ------TGKWLG 209
                  G+ LG
Sbjct: 63  NNYEIRNGRLLG 74

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 6/32 (18%)

Query: 171 ARVMWDQK------TGRSRGFGFVSFRNQQDA 196
            ++M D K       G+S+G+GFV F N + A
Sbjct: 39  VKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHA 70

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

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 16/79 (20%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY-----GFIHYFDRRSAAMAI 111
           R+V++ N+    TE  L+E+FS  G V+  +++ KDK +       F+ +  + SA   +
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIV-KDKLTGHSKGTAFVKFKTKESAQKCL 59

Query: 112 ----------LSLNGRHLF 120
                     LSL+GR L 
Sbjct: 60  EAADNAEDSGLSLDGRRLI 78

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

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK-DKSS--YGFIHYFDRRSAAMAILSLN 115
           + V N+  + T+  ++ +FSS G ++  ++ +K D+S+  + F+ +   + A  A+ +L 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 116 GRHLFGQPIKVNWA 129
             HL G+ + + +A
Sbjct: 63  DTHLLGRRLVLQYA 76

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

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 8/59 (13%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV-------QRDKGFGFVRYSTHAEAALAI 317
           +VG +    T+ ++   F  +  GV  +V V        +++GF FV Y +H  AA+A 
Sbjct: 5   FVGGIPKTKTKEEILEEFSKVTEGV-VDVIVYRSPDDKNKNRGFAFVEYESHRAAAMAR 62

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|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ-RDKG--FGFVRYSTHAEAALAIQMGN 321
           +YVG + P+ T+ +L   F   G   IEE  V  RD G  +GF+ Y    +A  A++ G 
Sbjct: 5   IYVGKIRPDTTRTELRDRFEVFGE--IEECTVNLRDDGDSYGFITYRYTCDAFAALENGY 62

Query: 322 TTQSS 326
           T + S
Sbjct: 63  TLRRS 67

This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA. . Length = 91

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           IFVG +  ++ +  L   F       D R+M D  TG +RG+ FV+F  ++ AQ A+
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

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

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +YVGN+   + E  ++++F   GP++   L  R+    + F+ + D R A  A+   +G 
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGY 61

Query: 118 HLFGQPIKV 126
              G  ++V
Sbjct: 62  DFDGYRLRV 70

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

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           +++V N+   VT+  L + FS   P++   ++   ++     YGF+ +     A  A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 114 LNGRHLFGQPIKVNWA 129
           L  + L G+ ++++ A
Sbjct: 61  LKNKKLHGRILRLDIA 76

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

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           T+ V NL+ +  + DL   F   G   I  V + +D      +GF FV + T  +A  AI
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGP--ISRVYLAKDKETGQSRGFAFVTFHTREDAERAI 58

Query: 318 Q 318
           +
Sbjct: 59  E 59

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRY 307
           + T++V  L  + T+  L R F   G   I+ +R+ RDK      G+ F+ +
Sbjct: 1   FKTLFVARLNYDTTESKLRREFEEYGP--IKRIRLVRDKKTGKPRGYAFIEF 50

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 8/66 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           +YV  L   +TQ +L   F   G   I   R+  D      +G GF+R+    EA  AI+
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGR--IITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60

Query: 319 MGNTTQ 324
             N T 
Sbjct: 61  ALNGTI 66

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

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

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++V D+  +VT+  L A FS      D RV  D  +     F F+ F +++ A++A++ L
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNS--VLRFAFIEFTDEEGARAALS-L 61

Query: 204 TGKWLGSRQIR 214
           +G  LG   +R
Sbjct: 62  SGTMLGFYPVR 72

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

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

 Score = 38.0 bits (88), Expect = 6e-04
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNG 116
           V N+    T    +E+  + G +E C L+  +       YGF+ Y  + SA+ A L L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 117 RHLFGQPIKVNWA 129
           + L    +   W 
Sbjct: 64  KQLGESTLFAQWM 76

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

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 18/83 (21%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHYFDRR 105
           R +YVGN+   +TE  L + F+              PV   + I  +K ++ F+ +   R
Sbjct: 2   RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQ-INPEK-NFAFVEF---R 56

Query: 106 SAAMAI--LSLNGRHLFGQPIKV 126
           +   A   L+L+G    GQP+K+
Sbjct: 57  TVEEATAALALDGIIFKGQPLKI 79

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

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

 Score = 40.7 bits (95), Expect = 7e-04
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 8/65 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           ++V NL+P+  +  L + F   GA  ++ V++ RD      KG+GFV  + + EAA+AI 
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGA--VQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAIL 329

Query: 319 MGNTT 323
             N  
Sbjct: 330 SLNGY 334

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

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMG 320
           ++VG L P+VT+ +   +F   G  V  ++    D    +GFGFV + + +        G
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 321 NTTQSSYLFGKQMKV 335
                  L GKQ++V
Sbjct: 62  MLE----LGGKQVEV 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 37.5 bits (88), Expect = 7e-04
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 8/66 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAIQ 318
           +YVGNL+   T+  ++  F     G I+ + +  D+      GF FV Y T  +A  A++
Sbjct: 1   LYVGNLSFYTTEEQIYELFSR--CGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 319 MGNTTQ 324
             N T+
Sbjct: 59  YLNGTK 64

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           ++V N+  +  E +L ++F   G V   K+IR   ++    +GF+   +   AAMAI SL
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 115 NGRHLFGQPIKVNW 128
           NG  L  + ++V++
Sbjct: 64  NGYRLGDRVLQVSF 77

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           ++V N+     E +L ++F   G V   K+IR   ++    +GF+   +   AAMAI SL
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 115 NGRHLFGQPIKVNW 128
           NG  L  + ++V++
Sbjct: 66  NGYRLGDRVLQVSF 79

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

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

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L  ++T+      FS Y   S+  +       + +GFGF+    + +A+ A  +L
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAEL 57

Query: 204 TGKWLGSRQIR 214
            G     RQ+R
Sbjct: 58  DGIMRKGRQLR 68

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

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

 Score = 37.0 bits (86), Expect = 7e-04
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++V    P+ +++ +   FS Y +  + +++          F FV F + + A  A + +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53

Query: 204 TGKWLGSRQIRC 215
            GK L +  +  
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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 3/44 (6%)

Query: 170 DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
           D +   D   GRS+GFG V F + +DAQ AI    G  L  R++
Sbjct: 29  DVKTDND---GRSKGFGTVLFESPEDAQRAIEMFNGYDLEGREL 69

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|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA 107
           PPG     C++V+VG +    TE +++EVF   G +     IR  K ++  I + +  + 
Sbjct: 3   PPG-----CKTVFVGGLPENATEEIIREVFEQCGEIIA---IRMSKKNFCHIRFAEEFAV 54

Query: 108 AMAIL 112
             AI 
Sbjct: 55  DKAIY 59

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|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 5/73 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +Y+GN+   VT   L+++F     P+ G  L+   KS Y F+ Y D+  A  AI +L+G+
Sbjct: 4   LYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLL---KSGYAFVDYPDQNWAIRAIETLSGK 60

Query: 118 -HLFGQPIKVNWA 129
             L G+ ++V+++
Sbjct: 61  VELHGKVMEVDYS 73

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 37.5 bits (87), Expect = 8e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG 320
           ++VG+L+PEVT   L   F +      A V+ +++  R +G+GFV + +  +A  AI   
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAI--- 58

Query: 321 NTTQSSYLFGKQMKV 335
           N     +L  + ++ 
Sbjct: 59  NEMNGKWLGSRPIRC 73

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 9/72 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ-MGNTT 323
           ++VGNL    T  +L   F   G  V E   V   K +GFV      +A  AI+ +    
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGT-VTECDVV---KNYGFVHMEEEEDAEDAIKALNGYE 57

Query: 324 QSSYLFGKQMKV 335
                 GK++ V
Sbjct: 58  ----FMGKRINV 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|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 37.1 bits (86), Expect = 8e-04
 Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           VYV NI  + TE  + + FS  G +    L   D  S      F++ SAA   L L+   
Sbjct: 1   VYVSNISPKTTEKQISDFFSFCGKISNLDL-TNDGESQTATITFEKPSAAKTALLLDNAL 59

Query: 119 LFGQPIKV 126
           L G+ I+V
Sbjct: 60  LGGKVIQV 67

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

>gnl|CDD|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 = 37.2 bits (87), Expect = 8e-04
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 179 TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            G  RGF FV F  +Q+AQ+A+  L    L  R +   +A
Sbjct: 37  DGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  LS     A L   FS Y     A+++ + ++  +R FGFV+  + ++A   I  
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 203 LTGKWLGSRQIR 214
           L    L  R I 
Sbjct: 61  LHRTELHGRVIS 72

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

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 9/60 (15%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-----VQRDKGFGFVRYSTH--AEAALA 316
           TV+V NL   V + +L + F     G I +VR       + KG+ +V +      + AL 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFS--KCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK 58

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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 36.8 bits (86), Expect = 9e-04
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)

Query: 265 VYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYST--HAEAALAIQMGN 321
           V+VGNL  + V++ DL   F   G   I  + +   KG+GFV++     A AA+A + G 
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGK--ILGISLH--KGYGFVQFDNEEDARAAVAGENGR 58

Query: 322 T 322
            
Sbjct: 59  E 59

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

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           T + V NL P VT+ D+   F ++GA  ++  R+ R  G   V Y    +A  AI   N 
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGA--LKRARLVR-PGVAEVVYVRKDDALTAIDKYNN 57

Query: 323 TQSSYLFGKQMKV 335
            +   L G+ MK 
Sbjct: 58  RE---LDGQPMKC 67

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

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

 Score = 37.0 bits (86), Expect = 9e-04
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 8/51 (15%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ------RDKGFGFVRYST 309
           ++VGNL+ E T+ +L  HF  +G   I  VR+       + KGF FV +  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGR--IRRVRMMTFEDSGKCKGFAFVDFEE 49

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.5 bits (87), Expect = 9e-04
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGR-----SRGFGFVSFRNQQDAQS 198
           +FV +L+   T+  L   F        ARV       R     S GFGFV F+ ++ AQ+
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 199 AINDLTGKWLGSRQI 213
           A+  + G  L    +
Sbjct: 63  ALKAMDGFVLDGHTL 77

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|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 = 36.4 bits (85), Expect = 0.001
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 8/59 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           V+VGN+  + T+  L   F     G +   R+  D      KG+GF  +     AA AI
Sbjct: 1   VFVGNIPYDATEEQLIEIFS--EVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57

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|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 = 37.1 bits (86), Expect = 0.001
 Identities = 20/79 (25%), Positives = 44/79 (55%), Gaps = 6/79 (7%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           +++G +     E  L++VFS  G +    ++ KD+ +     +GF+ + +   A  A+++
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVV-KDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 114 LNGRHLFGQPIKVNWAYAS 132
           +NG+ + G+ I+V+ A  S
Sbjct: 62  MNGKSVDGRQIRVDQAGKS 80

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLI---RKDKS-SYGFIHYFDRRSAAMAILSLNG 116
           V  +    TE  L+EVFS  GP+E  +++   +  +S  +GF+++     A  A   LNG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 117 RHLFGQPIKVNWA 129
             + G+ I+V+++
Sbjct: 64  MEIDGRRIRVDYS 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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG+L   V +  L+  F      +   +  D K G+ + FGFV F++ +    AI  L
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIALL 62

Query: 204 TGKWLGSRQIR 214
            G  L  R I+
Sbjct: 63  NGIRLYGRPIK 73

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           ++V N+     E +L ++F   G V   K+IR   ++    +GF+   +   AAMAI SL
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 115 NGRHLFGQPIKVNW 128
           NG  L  + ++V++
Sbjct: 66  NGYRLGDRVLQVSF 79

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

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 8/67 (11%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
           T +YV NL  ++T+ +L + F + G   I +  + RDK      G  FVRY    EA  A
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGN--IVQCNLLRDKSTGLPRGVAFVRYDKREEAQAA 58

Query: 317 IQMGNTT 323
           I   N T
Sbjct: 59  ISSLNGT 65

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

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 8/61 (13%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           TV+V  L+ +V + DL+  F    AG + +VR+ RD      KG  +V +       LA+
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSK--AGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58

Query: 318 Q 318
            
Sbjct: 59  G 59

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYST--HAEAA 314
           Q   ++VG L  + +   L RHF   G      V+ +   +R +GFGF+ +S+   A+ A
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 315 LAIQ 318
           +  Q
Sbjct: 61  MEAQ 64

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|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 = 37.2 bits (87), Expect = 0.001
 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 6/62 (9%)

Query: 267 VGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK-----GFGFVRYSTHAEAALAIQMGN 321
           V NL   +T+ +L  HF   G G I +V++ R +        F+ Y T  EA  A    N
Sbjct: 5   VKNLPASLTEAELKEHFSKHG-GEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFN 63

Query: 322 TT 323
            T
Sbjct: 64  NT 65

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +++ N+     E +L ++F   G V   K+IR   ++    +GF+   +   AAMAI SL
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 115 NGRHLFGQPIKVNW 128
           NG  L  + ++V++
Sbjct: 64  NGYRLGDKILQVSF 77

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

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 7/49 (14%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK-----GFGFVRY 307
           T++VGNL   +T+ +L R F     GV+E+V ++R        + FV++
Sbjct: 4   TLFVGNLEITITEEELRRAFERY--GVVEDVDIKRPPRGQGNAYAFVKF 50

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYGFIHY 101
           R +YVG I    T   L++ F   G +E   L  R D  +YGF+ Y
Sbjct: 3   RVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTY 48

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAI 317
           VY+G L     + D+ R F   G G I E+ ++   GFGFV +    +A  A+
Sbjct: 2   VYIGRLPYRARERDVERFFK--GYGRIREINLKN--GFGFVEFEDPRDADDAV 50

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L P  + A L   F  + +    R+ +D      R + ++ + + + AQ+A   L
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIR--RIDYD----PGRNYAYIEYESIEAAQAAKEAL 54

Query: 204 TGKWLGSRQIRC 215
            G  LG    R 
Sbjct: 55  RGFPLGGPGRRL 66

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

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           ++VG +    +   L+  F   G +            Y +I Y    +A  A  +L G  
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN--YAYIEYESIEAAQAAKEALRGFP 58

Query: 119 L--FGQPIKVNWA 129
           L   G+ ++V++A
Sbjct: 59  LGGPGRRLRVDFA 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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  L   VT   L   F  +      R++   ++G+ +G  +V + N+  A  A+  +
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLV-TNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 204 TGKWLGSRQI 213
            G  +  + I
Sbjct: 64  DGTEIKEKTI 73

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 10/58 (17%)

Query: 161 CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
           CF VY           + TG S+G+GFV +  +  A  A  +L GK LG   +   W 
Sbjct: 29  CFLVY----------SEVTGHSKGYGFVEYMKKDSASKARLELLGKQLGESTLFAQWM 76

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ---RDKGFGFVRYSTHAEAALAIQMGN 321
           ++V NL   VT  DL   F   G  +  +V+     R KGFG V + +  +A  AI+M N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

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

>gnl|CDD|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 = 37.2 bits (87), Expect = 0.001
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 61  VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---YGFIHYFDRRSAAMAILSLNGR 117
           V N+  + T+  L+E+FS  G V+  +L +K   S   + F+ +  ++ A  A+ +L   
Sbjct: 5   VRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

Query: 118 HLFGQPIKVNWA 129
           HL+G+ + + +A
Sbjct: 65  HLYGRHLVLEYA 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|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 146 VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           V +LSP V++  L   FS +     A V+ D + GRS G G V F  +  AQ+AI 
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFSRKPGAQAAIK 58

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 22/79 (27%)

Query: 144 IFVG----DLSPEVTDATLFACFS----VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
           +FVG    DL  +     L   F     +Y    + R+M D  +G +RG+ FV++ N++ 
Sbjct: 4   VFVGKIPRDLFED----ELVPLFEKAGPIY----ELRLMMD-FSGLNRGYAFVTYTNKEA 54

Query: 196 AQSAINDLTGKWLGSRQIR 214
           AQ A+     K L + +IR
Sbjct: 55  AQRAV-----KQLHNYEIR 68

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

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 6/58 (10%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYG------FIHYFDRRSAAMA 110
           V V N+  Q TE  ++ +F   G +E  +L   D           F+ Y D     +A
Sbjct: 2   VQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVA 59

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

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
           IFVG L+PE T+  +   F  +       +  D KT + RGF F++F+ + 
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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 45/261 (17%), Positives = 82/261 (31%), Gaps = 42/261 (16%)

Query: 24  QQQSLYHPGLLAAP--QIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSST- 80
            + ++  P  L A    I P+P             R +YVG I  +  E  + + F+   
Sbjct: 142 PRPAMTDPEKLLAEGSIITPLPVLPYQQQATRQA-RRLYVGGIPPEFVEEAVVDFFNDLM 200

Query: 81  ----------GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV---- 126
                     G       I K+K+ + F+ +     A  A ++L+        +K+    
Sbjct: 201 IATGYHKAEDGKHVSSVNINKEKN-FAFLEFRTVEEATFA-MALDSIIYSNVFLKIRRPH 258

Query: 127 ----------------------NWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSV 164
                                 N                I++G+L   + +  +      
Sbjct: 259 DYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLES 318

Query: 165 YPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGN 224
           +       ++ D  TG S+G+ F  +++      AI  L GK  G  ++    A  GA  
Sbjct: 319 FGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQ 378

Query: 225 NEDKQSSDAKSVVELTNGSSE 245
                S+    V  L    S+
Sbjct: 379 ATIDTSNGMAPVTLLAKALSQ 399

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 13/79 (16%)

Query: 60  YVGNIHTQVTEPLLQ----EVFSSTGPVEGCKL---IRKDKSSYG--FIHYFDRRSAAMA 110
           Y+ N++ ++ +  L+     +FS  GPV    L     K     G  F+ + D  SA  A
Sbjct: 3   YINNLNEKIKKDELKRSLYALFSQFGPV----LDIVASKTLKMRGQAFVVFKDVESATNA 58

Query: 111 ILSLNGRHLFGQPIKVNWA 129
           + +L G   + +P+++ +A
Sbjct: 59  LRALQGFPFYDKPMRIQYA 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|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +Y+GN+    +   L+ +F  +  P  G  L+   KS Y F+   D   A  AI +L+G+
Sbjct: 4   LYIGNLSENASPLDLESIFKDSKIPFSGPFLV---KSGYAFVDCPDESWAMKAIDTLSGK 60

Query: 118 -HLFGQPIKV 126
             L G+ I+V
Sbjct: 61  VELHGKVIEV 70

This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           RSV+V       +E  L + FS+ GPV    ++ KDK  Y  +  FD +     +LS   
Sbjct: 3   RSVFVSGFKRGTSEEQLMDYFSAFGPVMNV-IMDKDKGVYAIVE-FDSKEGVDKVLSEPQ 60

Query: 117 RHLFGQPIKV 126
             L G  ++V
Sbjct: 61  HTLNGHRLRV 70

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAAMAILSL 114
           R++++GN+    T   L+E F   G +     I+K     +Y FI Y D  S   A+  +
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDID-IKKQGGNPAYAFIQYADIASVVKAMRKM 61

Query: 115 NGRHLFGQPIKV 126
           +G +L    +K+
Sbjct: 62  DGEYLGNNRVKL 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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI--N 201
           +FVG+L  E  +  L+  F         R++ D KT   +GF +V F+++   + A+  N
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 202 DLTGKWLGSRQIR 214
           +     +  R++R
Sbjct: 62  EKKFPPMLPRELR 74

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 8/49 (16%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRY 307
           V+VGNL  E  +  L R F   G   IE VR+ RD      KGF +V++
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGG--IEYVRIVRDPKTNVGKGFAYVQF 48

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|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 10/65 (15%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGA--------GVIEEVRVQRDK--GFGFVRYSTHAEAA 314
           +Y+ NL P+ TQL+L   F   G            +E      K    GF  + +H EA 
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62

Query: 315 LAIQM 319
            A+ +
Sbjct: 63  EALAL 67

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           VYVGN+   + E  ++++F   GP+    L +      Y FI + D R A  AI   +G 
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGY 61

Query: 118 HLFGQPIKV 126
              GQ ++V
Sbjct: 62  DFDGQRLRV 70

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 19/64 (29%), Positives = 31/64 (48%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           V + N+   VT  +L +VFS  G VE   +  K+      + +    SA  A  +LNGR+
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 119 LFGQ 122
           ++  
Sbjct: 64  IYDG 67

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

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 14/79 (17%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-------KGFGFVRYSTHAEAALA 316
           T Y+GNL  +VT+ D+   F  L    +  VR+ R+       +GFG+  +        A
Sbjct: 3   TAYLGNLPYDVTEEDIKEFFRGLN---VSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA 59

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           + + + +    L  ++++V
Sbjct: 60  LSLNDES----LKNRRIRV 74

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

>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein MRN1 and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 10/59 (16%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRY---ST----HAEAAL 315
           TVY+GNL P  T  +L  H  S   G IE VR+  +K   F+ +   S     H++A L
Sbjct: 3   TVYLGNLPPNTTVKELLSHVRS---GPIENVRILPEKNCAFISFLDPSAATAFHSDAIL 58

This subgroup corresponds to the RRM1 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

>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 = 36.3 bits (84), Expect = 0.002
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 10/78 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSL-----GAGVIEEVRVQRDKGFGFVRYSTHAEAALA-I 317
           +++VG+L+PEV + DL   F S       A ++ +      +G+GFVR+S   +   A I
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 318 QMGNTTQSSYLFGKQMKV 335
           +M    Q  Y  G+ M++
Sbjct: 63  EM----QGVYCGGRPMRI 76

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAI 317
           T+++G+L P + +  ++  F   G      V++ R+K      G+GFV ++TH  A  A+
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTS--VKIIRNKQTGKSAGYGFVEFATHEAAEQAL 58

Query: 318 QMGNTTQ 324
           Q  N   
Sbjct: 59  QSLNGKP 65

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

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 8/59 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           ++V NL+P+  +  L + F   GA  +  V+V RD      KGFGFV  + + EAA+AI
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGA--VNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR---KDKS-SYGFIHYFDRRSAAMAIL 112
           ++++V  ++   TE  L+  F   GP++  +L+R     K   Y FI +   R    A  
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 113 SLNGRHLFGQPIKV 126
             +G+ + G+ + V
Sbjct: 62  YADGKKIDGRRVLV 75

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

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAI 317
           ++VG L  +V + DL  HF     G +E+  V  DK      GFGFV +  H  A  A 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQF--GPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           ++VG +   VTE  L+E FS  G VE  +++  DK +     + F+ + D       +L 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIV-TDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 114 ----LNGRHL 119
               +NG  +
Sbjct: 61  KYHTINGHRV 70

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 6/57 (10%)

Query: 264 TVYVG----NLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           T+YVG      A +  +  L RHF   G   IE++RV   KG  FVRY   A A  A
Sbjct: 3   TLYVGGIKAGSALKQIEEILRRHFGEWGD--IEDIRVLPSKGIAFVRYKYRASAEFA 57

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV---QRDKGFGFVRYSTHAEAALAI 317
            +YVGNL  ++ + D+   F+  G   I+ + +   +R   F FV +    +A  A+
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGP--IKAIDLKNRRRGPPFAFVEFEDPRDAEDAV 55

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 9/71 (12%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---YGFIHYFDRRSAAMAILSL 114
           +V+V N+   V E  L+++FS  G +   +L++  K     Y ++  F+   +    L L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVE-FENEESVQEALKL 59

Query: 115 -----NGRHLF 120
                 GR +F
Sbjct: 60  DRELIKGRPMF 70

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 8/64 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR------DKGFGFVRYSTHAEAALAI 317
           TVYV  L    T   L   F   G   +  V + R       KGF F+ + T  EA  A 
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYG--TVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58

Query: 318 QMGN 321
           +  N
Sbjct: 59  KHLN 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 36.7 bits (84), Expect = 0.002
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+++  L P  TD  L      Y      + + D+ T + +G+GFV F +   AQ A++ 
Sbjct: 9   NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSA 68

Query: 203 L 203
           L
Sbjct: 69  L 69

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSSYG--FIHYFDRRSAAMAIL 112
           R+V+   +  ++    L+E FS+ G V   ++I  R  + S G  ++ + D  S  +AI 
Sbjct: 2   RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI- 60

Query: 113 SLNGRHLFGQPIKVNWAYASGQR 135
            L G+ + G PI V  + A   R
Sbjct: 61  GLTGQRVLGVPIIVQASQAEKNR 83

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. 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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 16/80 (20%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTH--AEAAL 315
           +VYVGN+    T  +L  HFH  G G +  V +  D      KGF ++ +S       AL
Sbjct: 1   SVYVGNVDYGATAEELEAHFH--GCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL 58

Query: 316 AIQMGNTTQSSYLFGKQMKV 335
           A+        S   G+Q+KV
Sbjct: 59  AL------DESLFRGRQIKV 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|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 11/29 (37%), Positives = 18/29 (62%)

Query: 187 FVSFRNQQDAQSAINDLTGKWLGSRQIRC 215
           +V FR ++DA+ A+NDL  +W   + I  
Sbjct: 72  YVKFRREEDAEKAVNDLNNRWFNGQPIYA 100

This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain. . Length = 104

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           ++VGNL  ++T+ +  + F   G     EV + + KGFGF++  + A A +A
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEP--GEVFINKGKGFGFIKLESRALAEIA 53

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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFV +L  +V    L   FS+  +   A +  D K G+SRG G V+F    +A  AI+  
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 204 TGKWLGSRQI 213
            G++L  R +
Sbjct: 62  NGQFLFDRPM 71

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.9 bits (82), Expect = 0.002
 Identities = 18/61 (29%), Positives = 29/61 (47%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+++  L P  TD  L      Y      + + D+ T + +G+GFV F +   AQ A+  
Sbjct: 3   NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62

Query: 203 L 203
           L
Sbjct: 63  L 63

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 7/65 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGF-----GFVRYSTHAEAALAIQM 319
           +YVGNL P VT+  L + F     G ++ V++  DK       GFV Y    +A +A+Q 
Sbjct: 1   LYVGNLDPRVTEDILKQIFQV--GGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQT 58

Query: 320 GNTTQ 324
            N  Q
Sbjct: 59  LNGRQ 63

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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 13/76 (17%)

Query: 144 IFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRS--RGFGFVSFRNQQDAQSAI 200
           +FVG+L+ + V+   L   FS Y      +++     G S  +G+GFV F N++DA++A+
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKY-----GKIL-----GISLHKGYGFVQFDNEEDARAAV 52

Query: 201 NDLTGKWLGSRQIRCN 216
               G+ +  +++  N
Sbjct: 53  AGENGREIAGQKLDIN 68

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 7/68 (10%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSS--YGFIHYFDRRSA----AMAI 111
           ++VG I    TE  L++ FS  G V+  K+I  +   S  YGF+ +  +  A    AM  
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 112 LSLNGRHL 119
           L+  G+ L
Sbjct: 65  LNFRGKKL 72

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

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 10/77 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
           T++VGNL P+VT+  +   F    AG + +V++ +D     K F FV +        A+ 
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQ--AGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMN 60

Query: 319 MGNTTQSSYLFGKQMKV 335
           + N  +   L+G+ + +
Sbjct: 61  LLNGIK---LYGRPLNI 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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 13/79 (16%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI----- 111
            ++YVG +  +VTE  L++ F   G +    ++ + +    F+ +  R +A  A      
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ--CAFVTFTTREAAEKAAERLFN 59

Query: 112 -LSLNGRHLFGQPIKVNWA 129
            L +NGR L     K+ W 
Sbjct: 60  KLIINGRRL-----KLKWG 73

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 180 GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR 214
           GR RGFG+  F ++     A++ L  + L +R+IR
Sbjct: 40  GRLRGFGYAEFEDRDSLLQALS-LNDESLKNRRIR 73

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|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 179 TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC 215
                G G V F +Q+D + A+  L G     R++R 
Sbjct: 33  DRDQEGEGVVEFTSQEDMERALRKLDGTEFRGRRVRV 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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 31/100 (31%), Positives = 40/100 (40%), Gaps = 3/100 (3%)

Query: 27  SLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC 86
           S Y P   AAP    I S    P         +  G    +V    L  +F   G VE  
Sbjct: 249 SRYRPAYEAAPLAPAISS--YGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERV 306

Query: 87  KLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV 126
           K   K+K     I   D   A +A+  LNG  LFG+P++V
Sbjct: 307 K-FMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRV 345

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). Length = 481

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 4/81 (4%)

Query: 144 IFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++GDL P + +  +   + S+     + +V+  + +G + G+ FV F +   AQ+A++ 
Sbjct: 2   LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS- 60

Query: 203 LTGKWL--GSRQIRCNWATKG 221
           L G  +   +R  + NWA+ G
Sbjct: 61  LNGTPIPNSNRTFKLNWASGG 81

This subgroup corresponds to the RRM1 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 81

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 16/50 (32%), Positives = 25/50 (50%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           IFVG +  +  +  L   F  Y       +M D+ +G+ RGF FV+F + 
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 52

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

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 10/61 (16%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ------RDKGFGFVRYSTH--AEAALA 316
           ++VGNL  ++T+ +L   F   G   + EVR+       R   FGFV +      +  LA
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGN--VLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA 63

Query: 317 I 317
            
Sbjct: 64  N 64

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

>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 18/33 (54%), Positives = 22/33 (66%), Gaps = 1/33 (3%)

Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           P  +D R+M  +KTG SRGF FV F + QDA S
Sbjct: 32  PQPADVRLM-KRKTGVSRGFAFVEFYHLQDATS 63

This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 87

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 17/47 (36%), Positives = 25/47 (53%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           IFVG +  +  +  L   F  Y       VM D+++G+ RGF FV+F
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +LS   ++ +L     V+   +  R+   Q  GR +G+ FV F + +DA+ A+N  
Sbjct: 4   LVVNNLSYSASEDSLQ---EVFEKATSIRI--PQNNGRPKGYAFVEFESAEDAKEALNSC 58

Query: 204 TGKWLGSRQIR 214
               +  R IR
Sbjct: 59  NNTEIEGRSIR 69

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 35.6 bits (81), Expect = 0.003
 Identities = 18/61 (29%), Positives = 29/61 (47%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+++  L P  TD  L      Y      + + D+ T + +G+GFV F +   AQ A+  
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 203 L 203
           L
Sbjct: 66  L 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHS-----LGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           +++VG+L P+V    L+  F        GA V+ + +    +G+GFVR+S  +E   A+ 
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALT 61

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           +YV NL    T+  L   F   G   +E V+  +D  + FV +    +A  A++  N  
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGE--VERVKKIKD--YAFVHFEERDDAVKAMEEMNGK 58

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 13/78 (16%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG 320
           +YV ++ P++++ D+   F + G      +  +    + KG+GF+ Y     A  AI   
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 321 NTTQSSYLF---GKQMKV 335
           N      LF   G+Q++V
Sbjct: 63  N------LFDLGGQQLRV 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 144 IFVGDLSPEVTDA---TLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           +FVG++   V+D     L        S    RV  D  TG+ + FGF  F + + A  A+
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWK--RVK-DPSTGKLKAFGFCEFEDPEGALRAL 59

Query: 201 NDLTGKWLGSRQI--RCNWATK 220
             L G  LG +++  + +  T+
Sbjct: 60  RLLNGLELGGKKLLVKVDAKTR 81

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           Q   +++G L+ E T   L  HF   G      V+ +   +R +GFGFV YS+  E   A
Sbjct: 1   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

Query: 317 I 317
           +
Sbjct: 61  M 61

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 8/62 (12%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
           T VY+  L P  T  DL +       G I   +   D      KG+GFV + +   A  A
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQP--FGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58

Query: 317 IQ 318
           I+
Sbjct: 59  IE 60

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           Q   +++G L+ E T   L  HF   G      V+ + + +R +GFGFV YS   E   A
Sbjct: 1   QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

Query: 317 I 317
           +
Sbjct: 61  M 61

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FVG+L   +T+  L   F  Y    D  +    + G+   + FV F N   A  A   
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLNLDMAHRAKVA 62

Query: 203 LTGKWLGSRQIRCNW 217
           ++G+++G  QI+  +
Sbjct: 63  MSGQYIGRNQIKIGY 77

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG++S   T   L   F  +    +   +        + + FV    +++A +AI  L
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEAL 54

Query: 204 TGKWLGSRQI 213
            GK +  R+I
Sbjct: 55  NGKEVKGRRI 64

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDAR-VMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           I+VG+L P  T   L   FS      + + V       +   + FV F  Q    +A+  
Sbjct: 7   IYVGNLDPTTTADQLLEFFS---QAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK- 62

Query: 203 LTGKWLGSRQIRCNWAT 219
           L G   G R ++ N + 
Sbjct: 63  LNGAMFGGRPLKVNHSN 79

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

>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKDKSSYGFIHY 101
           R +YVG I    T   L++ F   G +E C + +R D  SYGFI Y
Sbjct: 3   RVIYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRDDGDSYGFITY 48

This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA. . Length = 91

>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 = 35.3 bits (82), Expect = 0.004
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 10/78 (12%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV-----QRDKGFGFVRYSTHAEAALAI 317
           T + V N+  E T+ +L   F   G   ++ VR+        +GF FV + T  EA  A+
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQ--VKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58

Query: 318 QMGNTTQSSYLFGKQMKV 335
                 +S++L+G+ + +
Sbjct: 59  ---EALKSTHLYGRHLVL 73

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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI-RKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           +YVGN+ + V E  L+++F   G +   +L  R+    + F+ + D R A  A+   NG 
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNG- 60

Query: 118 HLFGQ 122
           + FGQ
Sbjct: 61  YDFGQ 65

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           VYVG I    TE  ++  FS  G +E   L+    +       FI  F    AA   L+L
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFIT-FKTEEAAKRALAL 59

Query: 115 NGRHLFGQPIKV 126
           +G  + G+ +KV
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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 7/72 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG +  +V +  L   F       + R+M D   G++RG+ FV +  + +A+ A+ +L
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVREL 62

Query: 204 T------GKWLG 209
                  G+ LG
Sbjct: 63  NNYEIRPGRLLG 74

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|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.9 bits (85), Expect = 0.004
 Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 5/59 (8%)

Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAK 234
               GRSRG+GF+ F + + A  A+     +WL    +                + D  
Sbjct: 82  GSTAGRSRGYGFMEFISHKYALMAL-----RWLNGHAVTVKKIIDAEIEWARLPNIDYN 135

This subgroup corresponds to the RRM4 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 = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	335
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.96
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.96
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.96
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.96
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.95
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.94
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.93
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.93
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.92
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.91
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.89
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.89
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.89
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.88
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.87
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.85
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.85
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.85
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.85
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.84
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.82
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.82
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.8
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.78
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.76
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.75
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.75
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.74
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.73
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.7
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.68
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.66
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.66
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.65
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.64
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.64
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.61
KOG0122	270	consensus Translation initiation factor 3, subunit	99.61
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.6
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.6
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.6
PLN03120	260	nucleic acid binding protein; Provisional	99.59
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.56
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.54
KOG0122	270	consensus Translation initiation factor 3, subunit	99.53
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.52
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.51
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.5
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.5
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.48
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.48
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.48
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.48
PLN03213	759	repressor of silencing 3; Provisional	99.47
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.47
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.46
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.46
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.45
PLN03121	243	nucleic acid binding protein; Provisional	99.45
smart00362	72	RRM_2 RNA recognition motif.	99.45
PLN03120	260	nucleic acid binding protein; Provisional	99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.42
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.4
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.38
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.38
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.37
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.37
smart00362	72	RRM_2 RNA recognition motif.	99.37
smart00360	71	RRM RNA recognition motif.	99.35
PLN03213	759	repressor of silencing 3; Provisional	99.35
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.35
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.34
smart00360	71	RRM RNA recognition motif.	99.34
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.33
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.33
PLN03121	243	nucleic acid binding protein; Provisional	99.32
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.3
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.29
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.29
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.28
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.27
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.26
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.25
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.24
smart00361	70	RRM_1 RNA recognition motif.	99.23
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.22
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.19
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.12
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.11
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.11
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.1
smart00361	70	RRM_1 RNA recognition motif.	99.08
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.04
KOG0226	290	consensus RNA-binding proteins [General function p	99.01
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.01
KOG0151	877	consensus Predicted splicing regulator, contains R	98.97
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.92
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.92
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.91
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.81
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.79
KOG4210	285	consensus Nuclear localization sequence binding pr	98.79
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.76
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.74
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.71
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.7
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.69
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.64
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.64
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.6
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.59
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.57
KOG4210	285	consensus Nuclear localization sequence binding pr	98.57
KOG0226	290	consensus RNA-binding proteins [General function p	98.44
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.44
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.42
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.41
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.41
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.37
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.37
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.3
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.25
KOG0151	877	consensus Predicted splicing regulator, contains R	98.23
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.18
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.14
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.04
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.92
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.88
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.79
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.74
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.71
KOG3152	278	consensus TBP-binding protein, activator of basal	97.64
KOG3152	278	consensus TBP-binding protein, activator of basal	97.63
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.57
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.54
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.51
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.5
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.45
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.42
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.36
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.36
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.35
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.28
KOG2314	698	consensus Translation initiation factor 3, subunit	97.27
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.24
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.16
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.12
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.02
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.0
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.97
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.85
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.78
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.63
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.62
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.6
KOG2314	698	consensus Translation initiation factor 3, subunit	96.37
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.15
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	95.86
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.81
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.63
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.61
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.58
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.39
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.36
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.06
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.97
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.96
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.75
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.62
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.36
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.33
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.12
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.01
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.0
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.93
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	93.55
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.36
KOG2135	526	consensus Proteins containing the RNA recognition	93.17
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	93.11
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.73
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.5
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.21
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	91.95
KOG2135	526	consensus Proteins containing the RNA recognition	91.09
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	91.08
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.88
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.53
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	88.0
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	84.64
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	84.02
KOG2318	650	consensus Uncharacterized conserved protein [Funct	80.7

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=4.2e-46  Score=330.34  Aligned_cols=272  Identities=27%  Similarity=0.455  Sum_probs=215.7

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ..+|||+|||.++++++|+++|+.||+|.+|++++++    ++|||||+|.+.++|.+|++.|||..+.|++|+|.++.+
T Consensus         3 ~~~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~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            5689999999999999999999999999999999875    458999999999999999999999999999999999865


Q ss_pred             CCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-
Q 019811          132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS-  210 (335)
Q Consensus       132 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g-  210 (335)
                      ...   .....+|||+|||..+++++|.++|+.||.|..+.++++..++.++|||||+|.+.++|.+|++.|+|..+.| 
T Consensus        83 ~~~---~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~  159 (352)
T TIGR01661        83 SSD---SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGC  159 (352)
T ss_pred             ccc---ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCC
Confidence            432   2345689999999999999999999999999999999988788899999999999999999999999998876 


Q ss_pred             -eeeEEEEccCCCCCCCCCCCcc------cccch-------------hcc---------------------------CCC
Q 019811          211 -RQIRCNWATKGAGNNEDKQSSD------AKSVV-------------ELT---------------------------NGS  243 (335)
Q Consensus       211 -~~l~v~~~~~~~~~~~~~~~~~------~~~~~-------------~~~---------------------------~~~  243 (335)
                       ..|.|.|+..............      +....             ...                           ...
T Consensus       160 ~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (352)
T TIGR01661       160 TEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQH  239 (352)
T ss_pred             ceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccccc
Confidence             6788888865542111100000      00000             000                           000


Q ss_pred             C-cCCcCC----------CCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc------cceEEEE
Q 019811          244 S-EDGKET----------TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVR  306 (335)
Q Consensus       244 ~-~~~~~~----------~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~------~g~afV~  306 (335)
                      . ......          .....+.....+.+|||+|||+++++++|+++|++||  .|.++++..+      +|+|||+
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG--~v~~v~i~~d~~t~~skG~aFV~  317 (352)
T TIGR01661       240 AAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFG--AVQNVKIIRDLTTNQCKGYGFVS  317 (352)
T ss_pred             ccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCC--CeEEEEEeEcCCCCCccceEEEE
Confidence            0 000000          0000111122345799999999999999999999999  5888887654      7999999


Q ss_pred             eCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          307 YSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       307 f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      |.+.++|.+|+..|||.   .|+||.|+|
T Consensus       318 F~~~~~A~~Ai~~lnG~---~~~gr~i~V  343 (352)
T TIGR01661       318 MTNYDEAAMAILSLNGY---TLGNRVLQV  343 (352)
T ss_pred             ECCHHHHHHHHHHhCCC---EECCeEEEE
Confidence            99999999999999999   999999986

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

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=9.2e-42  Score=267.18  Aligned_cols=275  Identities=29%  Similarity=0.448  Sum_probs=223.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCC----CeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~----g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ......|.|.-||..+|++|++.+|...|+|+++++++|+.+    ||+||.|.+++||++|+..|||..+..++|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            344556889999999999999999999999999999999854    7999999999999999999999999999999999


Q ss_pred             eccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       129 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      +.+.+.   .....+|||++||..+|..||..+|++||.|..-+|+.|..+|.++|.+||.|+..++|++|+..|||..-
T Consensus       118 ARPSs~---~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P  194 (360)
T KOG0145|consen  118 ARPSSD---SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKP  194 (360)
T ss_pred             ccCChh---hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCC
Confidence            987654   34446899999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CC--eeeEEEEccCCCCCCCCCCCccc---------------ccchhc-------------cCCCCcCCcCCCCCCCCCC
Q 019811          209 GS--RQIRCNWATKGAGNNEDKQSSDA---------------KSVVEL-------------TNGSSEDGKETTNTEAPEN  258 (335)
Q Consensus       209 ~g--~~l~v~~~~~~~~~~~~~~~~~~---------------~~~~~~-------------~~~~~~~~~~~~~~~~~~~  258 (335)
                      .|  ..|.|.|+..+............               .....+             ++..............+..
T Consensus       195 ~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~  274 (360)
T KOG0145|consen  195 SGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGG  274 (360)
T ss_pred             CCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCC
Confidence            54  67999999876543322111110               000000             0000000011112222333


Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc------cceEEEEeCCHHHHHHHHHhhcCCCcccccCcc
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ  332 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~  332 (335)
                      .....+|||.||.++..|.-|..+|.+||.  +..|++.++      +|++||++.+.++|.-|+..|||+   .+++|.
T Consensus       275 ~~~g~ciFvYNLspd~de~~LWQlFgpFGA--v~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy---~lg~rv  349 (360)
T KOG0145|consen  275 PGGGWCIFVYNLSPDADESILWQLFGPFGA--VTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGY---RLGDRV  349 (360)
T ss_pred             CCCeeEEEEEecCCCchHhHHHHHhCcccc--eeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCc---cccceE
Confidence            445689999999999999999999999995  888888876      799999999999999999999999   999998


Q ss_pred             ccC
Q 019811          333 MKV  335 (335)
Q Consensus       333 l~v  335 (335)
                      |.|
T Consensus       350 LQV  352 (360)
T KOG0145|consen  350 LQV  352 (360)
T ss_pred             EEE
Confidence            864

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=9.4e-42  Score=286.21  Aligned_cols=237  Identities=24%  Similarity=0.413  Sum_probs=208.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCcccc-CceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLF-GQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~-g~~l~v~  127 (335)
                      +...+.|||+.||.++.|++|.-+|++.|.|.+++++.++    ++|||||.|++.+.|.+|++.||+..|. |+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            4567889999999999999999999999999999999984    5799999999999999999999999886 8999999


Q ss_pred             eeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          128 WAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKT-GRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       128 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      .+.         .++.|||+|+|.++++++|.+.+++.+ .|..|.+..++.+ .+++|||||+|.+...|..|.+.|-.
T Consensus       160 ~Sv---------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~  230 (506)
T KOG0117|consen  160 VSV---------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMP  230 (506)
T ss_pred             Eee---------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccC
Confidence            875         346899999999999999999999987 4777777766533 47899999999999999999887743


Q ss_pred             --ceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHh
Q 019811          206 --KWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHF  283 (335)
Q Consensus       206 --~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f  283 (335)
                        ..++|+.+.|.|+.+.......                              .....+.|||+||+.++|+|.|+++|
T Consensus       231 g~~klwgn~~tVdWAep~~e~ded------------------------------~ms~VKvLYVRNL~~~tTeE~lk~~F  280 (506)
T KOG0117|consen  231 GKIKLWGNAITVDWAEPEEEPDED------------------------------TMSKVKVLYVRNLMESTTEETLKKLF  280 (506)
T ss_pred             CceeecCCcceeeccCcccCCChh------------------------------hhhheeeeeeeccchhhhHHHHHHHH
Confidence              4689999999999886543322                              22234789999999999999999999


Q ss_pred             hhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          284 HSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       284 ~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +.||  .+..|+..+|  +|||+|.+.++|.+||+.+||+   .++|..|.|
T Consensus       281 ~~~G--~veRVkk~rD--YaFVHf~eR~davkAm~~~ngk---eldG~~iEv  325 (506)
T KOG0117|consen  281 NEFG--KVERVKKPRD--YAFVHFAEREDAVKAMKETNGK---ELDGSPIEV  325 (506)
T ss_pred             Hhcc--ceEEeecccc--eeEEeecchHHHHHHHHHhcCc---eecCceEEE
Confidence            9999  6999988877  9999999999999999999999   999998875

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=2e-40  Score=300.35  Aligned_cols=167  Identities=22%  Similarity=0.404  Sum_probs=150.5

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||+++++++|+++|+.||+|.+|++..++    ++|||||+|.+.++|.+|++.|||..+.|+.|+|.+..
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            35789999999999999999999999999999998764    57999999999999999999999999999999998754


Q ss_pred             cCCCc--------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 019811          131 ASGQR--------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND  202 (335)
Q Consensus       131 ~~~~~--------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  202 (335)
                      .....        ......++|||+|||+++++++|+++|+.||.|.++.+.+++.++.++|||||+|.+.++|.+|+..
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            33211        1123347899999999999999999999999999999999988899999999999999999999999


Q ss_pred             hCCceeCCeeeEEEEccCC
Q 019811          203 LTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       203 l~~~~~~g~~l~v~~~~~~  221 (335)
                      ||+..++|+.|+|.++..+
T Consensus       266 mNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             hCCCeeCCeEEEEEecCCC
Confidence            9999999999999998753

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.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=9.3e-41  Score=304.81  Aligned_cols=270  Identities=19%  Similarity=0.231  Sum_probs=207.0

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHH--hCCccccCceeEEeeeccC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILS--LNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~--l~~~~~~g~~l~v~~~~~~  132 (335)
                      ++++|||+|||.++++++|+++|+.||.|.+|+++++  ++||||+|.+.++|.+|+..  +++..+.|+.|+|.|+..+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~--k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG--KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC--CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            4689999999999999999999999999999999865  47999999999999999986  4788999999999998654


Q ss_pred             CCccC---------CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 019811          133 GQRED---------TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL  203 (335)
Q Consensus       133 ~~~~~---------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  203 (335)
                      .....         ......|+|.||+..+++++|+++|+.||.|.++.+.++.    .+++|||+|.+.++|.+|+..|
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~~~afVef~~~~~A~~A~~~L  154 (481)
T TIGR01649        79 EIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NVFQALVEFESVNSAQHAKAAL  154 (481)
T ss_pred             ccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----CceEEEEEECCHHHHHHHHHHh
Confidence            31111         1122478999999999999999999999999999988653    2468999999999999999999


Q ss_pred             CCceeCC--eeeEEEEccCCCCCC-----CCCCCccccc------ch------hcc------------CCC--C----c-
Q 019811          204 TGKWLGS--RQIRCNWATKGAGNN-----EDKQSSDAKS------VV------ELT------------NGS--S----E-  245 (335)
Q Consensus       204 ~~~~~~g--~~l~v~~~~~~~~~~-----~~~~~~~~~~------~~------~~~------------~~~--~----~-  245 (335)
                      +|..+.|  +.|+|.|++......     ..+.-..+..      ..      ...            .+.  .    . 
T Consensus       155 ng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  234 (481)
T TIGR01649       155 NGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAP  234 (481)
T ss_pred             cCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCc
Confidence            9999854  589999987644210     0000000000      00      000            000  0    0 


Q ss_pred             --C--CcCC--------------------CCCCCCCCCCCCCeEEEcCCCc-ccCHHHHHHHhhhcCCeeeEEEEEecc-
Q 019811          246 --D--GKET--------------------TNTEAPENNPQYTTVYVGNLAP-EVTQLDLHRHFHSLGAGVIEEVRVQRD-  299 (335)
Q Consensus       246 --~--~~~~--------------------~~~~~~~~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~i~~v~~~~~-  299 (335)
                        .  ...+                    .........+++++|||+|||+ .+++++|+++|+.||  .|..|+++++ 
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG--~V~~vki~~~~  312 (481)
T TIGR01649       235 LAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYG--NVERVKFMKNK  312 (481)
T ss_pred             ccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcC--CeEEEEEEeCC
Confidence              0  0000                    0000011234668999999998 699999999999999  5889988876 


Q ss_pred             cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 ~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +|+|||+|.+.++|.+|+..|||.   .|+|++|+|
T Consensus       313 ~g~afV~f~~~~~A~~Ai~~lng~---~l~g~~l~v  345 (481)
T TIGR01649       313 KETALIEMADPYQAQLALTHLNGV---KLFGKPLRV  345 (481)
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCC---EECCceEEE
Confidence            699999999999999999999999   999999975

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).

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

Probab=100.00  E-value=5.7e-41  Score=313.90  Aligned_cols=241  Identities=32%  Similarity=0.560  Sum_probs=208.6

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      +|||+|||.++||++|+++|++||.|.+|++.+++.    +|||||+|.+.++|.+|++.+++..+.|+.|+|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            699999999999999999999999999999988653    5899999999999999999999999999999999986433


Q ss_pred             CccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       134 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      .. ......+|||+|||.++++++|+++|+.||.|.++.+..+ .+|+++|||||+|.+.++|.+|++.+++..+.|+.|
T Consensus        82 ~~-~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i  159 (562)
T TIGR01628        82 SL-RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEV  159 (562)
T ss_pred             cc-cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceE
Confidence            22 2234568999999999999999999999999999999988 467899999999999999999999999999999999


Q ss_pred             EEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEE
Q 019811          214 RCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE  293 (335)
Q Consensus       214 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~  293 (335)
                      .|.....+....                              .......++|||+|||.++++++|+++|+.||  .|.+
T Consensus       160 ~v~~~~~~~~~~------------------------------~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG--~i~~  207 (562)
T TIGR01628       160 YVGRFIKKHERE------------------------------AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFG--EITS  207 (562)
T ss_pred             EEeccccccccc------------------------------cccccCCCeEEEeCCCCcCCHHHHHHHHHhcC--CEEE
Confidence            997654432211                              00112236799999999999999999999999  5778


Q ss_pred             EEEecc-----cceEEEEeCCHHHHHHHHHhhcCCCccccc----CccccC
Q 019811          294 VRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLF----GKQMKV  335 (335)
Q Consensus       294 v~~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~----g~~l~v  335 (335)
                      +.+.++     +|+|||+|.+.++|.+|++.|+|.   .+.    |+.|.|
T Consensus       208 ~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~---~i~~~~~g~~l~v  255 (562)
T TIGR01628       208 AAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGK---KIGLAKEGKKLYV  255 (562)
T ss_pred             EEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCc---EecccccceeeEe
Confidence            877644     689999999999999999999999   888    777653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=100.00  E-value=3.2e-40  Score=301.32  Aligned_cols=271  Identities=18%  Similarity=0.235  Sum_probs=210.6

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEeeecc
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWAYA  131 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~~~  131 (335)
                      ....+|+|+||++.+|+++|+++|+.||.|.+|+++++..+++|||+|.+.++|.+|++.|||..|.|  ++|+|.|+..
T Consensus        94 ~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~  173 (481)
T TIGR01649        94 NKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKP  173 (481)
T ss_pred             CceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecC
Confidence            34457999999999999999999999999999999888777899999999999999999999999965  4788888753


Q ss_pred             CCC--------------------cc-------------------------------------------------------
Q 019811          132 SGQ--------------------RE-------------------------------------------------------  136 (335)
Q Consensus       132 ~~~--------------------~~-------------------------------------------------------  136 (335)
                      ...                    +.                                                       
T Consensus       174 ~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (481)
T TIGR01649       174 TRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRP  253 (481)
T ss_pred             CCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcc
Confidence            110                    00                                                       


Q ss_pred             -----------------CCCCcceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHH
Q 019811          137 -----------------DTSGHFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS  198 (335)
Q Consensus       137 -----------------~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~  198 (335)
                                       ...++++|||+|||. .+++++|+++|+.||.|.+++++++     .+|+|||+|.+.++|..
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~-----~~g~afV~f~~~~~A~~  328 (481)
T TIGR01649       254 AYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN-----KKETALIEMADPYQAQL  328 (481)
T ss_pred             cccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC-----CCCEEEEEECCHHHHHH
Confidence                             011346899999998 6999999999999999999999865     25899999999999999


Q ss_pred             HHHHhCCceeCCeeeEEEEccCCCCCCCCCCCccccc--chhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCH
Q 019811          199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS--VVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQ  276 (335)
Q Consensus       199 a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~  276 (335)
                      |+..|++..+.|+.|+|.+++................  ..+.......+...+.........+++.+|||+|||..+++
T Consensus       329 Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~te  408 (481)
T TIGR01649       329 ALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSE  408 (481)
T ss_pred             HHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCH
Confidence            9999999999999999999866543222111000000  01111111111111111111223457789999999999999


Q ss_pred             HHHHHHhhhcCCeeeEEEEEecc----cceEEEEeCCHHHHHHHHHhhcCCCcccccCcc
Q 019811          277 LDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ  332 (335)
Q Consensus       277 ~~l~~~f~~~G~~~i~~v~~~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~  332 (335)
                      ++|+++|+.||...+..+++...    +++|||+|.+.++|.+|+..|||+   .|+|+.
T Consensus       409 e~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~---~l~~~~  465 (481)
T TIGR01649       409 EDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHH---QLNEPN  465 (481)
T ss_pred             HHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCC---ccCCCC
Confidence            99999999999545788887644    589999999999999999999999   999885

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).

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

Probab=100.00  E-value=6.7e-41  Score=313.43  Aligned_cols=258  Identities=30%  Similarity=0.479  Sum_probs=215.5

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ...+|||+|||.++++++|+++|+.||.|.+|++..+.   ++|||||+|.+.++|.+|++.+||..+.|+.|.|.....
T Consensus        87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628        87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccc
Confidence            45679999999999999999999999999999998764   579999999999999999999999999999999987765


Q ss_pred             CCCcc--CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          132 SGQRE--DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       132 ~~~~~--~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      +..+.  .....++|||+|||.++|+++|+++|+.||.|.++.+.++ .++.++|||||+|.+.++|.+|++.+++..+.
T Consensus       167 ~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~  245 (562)
T TIGR01628       167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG  245 (562)
T ss_pred             ccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEEC-CCCCcccEEEEEECCHHHHHHHHHHhCCcEec
Confidence            54432  3344568999999999999999999999999999999988 46789999999999999999999999999999


Q ss_pred             ----CeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhh
Q 019811          210 ----SRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHS  285 (335)
Q Consensus       210 ----g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~  285 (335)
                          |+.+.|.++..+........       ......          ...........+|||+||+..+++++|+++|+.
T Consensus       246 ~~~~g~~l~v~~a~~k~er~~~~~-------~~~~~~----------~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~  308 (562)
T TIGR01628       246 LAKEGKKLYVGRAQKRAEREAELR-------RKFEEL----------QQERKMKAQGVNLYVKNLDDTVTDEKLRELFSE  308 (562)
T ss_pred             ccccceeeEeecccChhhhHHHHH-------hhHHhh----------hhhhhcccCCCEEEEeCCCCccCHHHHHHHHHh
Confidence                99999988765443211000       000000          000011223478999999999999999999999


Q ss_pred             cCCeeeEEEEEecc-----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          286 LGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       286 ~G~~~i~~v~~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ||  .|.++++..+     +|+|||+|.+.++|.+|+..|||.   .|+|++|.|
T Consensus       309 ~G--~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~---~~~gk~l~V  358 (562)
T TIGR01628       309 CG--EITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGR---MLGGKPLYV  358 (562)
T ss_pred             cC--CeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCC---eeCCceeEE
Confidence            99  5888888654     699999999999999999999999   999999875

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=100.00  E-value=1.5e-40  Score=300.84  Aligned_cols=237  Identities=24%  Similarity=0.400  Sum_probs=199.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCcccc-CceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLF-GQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~-g~~l~v~~  128 (335)
                      +...++|||+|||.++++++|+++|++||.|.+++++++   +++|||||+|.+.++|.+|++.||+..+. |+.|.|.+
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            445689999999999999999999999999999999886   35799999999999999999999999886 78887776


Q ss_pred             eccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCC-ceeeEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-
Q 019811          129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPS-CSDARVM-WDQKTGRSRGFGFVSFRNQQDAQSAINDLTG-  205 (335)
Q Consensus       129 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~-v~~~~~~-~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~-  205 (335)
                      +.         ..++|||+|||.++++++|.+.|++++. +..+.+. .....++++|||||+|.+.++|.+|++.|+. 
T Consensus       135 S~---------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~g  205 (578)
T TIGR01648       135 SV---------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPG  205 (578)
T ss_pred             cc---------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhcc
Confidence            53         2468999999999999999999999864 4444333 2223457899999999999999999988864 


Q ss_pred             -ceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhh
Q 019811          206 -KWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFH  284 (335)
Q Consensus       206 -~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~  284 (335)
                       ..+.|+.|.|.|+.+......                              ......++|||+||+..+++++|+++|+
T Consensus       206 ki~l~Gr~I~VdwA~p~~~~d~------------------------------~~~~~~k~LfVgNL~~~~tee~L~~~F~  255 (578)
T TIGR01648       206 RIQLWGHVIAVDWAEPEEEVDE------------------------------DVMAKVKILYVRNLMTTTTEEIIEKSFS  255 (578)
T ss_pred             ceEecCceEEEEeecccccccc------------------------------cccccccEEEEeCCCCCCCHHHHHHHHH
Confidence             467899999999876432110                              1112237899999999999999999999


Q ss_pred             hc--CCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          285 SL--GAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       285 ~~--G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .|  |  .|..|.+.  +++|||+|.+.++|.+|++.|||.   .|+|+.|+|
T Consensus       256 ~f~~G--~I~rV~~~--rgfAFVeF~s~e~A~kAi~~lnG~---~i~Gr~I~V  301 (578)
T TIGR01648       256 EFKPG--KVERVKKI--RDYAFVHFEDREDAVKAMDELNGK---ELEGSEIEV  301 (578)
T ss_pred             hcCCC--ceEEEEee--cCeEEEEeCCHHHHHHHHHHhCCC---EECCEEEEE
Confidence            99  7  68888776  459999999999999999999999   999999986

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.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=100.00  E-value=7.4e-39  Score=293.29  Aligned_cols=277  Identities=25%  Similarity=0.393  Sum_probs=212.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ....++|||+|||..+++++|+++|+.||.|.+|+++.++    ++|||||+|.+.++|.+|+. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3457899999999999999999999999999999999864    46899999999999999995 899999999999987


Q ss_pred             eccCCCc---------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHH
Q 019811          129 AYASGQR---------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA  199 (335)
Q Consensus       129 ~~~~~~~---------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  199 (335)
                      +......         ......++|||+|||..+++++|.++|+.||.|..+.++++..+|.++|||||+|.+.++|.+|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence            6432211         1112357899999999999999999999999999999999988889999999999999999999


Q ss_pred             HHHhCCceeCCeeeEEEEccCCCCCCCCCCC---------ccc---------------------ccchhccCC-------
Q 019811          200 INDLTGKWLGSRQIRCNWATKGAGNNEDKQS---------SDA---------------------KSVVELTNG-------  242 (335)
Q Consensus       200 ~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~---------~~~---------------------~~~~~~~~~-------  242 (335)
                      +..|+|..+.|+.|.|.|+............         ...                     ....+....       
T Consensus       245 ~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  324 (457)
T TIGR01622       245 LEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQK  324 (457)
T ss_pred             HHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcc
Confidence            9999999999999999997532211100000         000                     000000000       


Q ss_pred             CCcCCc----------------CCCCCCC--CCCCCCCCeEEEcCCCcccC----------HHHHHHHhhhcCCeeeEEE
Q 019811          243 SSEDGK----------------ETTNTEA--PENNPQYTTVYVGNLAPEVT----------QLDLHRHFHSLGAGVIEEV  294 (335)
Q Consensus       243 ~~~~~~----------------~~~~~~~--~~~~~~~~~l~v~nlp~~~t----------~~~l~~~f~~~G~~~i~~v  294 (335)
                      ....+.                .......  .......++|+|.||....+          .+||++.|++||  .|..|
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G--~v~~v  402 (457)
T TIGR01622       325 LQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYG--GVVHI  402 (457)
T ss_pred             ccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcC--CeeEE
Confidence            000000                0000000  00234568999999965543          368999999999  47777


Q ss_pred             EEe--cccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          295 RVQ--RDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       295 ~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .+.  ...|++||+|.+.++|.+|+..|||+   .|+|+.|.+
T Consensus       403 ~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr---~f~gr~i~~  442 (457)
T TIGR01622       403 YVDTKNSAGKIYLKFSSVDAALAAFQALNGR---YFGGKMITA  442 (457)
T ss_pred             EEeCCCCceeEEEEECCHHHHHHHHHHhcCc---ccCCeEEEE
Confidence            775  44799999999999999999999999   999999874

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=2e-38  Score=294.43  Aligned_cols=269  Identities=17%  Similarity=0.250  Sum_probs=206.4

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhcc------------CCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSST------------GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHL  119 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~------------G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~  119 (335)
                      .....++|||+|||.++|+++|.++|..+            +.|..+.+  .+.+|||||+|.+.++|..|+ .|+|..|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~--~~~kg~afVeF~~~e~A~~Al-~l~g~~~  247 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI--NKEKNFAFLEFRTVEEATFAM-ALDSIIY  247 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE--CCCCCEEEEEeCCHHHHhhhh-cCCCeEe
Confidence            35567899999999999999999999975            24444544  345689999999999999999 5999999


Q ss_pred             cCceeEEeeeccCCCc--------------------------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEE
Q 019811          120 FGQPIKVNWAYASGQR--------------------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV  173 (335)
Q Consensus       120 ~g~~l~v~~~~~~~~~--------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~  173 (335)
                      .|+.|+|.........                          ......++|||+|||..+++++|.++|..||.|..+.+
T Consensus       248 ~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~  327 (509)
T TIGR01642       248 SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNL  327 (509)
T ss_pred             eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Confidence            9999999754322100                          01123468999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCC
Q 019811          174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNT  253 (335)
Q Consensus       174 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (335)
                      +++..+|.++|||||+|.+.++|..|+..|+|..++|+.|.|.++.................   ....  ..  .....
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~---~~~~--~~--~~~~~  400 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAP---VTLL--AK--ALSQS  400 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccc---cccc--cc--cchhh
Confidence            99988899999999999999999999999999999999999999865443221111100000   0000  00  00000


Q ss_pred             CCCCCCCCCCeEEEcCCCcc--c--------CHHHHHHHhhhcCCeeeEEEEEecc---------cceEEEEeCCHHHHH
Q 019811          254 EAPENNPQYTTVYVGNLAPE--V--------TQLDLHRHFHSLGAGVIEEVRVQRD---------KGFGFVRYSTHAEAA  314 (335)
Q Consensus       254 ~~~~~~~~~~~l~v~nlp~~--~--------t~~~l~~~f~~~G~~~i~~v~~~~~---------~g~afV~f~~~~~a~  314 (335)
                      .......+..+|+|.|+...  +        ..++|+++|++||  .|..|.++++         .|+|||+|.+.++|.
T Consensus       401 ~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G--~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~  478 (509)
T TIGR01642       401 ILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYG--PLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAE  478 (509)
T ss_pred             hccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcC--CeeEEEeeccCcCCCcCCCcceEEEEECCHHHHH
Confidence            00112345688999999642  1        2368999999999  5888888754         488999999999999


Q ss_pred             HHHHhhcCCCcccccCccccC
Q 019811          315 LAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       315 ~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +|+..|||.   .|+|+.|.|
T Consensus       479 ~A~~~lnGr---~~~gr~v~~  496 (509)
T TIGR01642       479 KAMEGMNGR---KFNDRVVVA  496 (509)
T ss_pred             HHHHHcCCC---EECCeEEEE
Confidence            999999999   999999864

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.2e-39  Score=256.77  Aligned_cols=228  Identities=41%  Similarity=0.727  Sum_probs=195.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ....+||||+||+.++||+-|..+|++.|+|.+++++.+                               .++|.|+...
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-------------------------------e~~v~wa~~p   51 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-------------------------------ELKVNWATAP   51 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh-------------------------------hhccccccCc
Confidence            356689999999999999999999999999999998877                               5677776554


Q ss_pred             CCccCC--CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          133 GQREDT--SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       133 ~~~~~~--~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      .....+  .....+||+.|.+.++-++|++.|.+||+|.+.+++||..+++++||+||.|.+.++|+.||..|+|.+|++
T Consensus        52 ~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~  131 (321)
T KOG0148|consen   52 GNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGR  131 (321)
T ss_pred             ccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeecc
Confidence            332222  224679999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCee
Q 019811          211 RQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGV  290 (335)
Q Consensus       211 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~  290 (335)
                      |.|+-+|+.++.......    .....++               .....+.+++||++|++..+++++|++.|+.||  .
T Consensus       132 R~IRTNWATRKp~e~n~~----~ltfdeV---------------~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG--~  190 (321)
T KOG0148|consen  132 RTIRTNWATRKPSEMNGK----PLTFDEV---------------YNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFG--P  190 (321)
T ss_pred             ceeeccccccCccccCCC----CccHHHH---------------hccCCCCCceEEeCCcCccccHHHHHHhcccCC--c
Confidence            999999998876221111    1111111               122334569999999999999999999999999  5


Q ss_pred             eEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          291 IEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       291 i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      |.+|++.+++|++||.|++.++|.+|+..+||.   +++|..++|
T Consensus       191 I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNnt---ei~G~~VkC  232 (321)
T KOG0148|consen  191 IQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNT---EIGGQLVRC  232 (321)
T ss_pred             ceEEEEecccceEEEEecchhhHHHHHHHhcCc---eeCceEEEE
Confidence            999999999999999999999999999999999   999998875

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=2e-36  Score=259.93  Aligned_cols=275  Identities=23%  Similarity=0.401  Sum_probs=210.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      .||||++||++++.++|.++|+.+|+|..+.++.++    ++||+||.|.-.+++.+|+....+..|.|+.|.|..+..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            789999999999999999999999999999998865    3699999999999999999999999999999999988654


Q ss_pred             CCcc---------------------C--CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEE
Q 019811          133 GQRE---------------------D--TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVS  189 (335)
Q Consensus       133 ~~~~---------------------~--~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~  189 (335)
                      ....                     .  ..+...|.|+|||+.+...+|..+|+.||.|..+.|++.+ .|.-.|||||.
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~  164 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQ  164 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEE
Confidence            4321                     0  1225789999999999999999999999999999999765 45555999999


Q ss_pred             eCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCC------------------Cccccc-c----------hhc-
Q 019811          190 FRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQ------------------SSDAKS-V----------VEL-  239 (335)
Q Consensus       190 f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~------------------~~~~~~-~----------~~~-  239 (335)
                      |.+..+|..|+..+|+..|+||+|.|.|+..+........                  ..+... .          ... 
T Consensus       165 fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe  244 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEE  244 (678)
T ss_pred             EeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhccccccccccc
Confidence            9999999999999999999999999999977664333110                  000000 0          000 


Q ss_pred             cCC----------CCcC------CcCCCC-------C--CCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEE
Q 019811          240 TNG----------SSED------GKETTN-------T--EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEV  294 (335)
Q Consensus       240 ~~~----------~~~~------~~~~~~-------~--~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v  294 (335)
                      ...          ....      ......       .  ..........+|||+|||+++++++|...|++||.+....+
T Consensus       245 ~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~i  324 (678)
T KOG0127|consen  245 TDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAII  324 (678)
T ss_pred             ccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEE
Confidence            000          0000      000000       0  00112223489999999999999999999999996444444


Q ss_pred             EEecc----cceEEEEeCCHHHHHHHHHhh-----cC-CCcccccCccccC
Q 019811          295 RVQRD----KGFGFVRYSTHAEAALAIQMG-----NT-TQSSYLFGKQMKV  335 (335)
Q Consensus       295 ~~~~~----~g~afV~f~~~~~a~~A~~~l-----~g-~~~~~~~g~~l~v  335 (335)
                      .+.++    +|+|||.|.+..+|.+++...     .| .   .++||.|+|
T Consensus       325 V~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~---ll~GR~Lkv  372 (678)
T KOG0127|consen  325 VKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSV---LLDGRLLKV  372 (678)
T ss_pred             EeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceE---EEeccEEee
Confidence            44443    799999999999999999877     23 4   788988875

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=3.8e-35  Score=245.44  Aligned_cols=169  Identities=28%  Similarity=0.458  Sum_probs=147.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCc-cccC--cee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGR-HLFG--QPI  124 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~-~~~g--~~l  124 (335)
                      .+.+.-.+||+-||..++|.||+++|++||.|.+|.+++|+.    +|||||.|.+.++|.+|+.+|++. ++.|  .+|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            345667799999999999999999999999999999999985    589999999999999999998774 5555  678


Q ss_pred             EEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 019811          125 KVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT  204 (335)
Q Consensus       125 ~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  204 (335)
                      .|+++....+  +...+++|||+-|++.+||.|++++|++||.|+++.|++| ..+.++|+|||+|.+.+-|..|++.||
T Consensus       110 qvk~Ad~E~e--r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~n  186 (510)
T KOG0144|consen  110 QVKYADGERE--RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALN  186 (510)
T ss_pred             eecccchhhh--ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhc
Confidence            8888865443  3345678999999999999999999999999999999999 468999999999999999999999999


Q ss_pred             Cce-eC--CeeeEEEEccCCCC
Q 019811          205 GKW-LG--SRQIRCNWATKGAG  223 (335)
Q Consensus       205 ~~~-~~--g~~l~v~~~~~~~~  223 (335)
                      +.. +.  ..+|.|+|++.++.
T Consensus       187 g~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  187 GTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             cceeeccCCCceEEEecccCCC
Confidence            964 54  46899999988773

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=2.2e-32  Score=236.39  Aligned_cols=169  Identities=24%  Similarity=0.441  Sum_probs=152.7

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|+.++    ++|||||+|.+.++|.+|++.|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            45567899999999999999999999999999999998875    35899999999999999999999999999999999


Q ss_pred             eeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          128 WAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       128 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      ++.+...   ....++|||+|||.++++++|+++|++||.|..+.+++++.++.++++|||+|.+.++|.+|++.|++..
T Consensus       183 ~a~p~~~---~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  259 (346)
T TIGR01659       183 YARPGGE---SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI  259 (346)
T ss_pred             ccccccc---ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCc
Confidence            9865432   2335689999999999999999999999999999999998899999999999999999999999999998


Q ss_pred             eCC--eeeEEEEccCCCC
Q 019811          208 LGS--RQIRCNWATKGAG  223 (335)
Q Consensus       208 ~~g--~~l~v~~~~~~~~  223 (335)
                      +.+  +.|.|.++.....
T Consensus       260 ~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       260 PEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             cCCCceeEEEEECCcccc
Confidence            865  7899999876543

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).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=5.6e-32  Score=222.03  Aligned_cols=166  Identities=22%  Similarity=0.407  Sum_probs=149.0

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      -|+||||.|.+.+.|+.|+..|..||+|++|.+.+|.    ++|||||+|+-++.|..|++.|||..++||.|+|....+
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            3779999999999999999999999999999998875    579999999999999999999999999999999986544


Q ss_pred             CCCc--------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 019811          132 SGQR--------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL  203 (335)
Q Consensus       132 ~~~~--------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  203 (335)
                      -+..        ++...-+.|||..+.++++++||+..|+.||+|.+|.+-+++..+.++||+|++|.+..+...|+..+
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasM  272 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  272 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhc
Confidence            3322        12233468999999999999999999999999999999999988999999999999999999999999


Q ss_pred             CCceeCCeeeEEEEccCC
Q 019811          204 TGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       204 ~~~~~~g~~l~v~~~~~~  221 (335)
                      |-..++|..|+|......
T Consensus       273 NlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  273 NLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             chhhcccceEecccccCC
Confidence            999999999999866443

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=6.2e-32  Score=234.66  Aligned_cols=231  Identities=29%  Similarity=0.530  Sum_probs=201.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCcc
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE  136 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~  136 (335)
                      +||||   +++|+.+|+++|+++|+|.++++.++- +-|||||.|.++++|++|+..+|...+.|++++|.|+.....  
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~--   77 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS--   77 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc--
Confidence            58999   999999999999999999999998876 338999999999999999999999999999999999975543  


Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                            .+||.||+++++..+|.+.|+.||.|.+|++..+.. | ++|| ||+|++++.|.+|+..+||..+.|+.|.|.
T Consensus        78 ------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg  148 (369)
T KOG0123|consen   78 ------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVG  148 (369)
T ss_pred             ------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEe
Confidence                  399999999999999999999999999999999853 4 8999 999999999999999999999999999998


Q ss_pred             EccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      ....+.........                           .......+++.|++.+++++.|.++|..+|  .+.++.+
T Consensus       149 ~~~~~~er~~~~~~---------------------------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g--~i~s~~v  199 (369)
T KOG0123|consen  149 LFERKEEREAPLGE---------------------------YKKRFTNVYVKNLEEDSTDEELKDLFSAYG--SITSVAV  199 (369)
T ss_pred             eccchhhhcccccc---------------------------hhhhhhhhheeccccccchHHHHHhhcccC--cceEEEE
Confidence            87665433222110                           111225689999999999999999999999  5888877


Q ss_pred             ecc-----cceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          297 QRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       297 ~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                      +++     ++++||.|.+.++|..|+..|++.   .+++..+-
T Consensus       200 ~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~---~~~~~~~~  239 (369)
T KOG0123|consen  200 MRDSIGKSKGFGFVNFENPEDAKKAVETLNGK---IFGDKELY  239 (369)
T ss_pred             eecCCCCCCCccceeecChhHHHHHHHhccCC---cCCcccee
Confidence            754     799999999999999999999999   88766654

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=9.4e-31  Score=227.30  Aligned_cols=253  Identities=32%  Similarity=0.493  Sum_probs=210.1

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCcc
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE  136 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~  136 (335)
                      |||.||+++++..+|.++|+.||.|.+|++..+.  ++|| ||+|.+.++|.+|++.+||..+.|+.|.|.....+..+.
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            9999999999999999999999999999999876  4689 999999999999999999999999999998887655443


Q ss_pred             CCC-----CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 019811          137 DTS-----GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSR  211 (335)
Q Consensus       137 ~~~-----~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~  211 (335)
                      ...     .-..+++.+++.+.+++.|...|..+|.+.++.++.+. .+.+++|+||.|++.++|..|+..+++..+++.
T Consensus       158 ~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~  236 (369)
T KOG0123|consen  158 APLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDK  236 (369)
T ss_pred             ccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCcc
Confidence            322     23578999999999999999999999999999999884 566999999999999999999999999999999


Q ss_pred             eeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeee
Q 019811          212 QIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVI  291 (335)
Q Consensus       212 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i  291 (335)
                      .+.|..+..+........           ...      ...............|||.|++..++.+.|++.|+.||  .+
T Consensus       237 ~~~V~~aqkk~e~~~~l~-----------~~~------~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~G--eI  297 (369)
T KOG0123|consen  237 ELYVGRAQKKSEREAELK-----------RKF------EQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFG--EI  297 (369)
T ss_pred             ceeecccccchhhHHHHh-----------hhh------HhhhhhccccccccccccccCccccchhHHHHHHhccc--ce
Confidence            999988766221111000           000      00000111122336799999999999999999999999  57


Q ss_pred             EEEEEecc-----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          292 EEVRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       292 ~~v~~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..++++.+     +|++||.|.+.++|.+|+..+||.   .++++.|.|
T Consensus       298 ~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~---~i~~k~l~v  343 (369)
T KOG0123|consen  298 TSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGR---LIGGKPLYV  343 (369)
T ss_pred             eeEEEEeccCCCccceEEEEcCCHHHHHHHHHhhChh---hhcCCchhh
Confidence            77777643     799999999999999999999999   999998764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=2.9e-30  Score=223.24  Aligned_cols=159  Identities=31%  Similarity=0.494  Sum_probs=139.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|.+++|++|+.++.++|||||+|.++++|.+|+..|++..+.++.|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      |+.+....                                   ....+|||.|||.++++++|+++|++||  .|..+++
T Consensus       183 ~a~p~~~~-----------------------------------~~~~~lfV~nLp~~vtee~L~~~F~~fG--~V~~v~i  225 (346)
T TIGR01659       183 YARPGGES-----------------------------------IKDTNLYVTNLPRTITDDQLDTIFGKYG--QIVQKNI  225 (346)
T ss_pred             cccccccc-----------------------------------cccceeEEeCCCCcccHHHHHHHHHhcC--CEEEEEE
Confidence            97642210                                   0125799999999999999999999999  5777777


Q ss_pred             ecc------cceEEEEeCCHHHHHHHHHhhcCCCcccccC--ccccC
Q 019811          297 QRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFG--KQMKV  335 (335)
Q Consensus       297 ~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g--~~l~v  335 (335)
                      .++      +++|||+|.+.++|.+|++.||+.   .+.+  ++|+|
T Consensus       226 ~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~---~~~g~~~~l~V  269 (346)
T TIGR01659       226 LRDKLTGTPRGVAFVRFNKREEAQEAISALNNV---IPEGGSQPLTV  269 (346)
T ss_pred             eecCCCCccceEEEEEECCHHHHHHHHHHhCCC---ccCCCceeEEE
Confidence            655      489999999999999999999999   7766  45543

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).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=6.7e-30  Score=201.81  Aligned_cols=169  Identities=26%  Similarity=0.572  Sum_probs=153.3

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec----CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~----~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +.+-.|||+.|...++.++|++.|.+||.|.+.++++|    +++||+||.|.+.++|++||..|||..|++|.|+-.|+
T Consensus        60 ~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWA  139 (321)
T KOG0148|consen   60 NQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWA  139 (321)
T ss_pred             ccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccc
Confidence            34667999999999999999999999999999999997    46799999999999999999999999999999999999


Q ss_pred             ccCCCc-------------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHH
Q 019811          130 YASGQR-------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA  196 (335)
Q Consensus       130 ~~~~~~-------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a  196 (335)
                      ..+...             .....+++||++|++..+++++|++.|+.||.|.+|++.++      +||+||+|++.|.|
T Consensus       140 TRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaA  213 (321)
T KOG0148|consen  140 TRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAA  213 (321)
T ss_pred             ccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhH
Confidence            887643             23456789999999999999999999999999999999955      68999999999999


Q ss_pred             HHHHHHhCCceeCCeeeEEEEccCCCCCCCCC
Q 019811          197 QSAINDLTGKWLGSRQIRCNWATKGAGNNEDK  228 (335)
Q Consensus       197 ~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~  228 (335)
                      ..||-.+|+..+.|+.++|.|.+.........
T Consensus       214 ahAIv~mNntei~G~~VkCsWGKe~~~~~~~~  245 (321)
T KOG0148|consen  214 AHAIVQMNNTEIGGQLVRCSWGKEGDDGINNQ  245 (321)
T ss_pred             HHHHHHhcCceeCceEEEEeccccCCCCCCch
Confidence            99999999999999999999998877554443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=9.8e-29  Score=219.22  Aligned_cols=168  Identities=29%  Similarity=0.524  Sum_probs=146.8

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNW  128 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~  128 (335)
                      ..++|||+|||..+++++|+++|+.||.|..+++..+.    ++|||||+|.+.++|.+|++.|||..+.|  .+|.|.+
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45679999999999999999999999999999988754    46899999999999999999999999987  5677777


Q ss_pred             eccCCCc-------------------------------------------------------------------------
Q 019811          129 AYASGQR-------------------------------------------------------------------------  135 (335)
Q Consensus       129 ~~~~~~~-------------------------------------------------------------------------  135 (335)
                      +......                                                                         
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            6422200                                                                         


Q ss_pred             ----------------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHH
Q 019811          136 ----------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA  199 (335)
Q Consensus       136 ----------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  199 (335)
                                      .....+.+|||+|||.++++++|+++|++||.|.++++++|+.++.++|||||+|.+.++|.+|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                            0011123699999999999999999999999999999999998999999999999999999999


Q ss_pred             HHHhCCceeCCeeeEEEEccCCC
Q 019811          200 INDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       200 ~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      +..|+|..++|+.|+|.|...+.
T Consensus       328 i~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       328 ILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999999987754

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

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.96  E-value=4e-29  Score=227.00  Aligned_cols=166  Identities=25%  Similarity=0.510  Sum_probs=141.3

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||+++++++|+++|..||.|.++.+++|+.++.++|||||+|.+.++|.+|+..|+|..++|+.|+|.+...
T Consensus       107 ~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~  186 (612)
T TIGR01645       107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  186 (612)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccccc
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999986432


Q ss_pred             CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-
Q 019811          221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-  299 (335)
                      .......                        ...........++|||+|||.++++++|+++|+.||  .|.++++.++ 
T Consensus       187 ~p~a~~~------------------------~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG--~I~svrl~~D~  240 (612)
T TIGR01645       187 MPQAQPI------------------------IDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG--EIVKCQLARAP  240 (612)
T ss_pred             ccccccc------------------------cccccccccccceEEeecCCCCCCHHHHHHHHhhcC--CeeEEEEEecC
Confidence            2110000                        000001112347899999999999999999999999  5888888653 


Q ss_pred             -----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 -----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                           +|+|||+|.+.++|.+|+..|||.   .++|+.|+|
T Consensus       241 ~tgksKGfGFVeFe~~e~A~kAI~amNg~---elgGr~LrV  278 (612)
T TIGR01645       241 TGRGHKGYGFIEYNNLQSQSEAIASMNLF---DLGGQYLRV  278 (612)
T ss_pred             CCCCcCCeEEEEECCHHHHHHHHHHhCCC---eeCCeEEEE
Confidence                 789999999999999999999999   999999986

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=7.6e-29  Score=213.53  Aligned_cols=265  Identities=24%  Similarity=0.409  Sum_probs=194.7

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ..+|.|+|||+.+.+.+|..+|+.||.|.+|.|.+.+.   .|||||+|.+..+|..|++.+|+..|.|++|-|.|+-++
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            56799999999999999999999999999999986543   599999999999999999999999999999999998432


Q ss_pred             CC------------------------------------------------------------------------------
Q 019811          133 GQ------------------------------------------------------------------------------  134 (335)
Q Consensus       133 ~~------------------------------------------------------------------------------  134 (335)
                      ..                                                                              
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            10                                                                              


Q ss_pred             ---------ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--
Q 019811          135 ---------REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL--  203 (335)
Q Consensus       135 ---------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--  203 (335)
                               +.+..-..+|||+|||+++++++|.+.|+.||.|.++.++.++.++.++|.|||.|.+..+|..||...  
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Asp  356 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASP  356 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCc
Confidence                     000011268999999999999999999999999999999999999999999999999999999999876  


Q ss_pred             ---CC-ceeCCeeeEEEEccCCCCCCCCCC------CcccccchhccCCCCcCC----cCC----------------CCC
Q 019811          204 ---TG-KWLGSRQIRCNWATKGAGNNEDKQ------SSDAKSVVELTNGSSEDG----KET----------------TNT  253 (335)
Q Consensus       204 ---~~-~~~~g~~l~v~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~----~~~----------------~~~  253 (335)
                         .| ..++||.|.|..+..+........      ..+.....-...+....+    ...                ...
T Consensus       357 a~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyLa~EG~I~~gt~aAeglS~~Dm~kRer~~~~k~k~l  436 (678)
T KOG0127|consen  357 ASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYLAREGLIRDGTPAAEGLSATDMAKRERIAERKRKKL  436 (678)
T ss_pred             cCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceeeeccCccccCChhhcccchhhHHHHHHHHHHHHHhh
Confidence               23 568999999998866553211100      000000000000000000    000                001


Q ss_pred             CCCCCCCCCCeEEEcCCCcccCHHHHHHHhhh----cCCeeeEEEEEec---------ccceEEEEeCCHHHHHHHHHhh
Q 019811          254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHS----LGAGVIEEVRVQR---------DKGFGFVRYSTHAEAALAIQMG  320 (335)
Q Consensus       254 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~----~G~~~i~~v~~~~---------~~g~afV~f~~~~~a~~A~~~l  320 (335)
                      ..+......+.|.|.|||..+++..|..+...    |-......++.+.         +.|++|+.|...+.|.+|+..+
T Consensus       437 knpnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~kk~~R~~~~le~~~k~~s~g~aF~~f~EhEhalkalk~~  516 (678)
T KOG0127|consen  437 KNPNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKVKKCIRQIKFLEEEKKNYSEGYAFVGFTEHEHALKALKVL  516 (678)
T ss_pred             cCCceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhcchhhhhhhhHHhhhhcccccccccCccHHHHHHHhhhcc
Confidence            12333344477999999999999998887653    2111222233221         2689999999999999999765

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.96  E-value=6.5e-27  Score=194.97  Aligned_cols=275  Identities=21%  Similarity=0.321  Sum_probs=230.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~  129 (335)
                      .++.-.+++|.|+-+.++-+-|..+|++||.|..|.-+.+...-.|+|+|.+.+.|..|...|+|..|..  ++|+|.++
T Consensus       146 ~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~S  225 (492)
T KOG1190|consen  146 GPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFS  225 (492)
T ss_pred             CCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehh
Confidence            4556677899999999999999999999999998766655555579999999999999999999998875  46666655


Q ss_pred             cc----------CCC--------c------------------------------------------cCCCCcceEEECCC
Q 019811          130 YA----------SGQ--------R------------------------------------------EDTSGHFNIFVGDL  149 (335)
Q Consensus       130 ~~----------~~~--------~------------------------------------------~~~~~~~~l~v~nl  149 (335)
                      .-          +++        .                                          .....+..|.|.||
T Consensus       226 klt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnl  305 (492)
T KOG1190|consen  226 KLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNL  305 (492)
T ss_pred             hcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecC
Confidence            21          110        0                                          00011356777887


Q ss_pred             Cc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCC
Q 019811          150 SP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDK  228 (335)
Q Consensus       150 p~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~  228 (335)
                      .. .+|.+.|..+|.-||+|.+|+|++++.     .-|+|+|.+...|..|+..|+|..+.|+.|+|.+++.........
T Consensus       306 n~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~e  380 (492)
T KOG1190|consen  306 NEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPRE  380 (492)
T ss_pred             chhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCC
Confidence            55 589999999999999999999997754     349999999999999999999999999999999999998888888


Q ss_pred             CCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeC
Q 019811          229 QSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYS  308 (335)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~  308 (335)
                      ...+.+...++.+....+...++........+++.+|++.|+|..+++|+++..|..-|+..-....+.+++.+|++.+.
T Consensus       381 gq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~  460 (492)
T KOG1190|consen  381 GQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLE  460 (492)
T ss_pred             CCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccC
Confidence            88888888888888888888888888888889999999999999999999999999998633444455678899999999


Q ss_pred             CHHHHHHHHHhhcCCCcccccCc-ccc
Q 019811          309 THAEAALAIQMGNTTQSSYLFGK-QMK  334 (335)
Q Consensus       309 ~~~~a~~A~~~l~g~~~~~~~g~-~l~  334 (335)
                      +.++|..|+..++++   .+++. .|+
T Consensus       461 sveeA~~ali~~hnh---~lgen~hlR  484 (492)
T KOG1190|consen  461 SVEEAIQALIDLHNH---YLGENHHLR  484 (492)
T ss_pred             ChhHhhhhccccccc---cCCCCceEE
Confidence            999999999999999   77765 444

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.96  E-value=2e-28  Score=211.82  Aligned_cols=278  Identities=23%  Similarity=0.386  Sum_probs=211.8

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ......++||+--|+..+++.+|.+||+.+|.|..|.++.++    ++|.|||+|.+.++.-.|+ .|.|..+.|.+|.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~v  252 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIV  252 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEe
Confidence            345667889999999999999999999999999999999876    4699999999999999998 79999999999999


Q ss_pred             eeeccCCCc----------c-CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHH
Q 019811          127 NWAYASGQR----------E-DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD  195 (335)
Q Consensus       127 ~~~~~~~~~----------~-~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~  195 (335)
                      ..+......          . -..+-..|||+||.+++++++|+.+|++||.|..|.+.+|..+|.++||+|++|.+.++
T Consensus       253 q~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~  332 (549)
T KOG0147|consen  253 QLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKED  332 (549)
T ss_pred             cccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHH
Confidence            876432211          0 01122239999999999999999999999999999999998899999999999999999


Q ss_pred             HHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCC---Ccc----------cccch----hccCCC---------------
Q 019811          196 AQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQ---SSD----------AKSVV----ELTNGS---------------  243 (335)
Q Consensus       196 a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~---~~~----------~~~~~----~~~~~~---------------  243 (335)
                      |.+|+..|||.++.|+.|+|......-.......   ..+          .....    ......               
T Consensus       333 ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~  412 (549)
T KOG0147|consen  333 ARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLL  412 (549)
T ss_pred             HHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhc
Confidence            9999999999999999999976543322111100   000          00000    000000               


Q ss_pred             --CcCCc----------CCCCCCCCCCCCCCCeEEEcCCCcccCH----------HHHHHHhhhcCCeeeEEEEEeccc-
Q 019811          244 --SEDGK----------ETTNTEAPENNPQYTTVYVGNLAPEVTQ----------LDLHRHFHSLGAGVIEEVRVQRDK-  300 (335)
Q Consensus       244 --~~~~~----------~~~~~~~~~~~~~~~~l~v~nlp~~~t~----------~~l~~~f~~~G~~~i~~v~~~~~~-  300 (335)
                        ...+.          .......+....++.|+.+.|+-...++          +||.+.+.+||  .+..|.+.++. 
T Consensus       413 ~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g--~v~hi~vd~ns~  490 (549)
T KOG0147|consen  413 AKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHG--KVCHIFVDKNSA  490 (549)
T ss_pred             cccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcC--CeeEEEEccCCC
Confidence              00000          0000001122256678899998554332          68999999999  59999998775 


Q ss_pred             ceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       301 g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                      |+.||.|.+.+.|..|+.+|||.   +|.||-|+
T Consensus       491 g~VYvrc~s~~~A~~a~~alhgr---WF~gr~It  521 (549)
T KOG0147|consen  491 GCVYVRCPSAEAAGTAVKALHGR---WFAGRMIT  521 (549)
T ss_pred             ceEEEecCcHHHHHHHHHHHhhh---hhccceeE
Confidence            99999999999999999999999   99999886

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.96  E-value=4.6e-28  Score=215.19  Aligned_cols=248  Identities=23%  Similarity=0.341  Sum_probs=199.9

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ...+.++|+|||..+..++|...|..||.|..|.+.  ...-.++|.|.++.+|..|++.|.+..+...++.+.|+....
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dv  460 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDV  460 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecC--cccceeeeeecCccchHHHHHHhchhhhccCccccccChhhh
Confidence            344679999999999999999999999999988443  332359999999999999999999999988888877763210


Q ss_pred             Cc--------------------------------cC---------------CCCcceEEECCCCccccHHHHHHHhccCC
Q 019811          134 QR--------------------------------ED---------------TSGHFNIFVGDLSPEVTDATLFACFSVYP  166 (335)
Q Consensus       134 ~~--------------------------------~~---------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g  166 (335)
                      -.                                .+               ....+.||+.||+++.+.+++...|...|
T Consensus       461 f~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G  540 (725)
T KOG0110|consen  461 FTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQG  540 (725)
T ss_pred             ccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcC
Confidence            00                                00               00113499999999999999999999999


Q ss_pred             CceeeEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCC
Q 019811          167 SCSDARVMWDQKT---GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGS  243 (335)
Q Consensus       167 ~v~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (335)
                      .|.++.|...+..   -.+.|||||+|.+.++|..|+..|+|..++|+.|.|.++.........+               
T Consensus       541 ~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK---------------  605 (725)
T KOG0110|consen  541 TVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGK---------------  605 (725)
T ss_pred             eEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCcccccccc---------------
Confidence            9999988754321   1256999999999999999999999999999999999997222111110               


Q ss_pred             CcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc------cceEEEEeCCHHHHHHHH
Q 019811          244 SEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI  317 (335)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~------~g~afV~f~~~~~a~~A~  317 (335)
                                 ..........|+|+|||+..+..+|+.+|..||  .+.+|++++.      +|+|||+|.++.+|.+|+
T Consensus       606 -----------~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFG--qlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~  672 (725)
T KOG0110|consen  606 -----------KKSKKKKGTKILVRNIPFEATKREVRKLFTAFG--QLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAF  672 (725)
T ss_pred             -----------ccccccccceeeeeccchHHHHHHHHHHHhccc--ceeeeccchhhcchhhccceeeeccCcHHHHHHH
Confidence                       001111246899999999999999999999999  6999999865      799999999999999999


Q ss_pred             HhhcCCCcccccCcccc
Q 019811          318 QMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       318 ~~l~g~~~~~~~g~~l~  334 (335)
                      .+|.+.   .+.||+|-
T Consensus       673 ~al~ST---HlyGRrLV  686 (725)
T KOG0110|consen  673 DALGST---HLYGRRLV  686 (725)
T ss_pred             Hhhccc---ceechhhh
Confidence            999988   89999874

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.95  E-value=1e-26  Score=211.20  Aligned_cols=218  Identities=20%  Similarity=0.297  Sum_probs=165.4

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCC-ceeEEEee-----cCCCCeEEEEEcCHHHHHHHHHHhCC--ccccCceeEE
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIR-----KDKSSYGFIHYFDRRSAAMAILSLNG--RHLFGQPIKV  126 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~-v~~v~~~~-----~~~~g~afv~f~~~~~A~~a~~~l~~--~~~~g~~l~v  126 (335)
                      ..++|||+|||.++++++|.+.|++++. +.++.+..     .+++|||||+|.+.++|..|++.|+.  ..+.|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4678999999999999999999999874 44544432     23579999999999999999988764  4578999999


Q ss_pred             eeeccCCCccC--CCCcceEEECCCCccccHHHHHHHhccC--CCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 019811          127 NWAYASGQRED--TSGHFNIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND  202 (335)
Q Consensus       127 ~~~~~~~~~~~--~~~~~~l~v~nlp~~~t~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  202 (335)
                      .|+.+......  ....++|||+||+.++++++|+++|+.|  |.|.++.++        ++||||+|.+.++|.+|++.
T Consensus       217 dwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~  288 (578)
T TIGR01648       217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDE  288 (578)
T ss_pred             EeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHH
Confidence            99976543322  2345789999999999999999999999  999999776        34899999999999999999


Q ss_pred             hCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHH
Q 019811          203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRH  282 (335)
Q Consensus       203 l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~  282 (335)
                      |++..|.|+.|+|.|+++..............       ............-.....+...++++.|++++.+++.+.++
T Consensus       289 lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~g-------g~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~  361 (578)
T TIGR01648       289 LNGKELEGSEIEVTLAKPVDKKSYVRYTRGTG-------GRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHF  361 (578)
T ss_pred             hCCCEECCEEEEEEEccCCCcccccccccccC-------CCcccccccccccCcccCccccccccccccccccccchhhc
Confidence            99999999999999997754321110000000       00000000011112223345689999999999999999999


Q ss_pred             hhhcC
Q 019811          283 FHSLG  287 (335)
Q Consensus       283 f~~~G  287 (335)
                      |..+|
T Consensus       362 f~~~g  366 (578)
T TIGR01648       362 PRMPG  366 (578)
T ss_pred             cccCc
Confidence            99988

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.95  E-value=5e-27  Score=175.11  Aligned_cols=172  Identities=32%  Similarity=0.599  Sum_probs=153.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      +.....+|||+||+..++++-|+++|-+.|+|.++++.+++    .+||||++|.+.++|+=|+.-||...+.|++|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            34556789999999999999999999999999999998765    46999999999999999999999999999999999


Q ss_pred             eeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCcee-eEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 019811          128 WAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD-ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK  206 (335)
Q Consensus       128 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  206 (335)
                      .+.  ........+.++||+||.+.++|.-|.+.|+.||.+.. -.++++..+|.++|++||.|.+.+.+.+|+..++++
T Consensus        85 kas--~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq  162 (203)
T KOG0131|consen   85 KAS--AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQ  162 (203)
T ss_pred             ecc--cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccc
Confidence            886  22233344578999999999999999999999998765 478888889999999999999999999999999999


Q ss_pred             eeCCeeeEEEEccCCCCCC
Q 019811          207 WLGSRQIRCNWATKGAGNN  225 (335)
Q Consensus       207 ~~~g~~l~v~~~~~~~~~~  225 (335)
                      .+.++.+.|.|+..+....
T Consensus       163 ~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  163 YLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             hhcCCceEEEEEEecCCCc
Confidence            9999999999998766544

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=5.4e-27  Score=196.79  Aligned_cols=150  Identities=27%  Similarity=0.461  Sum_probs=134.8

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-e--CCeeeEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW-L--GSRQIRC  215 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~-~--~g~~l~v  215 (335)
                      ...-++||+-+|..|+|.||+++|++||.|.+|.+++|+.++.++|+|||.|.+.++|.+|+.+|++.. +  ....|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            344589999999999999999999999999999999999999999999999999999999999998865 4  3478889


Q ss_pred             EEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEE
Q 019811          216 NWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR  295 (335)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~  295 (335)
                      +|++....+...                                  .+.|||+-|+..+||+||+++|++||  .|++|.
T Consensus       112 k~Ad~E~er~~~----------------------------------e~KLFvg~lsK~~te~evr~iFs~fG--~Ied~~  155 (510)
T KOG0144|consen  112 KYADGERERIVE----------------------------------ERKLFVGMLSKQCTENEVREIFSRFG--HIEDCY  155 (510)
T ss_pred             cccchhhhcccc----------------------------------chhhhhhhccccccHHHHHHHHHhhC--ccchhh
Confidence            998775544322                                  27799999999999999999999999  599999


Q ss_pred             Eecc-----cceEEEEeCCHHHHHHHHHhhcCCC
Q 019811          296 VQRD-----KGFGFVRYSTHAEAALAIQMGNTTQ  324 (335)
Q Consensus       296 ~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~  324 (335)
                      |+++     ||||||+|.+.+-|..|++.|||..
T Consensus       156 ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  156 ILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             heecccccccceeEEEEehHHHHHHHHHhhccce
Confidence            9886     8999999999999999999999984

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.94  E-value=6.8e-26  Score=207.78  Aligned_cols=168  Identities=29%  Similarity=0.500  Sum_probs=141.6

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+. |+|..+.|+.|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            346799999999999999999999999999999999999899999999999999999999996 8999999999999886


Q ss_pred             cCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec
Q 019811          219 TKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~  298 (335)
                      ...........                       .......+..++|||+|||..+++++|+++|+.||  .|..|.+..
T Consensus       166 ~~~~~~~~~~~-----------------------~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G--~i~~v~~~~  220 (457)
T TIGR01622       166 QAEKNRAAKAA-----------------------THQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFG--DIEDVQLHR  220 (457)
T ss_pred             chhhhhhhhcc-----------------------cccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcC--CeEEEEEEE
Confidence            54322111000                       00000112258999999999999999999999999  477887763


Q ss_pred             ------ccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          299 ------DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       299 ------~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                            .+|+|||+|.+.++|.+|+..|+|.   .|+|++|+|
T Consensus       221 d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~---~i~g~~i~v  260 (457)
T TIGR01622       221 DPETGRSKGFGFIQFHDAEEAKEALEVMNGF---ELAGRPIKV  260 (457)
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHhcCCc---EECCEEEEE
Confidence                  3689999999999999999999999   999999876

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=4.6e-26  Score=179.19  Aligned_cols=150  Identities=30%  Similarity=0.501  Sum_probs=135.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|.|.-||.++|++|++.+|...|+|++++++||+.+|.+-||+||.|.++++|++|+..|||..+..++|+|+|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEe
Q 019811          218 ATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ  297 (335)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~  297 (335)
                      +.+.......                                   ..|||.+||..+|..||..+|+.||.  |...++.
T Consensus       118 ARPSs~~Ik~-----------------------------------aNLYvSGlPktMtqkelE~iFs~fGr--IItSRiL  160 (360)
T KOG0145|consen  118 ARPSSDSIKD-----------------------------------ANLYVSGLPKTMTQKELEQIFSPFGR--IITSRIL  160 (360)
T ss_pred             ccCChhhhcc-----------------------------------cceEEecCCccchHHHHHHHHHHhhh--hhhhhhh
Confidence            9876544332                                   46999999999999999999999994  6555555


Q ss_pred             cc------cceEEEEeCCHHHHHHHHHhhcCCC
Q 019811          298 RD------KGFGFVRYSTHAEAALAIQMGNTTQ  324 (335)
Q Consensus       298 ~~------~g~afV~f~~~~~a~~A~~~l~g~~  324 (335)
                      .+      ||.+||.|+...+|..|+..|||..
T Consensus       161 ~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  161 VDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             hhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            43      8999999999999999999999983

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.93  E-value=3.2e-23  Score=174.45  Aligned_cols=165  Identities=22%  Similarity=0.290  Sum_probs=136.0

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHH-hccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVF-SSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f-~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .....+.+||+|||++....+|+++| ++.|.|+.|.++.|.   .+|+|.|+|+++|.+++|++.||...+.|++|.|+
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            34455679999999999999999999 468899999998874   57999999999999999999999999999999997


Q ss_pred             eeccCC------------------------------------------Cc------------------------------
Q 019811          128 WAYASG------------------------------------------QR------------------------------  135 (335)
Q Consensus       128 ~~~~~~------------------------------------------~~------------------------------  135 (335)
                      --....                                          .+                              
T Consensus       120 Ed~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl  199 (608)
T KOG4212|consen  120 EDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGL  199 (608)
T ss_pred             ccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccc
Confidence            542210                                          00                              


Q ss_pred             ----------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          136 ----------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       136 ----------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                                -.+.-...+||.||...+....|.+.|.-.|.+..+.+-.|+. |.++|+|.++|..+-.|..|+..+++
T Consensus       200 ~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  200 SASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhcc
Confidence                      0111125689999999999999999999999999999988865 58899999999999999999999987


Q ss_pred             ceeCCeeeEEEE
Q 019811          206 KWLGSRQIRCNW  217 (335)
Q Consensus       206 ~~~~g~~l~v~~  217 (335)
                      .-+..++..++.
T Consensus       279 ~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  279 QGLFDRRMTVRL  290 (608)
T ss_pred             CCCccccceeec
Confidence            665555555544

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.93  E-value=1.6e-25  Score=178.96  Aligned_cols=148  Identities=28%  Similarity=0.513  Sum_probs=138.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCccC
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRED  137 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~  137 (335)
                      .|||+|||..+++.+|+.+|++||.|.++.|+++    ||||..++...|+.|++.|+|-.+.|..|.|+.+++++    
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN----YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs----   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN----YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS----   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc----cceEEeecccccHHHHhhcccceecceEEEEEeccccC----
Confidence            4999999999999999999999999999999775    89999999999999999999999999999999998763    


Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                       ..+++++|+|+.+.++..|++..|++||.|..+.|++|        |+||.|+..++|..|++.|++.++.|+.++|..
T Consensus        76 -k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   76 -KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             -CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeee
Confidence             45578999999999999999999999999999999854        899999999999999999999999999999998


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +...-
T Consensus       147 stsrl  151 (346)
T KOG0109|consen  147 STSRL  151 (346)
T ss_pred             ecccc
Confidence            86643

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.93  E-value=3.9e-24  Score=198.88  Aligned_cols=167  Identities=18%  Similarity=0.285  Sum_probs=140.8

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.+.    ++|||||+|.+.++|..|+..|+|..|.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            456789999999999999999999999999999998764    4699999999999999999999999999999999987


Q ss_pred             ccCCCc-------------------------cCCCCcceEEECCCCccc----------cHHHHHHHhccCCCceeeEEe
Q 019811          130 YASGQR-------------------------EDTSGHFNIFVGDLSPEV----------TDATLFACFSVYPSCSDARVM  174 (335)
Q Consensus       130 ~~~~~~-------------------------~~~~~~~~l~v~nlp~~~----------t~~~l~~~f~~~g~v~~~~~~  174 (335)
                      ......                         ....++.+|+|.|+....          ..++|+++|.+||.|..|.|+
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            432210                         001245678999996421          236899999999999999998


Q ss_pred             ecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          175 WDQ---KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       175 ~~~---~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      ++.   .++...|++||+|.+.++|.+|+..|+|..|.|+.|.|.|...
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            652   2345678999999999999999999999999999999999765

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.93  E-value=3.4e-25  Score=165.33  Aligned_cols=160  Identities=31%  Similarity=0.493  Sum_probs=139.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      .....+|||+||+..++++-|.++|-..|+|..+.+++|+.+..+.||||++|.++++|+.|++-|+...+.|++|+|+.
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            34557999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEe
Q 019811          218 ATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ  297 (335)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~  297 (335)
                      +......                                  ...+..|||+||.+.+.+..|.+.|+.|| +.+....++
T Consensus        86 as~~~~n----------------------------------l~vganlfvgNLd~~vDe~~L~dtFsafG-~l~~~P~i~  130 (203)
T KOG0131|consen   86 ASAHQKN----------------------------------LDVGANLFVGNLDPEVDEKLLYDTFSAFG-VLISPPKIM  130 (203)
T ss_pred             ccccccc----------------------------------ccccccccccccCcchhHHHHHHHHHhcc-ccccCCccc
Confidence            8622111                                  11125799999999999999999999999 344544554


Q ss_pred             cc------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          298 RD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       298 ~~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ++      +|++||.|.+.+.+.+|+..|+|.   .+++++++|
T Consensus       131 rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq---~l~nr~itv  171 (203)
T KOG0131|consen  131 RDPDTGNPKGFGFINYASFEASDAAIGSMNGQ---YLCNRPITV  171 (203)
T ss_pred             ccccCCCCCCCeEEechhHHHHHHHHHHhccc---hhcCCceEE
Confidence            43      689999999999999999999999   999999875

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=2e-24  Score=182.29  Aligned_cols=166  Identities=22%  Similarity=0.354  Sum_probs=143.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCC-ceeEEEeec-----CCCCeEEEEEcCHHHHHHHHHHhCC--ccccCcee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIRK-----DKSSYGFIHYFDRRSAAMAILSLNG--RHLFGQPI  124 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~-v~~v~~~~~-----~~~g~afv~f~~~~~A~~a~~~l~~--~~~~g~~l  124 (335)
                      +...++|||+|||..+++++|.+.+++.++ |..|.+..+     +++|||||+|.+...|..|.+.|-.  ..+.|+.+
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            345678999999999999999999999985 777777653     4679999999999999999987644  45579999


Q ss_pred             EEeeeccCCCccCCC--CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 019811          125 KVNWAYASGQREDTS--GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND  202 (335)
Q Consensus       125 ~v~~~~~~~~~~~~~--~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  202 (335)
                      .|.|+.+........  .-..|||+||+.++|++.|+++|+.||.|++|+.++|        ||||.|.+.++|.+|++.
T Consensus       241 tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~  312 (506)
T KOG0117|consen  241 TVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKE  312 (506)
T ss_pred             eeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHH
Confidence            999998877654432  2357999999999999999999999999999988855        999999999999999999


Q ss_pred             hCCceeCCeeeEEEEccCCCCCCC
Q 019811          203 LTGKWLGSRQIRCNWATKGAGNNE  226 (335)
Q Consensus       203 l~~~~~~g~~l~v~~~~~~~~~~~  226 (335)
                      +|+..++|..|.|.++++......
T Consensus       313 ~ngkeldG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  313 TNGKELDGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             hcCceecCceEEEEecCChhhhcc
Confidence            999999999999999988765443

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.91  E-value=8.2e-23  Score=170.66  Aligned_cols=272  Identities=19%  Similarity=0.226  Sum_probs=190.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC--CccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN--GRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~--~~~~~g~~l~v~~~~  130 (335)
                      ..+++.|++||||.+++|+||.+++.+||.|..+.+.+.++  .||++|.+.++|..-+....  --.+.|++|.|.++.
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn--QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn  102 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN--QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSN  102 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch--hhhhhhcchhhhhheeecccccCccccCcceeehhhh
Confidence            34778899999999999999999999999999999988876  89999999999877332221  124456777776652


Q ss_pred             cCC------------------------------C-----cc--CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEE
Q 019811          131 ASG------------------------------Q-----RE--DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV  173 (335)
Q Consensus       131 ~~~------------------------------~-----~~--~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~  173 (335)
                      -..                              .     ..  .+..--.++|.|+-+.+|-+-|..+|++||.|..+.-
T Consensus       103 ~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiT  182 (492)
T KOG1190|consen  103 HSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIIT  182 (492)
T ss_pred             HHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEE
Confidence            110                              0     00  0011135778999999999999999999999988855


Q ss_pred             eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeeeEEEEccCCCCCCCCC---C--Ccccccchh--------
Q 019811          174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL--GSRQIRCNWATKGAGNNEDK---Q--SSDAKSVVE--------  238 (335)
Q Consensus       174 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~--~g~~l~v~~~~~~~~~~~~~---~--~~~~~~~~~--------  238 (335)
                      . .   ..+.-.|+|+|.+.+.|..|...|+|+.|  +.+.|++.|++...-.....   .  ..++.....        
T Consensus       183 F-~---Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~  258 (492)
T KOG1190|consen  183 F-T---KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQ  258 (492)
T ss_pred             E-e---cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccch
Confidence            4 2   12334599999999999999999999877  45778888886644211110   0  000000000        


Q ss_pred             -----c--------cCCCCcCCcCCCCCCCCCCCC--CCCeEEEcCCCc-ccCHHHHHHHhhhcCCeeeEEEEEeccc-c
Q 019811          239 -----L--------TNGSSEDGKETTNTEAPENNP--QYTTVYVGNLAP-EVTQLDLHRHFHSLGAGVIEEVRVQRDK-G  301 (335)
Q Consensus       239 -----~--------~~~~~~~~~~~~~~~~~~~~~--~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~i~~v~~~~~~-g  301 (335)
                           .        .+...+.+...+.........  .+..|-|.||.. .+|.+.|..+|.-||  +|..|++..++ .
T Consensus       259 ~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYG--dVqRVkil~nkkd  336 (492)
T KOG1190|consen  259 LMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYG--DVQRVKILYNKKD  336 (492)
T ss_pred             hhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhc--ceEEEEeeecCCc
Confidence                 0        000000000000000011111  257888899876 689999999999999  69999998765 5


Q ss_pred             eEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          302 FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       302 ~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .|.|.|.+...|.-|+++|+|.   .+.|++|+|
T Consensus       337 ~ALIQmsd~~qAqLA~~hL~g~---~l~gk~lrv  367 (492)
T KOG1190|consen  337 NALIQMSDGQQAQLAMEHLEGH---KLYGKKLRV  367 (492)
T ss_pred             ceeeeecchhHHHHHHHHhhcc---eecCceEEE
Confidence            7999999999999999999999   999999986

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.89  E-value=6.1e-23  Score=182.81  Aligned_cols=164  Identities=24%  Similarity=0.416  Sum_probs=145.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      |||.||++++|.++|...|..+|.|.++.|...+.       .|||||+|.++++|..|++.|+|+.+.|+.|.|.++..
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~  597 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISEN  597 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccC
Confidence            99999999999999999999999999998876543       39999999999999999999999999999999999872


Q ss_pred             CCC------ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          132 SGQ------REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       132 ~~~------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      ...      .......+.|+|.|+|+.++..+++.+|..||.+.+++++.....+.++|||||.|-+..+|..|+.+|.+
T Consensus       598 k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~S  677 (725)
T KOG0110|consen  598 KPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGS  677 (725)
T ss_pred             ccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcc
Confidence            221      11122357899999999999999999999999999999997644556799999999999999999999999


Q ss_pred             ceeCCeeeEEEEccCCC
Q 019811          206 KWLGSRQIRCNWATKGA  222 (335)
Q Consensus       206 ~~~~g~~l~v~~~~~~~  222 (335)
                      ..+.||.|.+.|++...
T Consensus       678 THlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  678 THLYGRRLVLEWAKSDN  694 (725)
T ss_pred             cceechhhheehhccch
Confidence            99999999999997643

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.89  E-value=4e-23  Score=165.26  Aligned_cols=142  Identities=27%  Similarity=0.485  Sum_probs=130.8

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ..|||+|||...++.+|+.+|++||.|..+.|+++        |+||..++...+..|+..|++-.+.|..|+|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            46999999999999999999999999999999944        8999999999999999999999999999999988765


Q ss_pred             CCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccc
Q 019811          222 AGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG  301 (335)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g  301 (335)
                      ..                                     .+.+|+|+|+.+.++-.+|+..|++||+  +.++.|.++  
T Consensus        75 sk-------------------------------------~stkl~vgNis~tctn~ElRa~fe~ygp--viecdivkd--  113 (346)
T KOG0109|consen   75 SK-------------------------------------ASTKLHVGNISPTCTNQELRAKFEKYGP--VIECDIVKD--  113 (346)
T ss_pred             CC-------------------------------------CccccccCCCCccccCHHHhhhhcccCC--ceeeeeecc--
Confidence            21                                     1267999999999999999999999994  888888866  


Q ss_pred             eEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          302 FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       302 ~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ++||+|+-.++|..|+..|+|.   +|.|++|+|
T Consensus       114 y~fvh~d~~eda~~air~l~~~---~~~gk~m~v  144 (346)
T KOG0109|consen  114 YAFVHFDRAEDAVEAIRGLDNT---EFQGKRMHV  144 (346)
T ss_pred             eeEEEEeeccchHHHHhccccc---ccccceeee
Confidence            9999999999999999999999   999999986

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.89  E-value=2e-23  Score=171.92  Aligned_cols=165  Identities=25%  Similarity=0.523  Sum_probs=140.9

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      +.+||+.+.+.+.|+.|+..|.+||+|+++.+.+|+.+++++|||||+|+-.+.|..|++.+||..++||.|+|.+...-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999854221


Q ss_pred             CCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc--
Q 019811          222 AGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--  299 (335)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~--  299 (335)
                      ....                        +......+.....++|||..++++++++||+.+|+.||  .|..|.+-++  
T Consensus       194 pQAQ------------------------piID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG--~I~~C~LAr~pt  247 (544)
T KOG0124|consen  194 PQAQ------------------------PIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG--EIVKCQLARAPT  247 (544)
T ss_pred             cccc------------------------hHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhc--ceeeEEeeccCC
Confidence            1000                        00000011112337899999999999999999999999  6999999765  


Q ss_pred             ----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 ----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 ----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                          +|++||+|.+..+...|+..||-.   .++|.-|+|
T Consensus       248 ~~~HkGyGfiEy~n~qs~~eAiasMNlF---DLGGQyLRV  284 (544)
T KOG0124|consen  248 GRGHKGYGFIEYNNLQSQSEAIASMNLF---DLGGQYLRV  284 (544)
T ss_pred             CCCccceeeEEeccccchHHHhhhcchh---hcccceEec
Confidence                799999999999999999999999   899998876

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.88  E-value=3.1e-20  Score=153.58  Aligned_cols=260  Identities=15%  Similarity=0.152  Sum_probs=205.1

Q ss_pred             EeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEeeeccCCC----
Q 019811           61 VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWAYASGQ----  134 (335)
Q Consensus        61 v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~~~~~~----  134 (335)
                      |-|--+.+|.+-|+.++...|.|.+|.|++. +.-.|.|+|++.+.|.+|...|||..|..  .+|+|+++++...    
T Consensus       127 IlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~k  205 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQK  205 (494)
T ss_pred             eecCccccchhhhhhhcCCCCceEEEEEEec-cceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeee
Confidence            3355588999999999999999999988876 44589999999999999999999998863  6889988855210    


Q ss_pred             ---------------------------------------------------------------------------ccCCC
Q 019811          135 ---------------------------------------------------------------------------REDTS  139 (335)
Q Consensus       135 ---------------------------------------------------------------------------~~~~~  139 (335)
                                                                                                 .....
T Consensus       206 nd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~  285 (494)
T KOG1456|consen  206 NDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGA  285 (494)
T ss_pred             cCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCC
Confidence                                                                                       00011


Q ss_pred             CcceEEECCCCcc-ccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          140 GHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       140 ~~~~l~v~nlp~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ++..++|.+|... ++-+.|.++|..||.|..|++++.+     .|.|+|++.|..+.++|+..|++..+.|.+|.|.++
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~S  360 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVS  360 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeec
Confidence            2367889999865 7789999999999999999999653     467999999999999999999999999999999999


Q ss_pred             cCCCCCCCC--CCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          219 TKGAGNNED--KQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       219 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      +........  .......+..+++.....+...+.........+++++|++-|.|..+||+.|.++|..-+ +...++++
T Consensus       361 kQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~-v~~~svkv  439 (494)
T KOG1456|consen  361 KQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKD-VPPTSVKV  439 (494)
T ss_pred             cccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcC-CCcceEEe
Confidence            876644332  122233334444444444445555556667778889999999999999999999999876 35677777


Q ss_pred             eccc----ceEEEEeCCHHHHHHHHHhhcCCCcccccC
Q 019811          297 QRDK----GFGFVRYSTHAEAALAIQMGNTTQSSYLFG  330 (335)
Q Consensus       297 ~~~~----g~afV~f~~~~~a~~A~~~l~g~~~~~~~g  330 (335)
                      ...+    ..+.++|++.++|..|+..+|..   .+.+
T Consensus       440 Fp~kserSssGllEfe~~s~Aveal~~~NH~---pi~~  474 (494)
T KOG1456|consen  440 FPLKSERSSSGLLEFENKSDAVEALMKLNHY---PIEG  474 (494)
T ss_pred             ecccccccccceeeeehHHHHHHHHHHhccc---cccC
Confidence            6442    47899999999999999999998   5554

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.87  E-value=6.4e-20  Score=151.76  Aligned_cols=272  Identities=18%  Similarity=0.214  Sum_probs=200.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHH--hCCccccCceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILS--LNGRHLFGQPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~--l~~~~~~g~~l~v~~~  129 (335)
                      .++.+..|.|++|-..++|.+|.+.++.||+|.-|.++..+.  .|.|+|++.+.|+.++..  -+...+.|..-.+.++
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r--~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyS  104 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR--QALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYS  104 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccc--eeeeeeccccchhhheehhccCcccccCchhhcccc
Confidence            356677899999999999999999999999998888776654  799999999999998843  3556777888888888


Q ss_pred             ccCCC----ccCCCCcceEE--ECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 019811          130 YASGQ----REDTSGHFNIF--VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL  203 (335)
Q Consensus       130 ~~~~~----~~~~~~~~~l~--v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  203 (335)
                      +....    .+...++..|.  |-|--+.+|.+-|..++...|.|.+|.|.+.     +.-.|+|+|++.+.|.+|...|
T Consensus       105 tsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-----ngVQAmVEFdsv~~AqrAk~al  179 (494)
T KOG1456|consen  105 TSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-----NGVQAMVEFDSVEVAQRAKAAL  179 (494)
T ss_pred             hhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-----cceeeEEeechhHHHHHHHhhc
Confidence            54322    22333444444  4455567999999999999999999988743     3346999999999999999999


Q ss_pred             CCcee--CCeeeEEEEccCCCCCCCCCCCc-------------ccccc----------hhccCCCCc-------------
Q 019811          204 TGKWL--GSRQIRCNWATKGAGNNEDKQSS-------------DAKSV----------VELTNGSSE-------------  245 (335)
Q Consensus       204 ~~~~~--~g~~l~v~~~~~~~~~~~~~~~~-------------~~~~~----------~~~~~~~~~-------------  245 (335)
                      ||..|  +.++|+|+|+++....-.+....             +++..          ....+.+..             
T Consensus       180 NGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~  259 (494)
T KOG1456|consen  180 NGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHG  259 (494)
T ss_pred             ccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCC
Confidence            99866  56889999998765211110000             00000          000000000             


Q ss_pred             ----------CC-cCCCCCCCCCCCCCCCeEEEcCCCc-ccCHHHHHHHhhhcCCeeeEEEEEecc-cceEEEEeCCHHH
Q 019811          246 ----------DG-KETTNTEAPENNPQYTTVYVGNLAP-EVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAE  312 (335)
Q Consensus       246 ----------~~-~~~~~~~~~~~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~i~~v~~~~~-~g~afV~f~~~~~  312 (335)
                                .. ........+....+++.++|.+|.- .++.+.|..+|..||  .|..|++++. .|.|.|++.|..+
T Consensus       260 p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYG--NV~rvkFmkTk~gtamVemgd~~a  337 (494)
T KOG1456|consen  260 PPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYG--NVERVKFMKTKPGTAMVEMGDAYA  337 (494)
T ss_pred             CCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcC--ceeeEEEeecccceeEEEcCcHHH
Confidence                      00 0001122234556678999999986 688999999999999  6999999987 5899999999999


Q ss_pred             HHHHHHhhcCCCcccccCccccC
Q 019811          313 AALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       313 a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .++|+..||+.   .+-|.+|.|
T Consensus       338 ver~v~hLnn~---~lfG~kl~v  357 (494)
T KOG1456|consen  338 VERAVTHLNNI---PLFGGKLNV  357 (494)
T ss_pred             HHHHHHHhccC---ccccceEEE
Confidence            99999999999   777877754

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=7.5e-21  Score=150.53  Aligned_cols=170  Identities=27%  Similarity=0.465  Sum_probs=147.2

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccc-cC--ceeEEe
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHL-FG--QPIKVN  127 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~-~g--~~l~v~  127 (335)
                      .+.+.|||+-|...-+|+|++.+|..||.|+++.+.+..   ++|+|||.|.+..+|..||..|+|..- .|  ..|.|+
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            366889999999999999999999999999999998854   579999999999999999999999644 34  467777


Q ss_pred             eeccCC--------------------------------------------------------------------------
Q 019811          128 WAYASG--------------------------------------------------------------------------  133 (335)
Q Consensus       128 ~~~~~~--------------------------------------------------------------------------  133 (335)
                      ++....                                                                          
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            763221                                                                          


Q ss_pred             --------------------------------------------------------------------------------
Q 019811          134 --------------------------------------------------------------------------------  133 (335)
Q Consensus       134 --------------------------------------------------------------------------------  133 (335)
                                                                                                      
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                                                                                            


Q ss_pred             ---------------------CccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCC
Q 019811          134 ---------------------QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN  192 (335)
Q Consensus       134 ---------------------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~  192 (335)
                                           ...+...+++|||-.||.+....||...|-+||.|.+.++..|+.++.++.|+||.|++
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                                 00112235899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeeEEEEccCCCC
Q 019811          193 QQDAQSAINDLTGKWLGSRQIRCNWATKGAG  223 (335)
Q Consensus       193 ~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~  223 (335)
                      ..+|..||..+||..|+=++|+|....++..
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            9999999999999999999999988776553

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=1e-20  Score=166.52  Aligned_cols=263  Identities=21%  Similarity=0.323  Sum_probs=197.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcc-----------C-CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSST-----------G-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~-----------G-~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      ....+.++|+++|..++++++..+|..-           | .+..+.+-.  .+++||++|.+.++|..|. .+++..+.
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~--~~nfa~ie~~s~~~at~~~-~~~~~~f~  248 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL--EKNFAFIEFRSISEATEAM-ALDGIIFE  248 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc--cccceeEEecCCCchhhhh-cccchhhC
Confidence            4456789999999999999999999753           3 255555544  4469999999999999987 58899999


Q ss_pred             CceeEEeeeccCCC--------------------ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCC
Q 019811          121 GQPIKVNWAYASGQ--------------------REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG  180 (335)
Q Consensus       121 g~~l~v~~~~~~~~--------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~  180 (335)
                      |..+++.-......                    .........++|++||..++++.+.++...||.+....++.+..+|
T Consensus       249 g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g  328 (500)
T KOG0120|consen  249 GRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATG  328 (500)
T ss_pred             CCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccc
Confidence            99888754322211                    1122345679999999999999999999999999999999998889


Q ss_pred             CcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCC
Q 019811          181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNP  260 (335)
Q Consensus       181 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (335)
                      .++||||.+|.+......|++.|+|..++++.+.|..+..................           .............
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~-----------~~i~~~~~q~~g~  397 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQV-----------PGIPLLMTQMAGI  397 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCcccccc-----------ccchhhhcccCCC
Confidence            99999999999999999999999999999999999998776544333222000000           0000000122223


Q ss_pred             CCCeEEEcCCC--cccCH--------HHHHHHhhhcCCeeeEEEEEecc---------cceEEEEeCCHHHHHHHHHhhc
Q 019811          261 QYTTVYVGNLA--PEVTQ--------LDLHRHFHSLGAGVIEEVRVQRD---------KGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       261 ~~~~l~v~nlp--~~~t~--------~~l~~~f~~~G~~~i~~v~~~~~---------~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      +...|.+.|+=  .++.+        |+++..|.+||  .+..|.++++         -|..||+|.+.++|.+|+..|+
T Consensus       398 ~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g--~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~  475 (500)
T KOG0120|consen  398 PTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFG--AVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELT  475 (500)
T ss_pred             cchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccC--ceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHcc
Confidence            34566666662  22221        46777788999  4888888766         4789999999999999999999


Q ss_pred             CCCcccccCcccc
Q 019811          322 TTQSSYLFGKQMK  334 (335)
Q Consensus       322 g~~~~~~~g~~l~  334 (335)
                      |+   .|.||.+.
T Consensus       476 Gr---KF~nRtVv  485 (500)
T KOG0120|consen  476 GR---KFANRTVV  485 (500)
T ss_pred             Cc---eeCCcEEE
Confidence            99   99999863

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.85  E-value=2e-19  Score=154.32  Aligned_cols=262  Identities=18%  Similarity=0.201  Sum_probs=177.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec--CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~--~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      .....-|.+++||.++|++||.+||+.++ |+++.+.+.  +.+|-|||+|.+.+++++|++ .+-..+..+-|.|-.+.
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            34456689999999999999999999986 556666654  457999999999999999996 57778888888886653


Q ss_pred             cCC--------CccCCCCcceEEECCCCccccHHHHHHHhccCCCcee-eEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 019811          131 ASG--------QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD-ARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN  201 (335)
Q Consensus       131 ~~~--------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~  201 (335)
                      ...        ..........|.+.+||+.+|++||.++|+..-.+.. +.++.+ ..+++.|-|||+|++.+.|+.|+.
T Consensus        85 ~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~  163 (510)
T KOG4211|consen   85 GAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALG  163 (510)
T ss_pred             CccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHH
Confidence            322        2223345678999999999999999999998755555 334545 456789999999999999999997


Q ss_pred             HhCCceeCCeeeEEEEccCCCCCCCC------C---C-----Ccccc---------------c-------c---------
Q 019811          202 DLTGKWLGSRQIRCNWATKGAGNNED------K---Q-----SSDAK---------------S-------V---------  236 (335)
Q Consensus       202 ~l~~~~~~g~~l~v~~~~~~~~~~~~------~---~-----~~~~~---------------~-------~---------  236 (335)
                      . +...|+.+-|.|..+.........      .   .     .....               .       .         
T Consensus       164 r-hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~  242 (510)
T KOG4211|consen  164 R-HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSL  242 (510)
T ss_pred             H-HHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccc
Confidence            4 777888888888654221110000      0   0     00000               0       0         


Q ss_pred             hhc-cCCCC---------c---CCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec---cc
Q 019811          237 VEL-TNGSS---------E---DGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR---DK  300 (335)
Q Consensus       237 ~~~-~~~~~---------~---~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~---~~  300 (335)
                      .+. .....         .   ...................++.++||++.++.+|.++|+..-. .-+.|.+..   ..
T Consensus       243 ~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p-~~v~i~ig~dGr~T  321 (510)
T KOG4211|consen  243 QDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNP-YRVHIEIGPDGRAT  321 (510)
T ss_pred             cccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCc-eeEEEEeCCCCccC
Confidence            000 00000         0   0000000000111122267999999999999999999997642 234444443   36


Q ss_pred             ceEEEEeCCHHHHHHHHHh
Q 019811          301 GFGFVRYSTHAEAALAIQM  319 (335)
Q Consensus       301 g~afV~f~~~~~a~~A~~~  319 (335)
                      |-|+|+|.+.++|..||..
T Consensus       322 GEAdveF~t~edav~Amsk  340 (510)
T KOG4211|consen  322 GEADVEFATGEDAVGAMGK  340 (510)
T ss_pred             CcceeecccchhhHhhhcc
Confidence            8999999999999999854

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=2.6e-20  Score=139.47  Aligned_cols=157  Identities=20%  Similarity=0.329  Sum_probs=131.7

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ..+++|||+|||.++.+.+|.++|-+||.|..|.+-.... ..||||+|+++.+|+.|+..-+|-.+.|..|+|+++...
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            4568899999999999999999999999999988744332 479999999999999999999999999999999997543


Q ss_pred             CC-----------------------ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEE
Q 019811          133 GQ-----------------------REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVS  189 (335)
Q Consensus       133 ~~-----------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~  189 (335)
                      ..                       .......+.|.|++||++.++.+|++...+.|+|-...+.+|       |++.|+
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~  156 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVE  156 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeee
Confidence            11                       112233478999999999999999999999999998888866       369999


Q ss_pred             eCCHHHHHHHHHHhCCcee--CCeeeEEEE
Q 019811          190 FRNQQDAQSAINDLTGKWL--GSRQIRCNW  217 (335)
Q Consensus       190 f~~~~~a~~a~~~l~~~~~--~g~~l~v~~  217 (335)
                      |...++.+.|+..|+...+  .|.+..+..
T Consensus       157 ~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  157 YLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             eeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            9999999999999988765  344444443

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.84  E-value=8.2e-21  Score=150.29  Aligned_cols=208  Identities=25%  Similarity=0.365  Sum_probs=150.1

Q ss_pred             CceeEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 019811          121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI  200 (335)
Q Consensus       121 g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~  200 (335)
                      +|.|.|+.+...++.   ..+++|||+-|.+.-+|+|++.+|..||.++++.+++. ..|.++|.+||+|.+.-+|..||
T Consensus         2 nrpiqvkpadsesrg---~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~s~~eAqaAI   77 (371)
T KOG0146|consen    2 NRPIQVKPADSESRG---GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG-PDGNSKGCAFVKFSSHAEAQAAI   77 (371)
T ss_pred             CCCccccccccccCC---ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC-CCCCCCCceEEEeccchHHHHHH
Confidence            466777777655433   24578999999999999999999999999999999987 46899999999999999999999


Q ss_pred             HHhCCce-eC--CeeeEEEEccCCCCCCCCCCCc--------cc---------------------------ccc------
Q 019811          201 NDLTGKW-LG--SRQIRCNWATKGAGNNEDKQSS--------DA---------------------------KSV------  236 (335)
Q Consensus       201 ~~l~~~~-~~--g~~l~v~~~~~~~~~~~~~~~~--------~~---------------------------~~~------  236 (335)
                      ..|+|.. +-  ...|.|+|++..+++..++-..        .+                           ...      
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~  157 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAA  157 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhh
Confidence            9999964 43  4678899987766211100000        00                           000      


Q ss_pred             -------------------hhc----------------------------------------------cCC---CCcCC-
Q 019811          237 -------------------VEL----------------------------------------------TNG---SSEDG-  247 (335)
Q Consensus       237 -------------------~~~----------------------------------------------~~~---~~~~~-  247 (335)
                                         .++                                              .++   ..... 
T Consensus       158 ~~~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp  237 (371)
T KOG0146|consen  158 FAAAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSP  237 (371)
T ss_pred             hHHHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCc
Confidence                               000                                              000   00000 


Q ss_pred             ---------------------------------cCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEE
Q 019811          248 ---------------------------------KETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEV  294 (335)
Q Consensus       248 ---------------------------------~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v  294 (335)
                                                       ............++++.|||..||....+.||..+|-.||.+....|
T Consensus       238 ~va~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKV  317 (371)
T KOG0146|consen  238 TVADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKV  317 (371)
T ss_pred             cccchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeee
Confidence                                             00000011234567799999999999999999999999996333444


Q ss_pred             EEec----ccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          295 RVQR----DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       295 ~~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .++|    +++++||.|+++.+|..|+..|||.   .|+-++|+|
T Consensus       318 FvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGF---QIGMKRLKV  359 (371)
T KOG0146|consen  318 FVDRATNQSKCFGFVSFDNPASAQAAIQAMNGF---QIGMKRLKV  359 (371)
T ss_pred             eehhccccccceeeEecCCchhHHHHHHHhcch---hhhhhhhhh
Confidence            4443    3789999999999999999999999   999999986

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.82  E-value=5.6e-19  Score=137.68  Aligned_cols=159  Identities=18%  Similarity=0.398  Sum_probs=137.2

Q ss_pred             cceEEEeCCCCCCCHHHHHH----HHhccCCceeEEEeec-CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           56 CRSVYVGNIHTQVTEPLLQE----VFSSTGPVEGCKLIRK-DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~----~f~~~G~v~~v~~~~~-~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..||||.||+..+..++|+.    +|++||.|.+|...+. +.+|.|||.|.+.+.|..|+..|+|..|.|+.++|.|+.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            34899999999999999888    9999999999988864 568999999999999999999999999999999999986


Q ss_pred             cCCCc-----------------------------------------------cCCCCcceEEECCCCccccHHHHHHHhc
Q 019811          131 ASGQR-----------------------------------------------EDTSGHFNIFVGDLSPEVTDATLFACFS  163 (335)
Q Consensus       131 ~~~~~-----------------------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~  163 (335)
                      .++..                                               ....++..+++.|||...+.+.+..+|.
T Consensus        89 s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~  168 (221)
T KOG4206|consen   89 SDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFE  168 (221)
T ss_pred             CccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHh
Confidence            54210                                               0123457899999999999999999999


Q ss_pred             cCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeeeEEEEcc
Q 019811          164 VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG-SRQIRCNWAT  219 (335)
Q Consensus       164 ~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~~~  219 (335)
                      .|.....++++..     ..+.|||+|.+...|..|...+.+..+. ...+.|.+++
T Consensus       169 qf~g~keir~i~~-----~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  169 QFPGFKEIRLIPP-----RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hCcccceeEeccC-----CCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999988843     3568999999999999999999998875 7888887764

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.82  E-value=1.2e-18  Score=135.89  Aligned_cols=185  Identities=19%  Similarity=0.263  Sum_probs=140.0

Q ss_pred             CcceEEECCCCccccHHHHHH----HhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFA----CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ++.+|||.||+..+..++|++    +|+.||.|..|...   .+.+.+|-|||.|++.+.|-.|+..|+|..+.|+.+++
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            344999999999999999998    99999999999887   45688999999999999999999999999999999999


Q ss_pred             EEccCCCCCCCCCCCcccccchh-------------ccCCCC---cCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHH
Q 019811          216 NWATKGAGNNEDKQSSDAKSVVE-------------LTNGSS---EDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDL  279 (335)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~---~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l  279 (335)
                      .|++.+..........-......             ..++..   .....+.+. .....+++..+++.|||..++.+.+
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~-~~~~~ppn~ilf~~niP~es~~e~l  163 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPF-LAQMAPPNNILFLTNIPSESESEML  163 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCc-cccCCCCceEEEEecCCcchhHHHH
Confidence            99987664443321100000000             000000   000011111 1344677899999999999999999


Q ss_pred             HHHhhhcCCeeeEEEEEecc-cceEEEEeCCHHHHHHHHHhhcCCCccccc-Cccc
Q 019811          280 HRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAIQMGNTTQSSYLF-GKQM  333 (335)
Q Consensus       280 ~~~f~~~G~~~i~~v~~~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~~~~-g~~l  333 (335)
                      ..+|+.|.+  ...+++... ++.|||+|.+...|..|...+.|.   .+. ...|
T Consensus       164 ~~lf~qf~g--~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~---~it~~~~m  214 (221)
T KOG4206|consen  164 SDLFEQFPG--FKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGF---KITKKNTM  214 (221)
T ss_pred             HHHHhhCcc--cceeEeccCCCceeEEecchhhhhHHHhhhhccc---eeccCceE
Confidence            999999984  888888875 689999999999999999999998   554 4443

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.80  E-value=3.4e-19  Score=149.79  Aligned_cols=170  Identities=22%  Similarity=0.416  Sum_probs=148.7

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      +.+.|||++|+.+++++.|++.|.+||.|.++.++++.    ++||+||.|.+++...+++. .....+.|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            67889999999999999999999999999999999875    35899999999999988874 44678899999998887


Q ss_pred             cCCCccCC---CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          131 ASGQREDT---SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       131 ~~~~~~~~---~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      ++......   .....+||++||.+++++++++.|.+||.|..+.++.|..+..+++|+||.|.+++++.+++. ..-..
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~  162 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHD  162 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceee
Confidence            66543332   245689999999999999999999999999999999999999999999999999999999986 57788


Q ss_pred             eCCeeeEEEEccCCCCCCC
Q 019811          208 LGSRQIRCNWATKGAGNNE  226 (335)
Q Consensus       208 ~~g~~l~v~~~~~~~~~~~  226 (335)
                      |.|+.+.|..+.++.....
T Consensus       163 ~~gk~vevkrA~pk~~~~~  181 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVMQS  181 (311)
T ss_pred             ecCceeeEeeccchhhccc
Confidence            9999999999988765443

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.78  E-value=1e-17  Score=125.73  Aligned_cols=169  Identities=22%  Similarity=0.341  Sum_probs=127.9

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .++.|||+|||.++-+.+|.++|.+||.|..|.+...   .....||||+|++..+|+.|+..-+|-.++|..|+|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4578999999999999999999999999999987632   2456799999999999999999889999999999999987


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~  299 (335)
                      ...........-.     .-...    +......-.+..-.....|.|.+||+.-++.||++.+.+-|  ++....+.++
T Consensus        82 ggr~s~~~~G~y~-----gggrg----Ggg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaG--dvCfadv~rD  150 (241)
T KOG0105|consen   82 GGRSSSDRRGSYS-----GGGRG----GGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAG--DVCFADVQRD  150 (241)
T ss_pred             CCCcccccccccC-----CCCCC----CCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhC--Ceeeeeeecc
Confidence            6542221111000     00000    11111111112222236799999999999999999999999  5776666664


Q ss_pred             cceEEEEeCCHHHHHHHHHhhcCC
Q 019811          300 KGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       300 ~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                       |.+.|+|...++.+.|+..|...
T Consensus       151 -g~GvV~~~r~eDMkYAvr~ld~~  173 (241)
T KOG0105|consen  151 -GVGVVEYLRKEDMKYAVRKLDDQ  173 (241)
T ss_pred             -cceeeeeeehhhHHHHHHhhccc
Confidence             69999999999999999999877

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.76  E-value=2.1e-18  Score=145.07  Aligned_cols=160  Identities=29%  Similarity=0.507  Sum_probs=133.6

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ....+||++|+..++++.|++.|..||+|..+.+++|+.+++++||+||+|++.+...+++. .....++|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            45789999999999999999999999999999999999999999999999999999888886 46678999999988887


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~  299 (335)
                      +........                             .......|||++||.++++++++++|++||  .+..+.++.+
T Consensus        84 ~r~~~~~~~-----------------------------~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g--~v~~~~~~~d  132 (311)
T KOG4205|consen   84 SREDQTKVG-----------------------------RHLRTKKIFVGGLPPDTTEEDFKDYFEQFG--KVADVVIMYD  132 (311)
T ss_pred             Ccccccccc-----------------------------cccceeEEEecCcCCCCchHHHhhhhhccc--eeEeeEEeec
Confidence            755332221                             111347899999999999999999999999  5666666533


Q ss_pred             ------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 ------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 ------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                            ++++||+|.+.++..+++ ..+-+   .|+|+.+.|
T Consensus       133 ~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~---~~~gk~vev  170 (311)
T KOG4205|consen  133 KTTSRPRGFGFVTFDSEDSVDKVT-LQKFH---DFNGKKVEV  170 (311)
T ss_pred             ccccccccceeeEeccccccceec-cccee---eecCceeeE
Confidence                  799999999999999987 44555   788887764

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.75  E-value=5.4e-17  Score=125.49  Aligned_cols=184  Identities=16%  Similarity=0.261  Sum_probs=126.7

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC---CeeeEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMW-DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG---SRQIRC  215 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~-~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~---g~~l~v  215 (335)
                      .-++|||.+||.++...||..+|..|-..+...+.. ++.....+-+||+.|.+...|..|+..|||..|+   +..|++
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            357999999999999999999999997777665543 2222345679999999999999999999999985   788999


Q ss_pred             EEccCCCCCCCCCCCcccccchhc---------------------------cCCCCcCCcCCC-----------------
Q 019811          216 NWATKGAGNNEDKQSSDAKSVVEL---------------------------TNGSSEDGKETT-----------------  251 (335)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~~~~-----------------  251 (335)
                      ++++........+....+.....+                           ............                 
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            987654433322222211110000                           000000000000                 


Q ss_pred             -------CCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          252 -------NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       252 -------~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                             ..+.......+.||||.||..+++|++|+.+|+.|.+-.+..++-......||++|++.+.|..||..|.|.
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~  271 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGN  271 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcc
Confidence                   000011122236899999999999999999999997534555555555678999999999999999999998

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.75  E-value=9.2e-17  Score=124.21  Aligned_cols=153  Identities=22%  Similarity=0.369  Sum_probs=121.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEee-cCC----CCeEEEEEcCHHHHHHHHHHhCCcccc---Cce
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDK----SSYGFIHYFDRRSAAMAILSLNGRHLF---GQP  123 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~-~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~---g~~  123 (335)
                      .+...+||||.+||.++...||+.+|..|--.+...+.. ++.    +..|||.|.+..+|..|+.+|||..|+   +.+
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            466689999999999999999999999986665554432 222    369999999999999999999999997   788


Q ss_pred             eEEeeeccCCCcc-------------------------------------------------------------------
Q 019811          124 IKVNWAYASGQRE-------------------------------------------------------------------  136 (335)
Q Consensus       124 l~v~~~~~~~~~~-------------------------------------------------------------------  136 (335)
                      |+|++++......                                                                   
T Consensus       110 LhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~  189 (284)
T KOG1457|consen  110 LHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSK  189 (284)
T ss_pred             eEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhc
Confidence            9998875432100                                                                   


Q ss_pred             ----------------CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 019811          137 ----------------DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI  200 (335)
Q Consensus       137 ----------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~  200 (335)
                                      ......+|||.||..+++|++|+.+|+.|.....++|.-    ......||++|++.+.|..|+
T Consensus       190 ~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g~~vaf~~~~~~~~at~am  265 (284)
T KOG1457|consen  190 APSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGGMPVAFADFEEIEQATDAM  265 (284)
T ss_pred             CCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCCcceEeecHHHHHHHHHHH
Confidence                            001125799999999999999999999998877776652    233457999999999999999


Q ss_pred             HHhCCcee
Q 019811          201 NDLTGKWL  208 (335)
Q Consensus       201 ~~l~~~~~  208 (335)
                      ..|.|..+
T Consensus       266 ~~lqg~~~  273 (284)
T KOG1457|consen  266 NHLQGNLL  273 (284)
T ss_pred             HHhhccee
Confidence            99998765

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.74  E-value=1.9e-16  Score=130.25  Aligned_cols=166  Identities=23%  Similarity=0.354  Sum_probs=134.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCcee--------EEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG--------CKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      .+..+..|||.|||.++|.+++.++|++||.|.+        |++.++..   +|-|++.|...+++..|+..|++..+.
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            3556677999999999999999999999998753        67777653   689999999999999999999999999


Q ss_pred             CceeEEeeeccCC-----------------------------------CccCCCCcceEEECCCCcc----cc-------
Q 019811          121 GQPIKVNWAYASG-----------------------------------QREDTSGHFNIFVGDLSPE----VT-------  154 (335)
Q Consensus       121 g~~l~v~~~~~~~-----------------------------------~~~~~~~~~~l~v~nlp~~----~t-------  154 (335)
                      |+.|+|..+.-..                                   ........++|.+.|+-..    .+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            9999998662110                                   0112234578888888321    22       


Q ss_pred             HHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          155 DATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       155 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      .++|.+-+.+||.|.+|.+. +   ..+.|.+-|.|.+.+.|..|++.|+|++|+||.|......-+
T Consensus       290 kedl~eec~K~G~v~~vvv~-d---~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVY-D---RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEe-c---cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            46777889999999999776 2   367889999999999999999999999999999998876543

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.74  E-value=1.2e-18  Score=151.56  Aligned_cols=168  Identities=27%  Similarity=0.412  Sum_probs=136.3

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .+++|+.-++-..+.-+|.++|+.+|.|..|.++.|+.++.++|.|||+|.|.+....|+. |.|..+.|.+|.|..+..
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHH
Confidence            4677777788888899999999999999999999999999999999999999999999995 899999999999987654


Q ss_pred             CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-
Q 019811          221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-  299 (335)
                      .+...  .....                   .........+...|||+||++++++++|+..|++||.  |..|.+.++ 
T Consensus       258 eknr~--a~~s~-------------------a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~--Ie~v~l~~d~  314 (549)
T KOG0147|consen  258 EKNRA--ANASP-------------------ALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGK--IENVQLTKDS  314 (549)
T ss_pred             HHHHH--Hhccc-------------------cccccccccchhhhhhcccccCchHHHHhhhccCccc--ceeeeecccc
Confidence            33210  00000                   0000111112234999999999999999999999994  666666544 


Q ss_pred             -----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 -----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                           +|++||+|.+.++|.+|+..|||.   ++-|+.|+|
T Consensus       315 ~tG~skgfGfi~f~~~~~ar~a~e~lngf---elAGr~ikV  352 (549)
T KOG0147|consen  315 ETGRSKGFGFITFVNKEDARKALEQLNGF---ELAGRLIKV  352 (549)
T ss_pred             ccccccCcceEEEecHHHHHHHHHHhccc---eecCceEEE
Confidence                 799999999999999999999999   999999986

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

Probab=99.73  E-value=4.7e-17  Score=123.64  Aligned_cols=85  Identities=40%  Similarity=0.615  Sum_probs=79.6

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ...+++|||+|||.++++++|+++|++||.|.++.+++++.++.++|||||+|.+.++|..|++.|++..+.|+.|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +..+.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            87644

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

Probab=99.70  E-value=2.9e-16  Score=119.32  Aligned_cols=81  Identities=25%  Similarity=0.451  Sum_probs=74.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ...+++|||+|||.++++++|+++|++||.|.++++..++    ++|||||+|.+.++|+.|++.||+..|.|+.|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4456789999999999999999999999999999998764    468999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +..+.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            87654

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.70  E-value=4.3e-16  Score=128.21  Aligned_cols=187  Identities=17%  Similarity=0.230  Sum_probs=134.5

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCce--------eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCS--------DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      .-++.|||+|||.++|.+++.++|++||.|.        .|++.++ ..|..+|-|++.|-..+++..|+..|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            4456799999999999999999999999763        4788888 458999999999999999999999999999999


Q ss_pred             eeeEEEEccCCCCCCCCCCCc---ccccchh---ccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcc----cC-----
Q 019811          211 RQIRCNWATKGAGNNEDKQSS---DAKSVVE---LTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPE----VT-----  275 (335)
Q Consensus       211 ~~l~v~~~~~~~~~~~~~~~~---~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~----~t-----  275 (335)
                      +.|+|..+.......-.....   .+.....   ............   ..+......++|.+.|+-..    .+     
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~---~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~  287 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDR---DDPSKARADRTVILKNMFTPEDFEKNPDLLN  287 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCc---cccccccCCcEEEeeecCCHHHhccCHHHHH
Confidence            999999876533211111000   0000000   000000000000   11222334489999998321    22     


Q ss_pred             --HHHHHHHhhhcCCeeeEEEEEe--cccceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          276 --QLDLHRHFHSLGAGVIEEVRVQ--RDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       276 --~~~l~~~f~~~G~~~i~~v~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                        .++|++-+++||.  +..|.+.  .+.|.+.|.|.+.++|..++..|+|+   .|+||+|+
T Consensus       288 dlkedl~eec~K~G~--v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR---~fdgRql~  345 (382)
T KOG1548|consen  288 DLKEDLTEECEKFGQ--VRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGR---WFDGRQLT  345 (382)
T ss_pred             HHHHHHHHHHHHhCC--cceEEEeccCCCceeEEEeCChHHHHHHHHHhcCe---eecceEEE
Confidence              4677888999994  7777665  55899999999999999999999999   99999985

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.68  E-value=2.1e-16  Score=131.61  Aligned_cols=270  Identities=16%  Similarity=0.143  Sum_probs=174.9

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCce----eEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVE----GCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~----~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ....|..++||...+..+|..+|+......    -+.....+..|.+.|.|.+.+.-+.|++. +...++++.+.|-.+.
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~  137 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKAT  137 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccC
Confidence            344578899999999999999998542221    11112233458999999999999999865 4566677777775443


Q ss_pred             cCC-------------CccCCCCcceEEECCCCccccHHHHHHHhccC----CCceeeEEeecCCCCCcceEEEEEeCCH
Q 019811          131 ASG-------------QREDTSGHFNIFVGDLSPEVTDATLFACFSVY----PSCSDARVMWDQKTGRSRGFGFVSFRNQ  193 (335)
Q Consensus       131 ~~~-------------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~----g~v~~~~~~~~~~~~~~~g~afv~f~~~  193 (335)
                      ...             ...+...--.|.+++||+++++.++.++|..-    |..+.+-+++. .+|+..|-|||.|..+
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACE  216 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCH
Confidence            221             11111223467889999999999999999632    35556655544 4688999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcc
Q 019811          194 QDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPE  273 (335)
Q Consensus       194 ~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~  273 (335)
                      ++|..|+.. +...++-|.|.+-.+...............    +.............+...-.......+|.+++||+.
T Consensus       217 e~aq~aL~k-hrq~iGqRYIElFRSTaaEvqqvlnr~~s~----pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~  291 (508)
T KOG1365|consen  217 EDAQFALRK-HRQNIGQRYIELFRSTAAEVQQVLNREVSE----PLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYE  291 (508)
T ss_pred             HHHHHHHHH-HHHHHhHHHHHHHHHhHHHHHHHHHhhccc----cccCCCCCCCCCCCccccCCCCCCCCeeEecCCChh
Confidence            999999975 666677777666555432210000000000    000000000000001111112222478999999999


Q ss_pred             cCHHHHHHHhhhcCCeeeEE--EEEe-----cccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          274 VTQLDLHRHFHSLGAGVIEE--VRVQ-----RDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       274 ~t~~~l~~~f~~~G~~~i~~--v~~~-----~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .+.|||.++|..|- ..+..  |.+.     +..|.|||+|.+.++|..|+...+++   .+.+|-|.|
T Consensus       292 AtvEdIL~FlgdFa-~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~---~mk~RYiEv  356 (508)
T KOG1365|consen  292 ATVEDILDFLGDFA-TDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKK---LMKSRYIEV  356 (508)
T ss_pred             hhHHHHHHHHHHHh-hhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHh---hcccceEEE
Confidence            99999999999875 23333  3332     34689999999999999999998888   666776654

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=2.3e-16  Score=124.52  Aligned_cols=162  Identities=25%  Similarity=0.417  Sum_probs=127.5

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      .+||++||+.+.+.+|.++|..||.+..+.+.        .||+||+|.+..+|..|+..+++..+.|..+.|.|+....
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            58999999999999999999999999998765        3578999999999999999999999999888888887532


Q ss_pred             CCCCCCCCcccccchhccCCCCcCCcCC-CCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccc
Q 019811          223 GNNEDKQSSDAKSVVELTNGSSEDGKET-TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG  301 (335)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g  301 (335)
                      .....                +..+... ............+.+.|.+++..+.+.+|.+.|+++|.  +.....  .++
T Consensus        75 ~~~g~----------------~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~--~~~~~~--~~~  134 (216)
T KOG0106|consen   75 RGRGR----------------PRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGE--VTYVDA--RRN  134 (216)
T ss_pred             cccCC----------------CCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCC--Cchhhh--hcc
Confidence            21100                0000000 01111122334478999999999999999999999994  444333  567


Q ss_pred             eEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          302 FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       302 ~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .+||+|.+..+|.+|++.|+|.   .+.|++|++
T Consensus       135 ~~~v~Fs~~~da~ra~~~l~~~---~~~~~~l~~  165 (216)
T KOG0106|consen  135 FAFVEFSEQEDAKRALEKLDGK---KLNGRRISV  165 (216)
T ss_pred             ccceeehhhhhhhhcchhccch---hhcCceeee
Confidence            9999999999999999999999   999999875

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.66  E-value=2.7e-16  Score=128.47  Aligned_cols=82  Identities=27%  Similarity=0.355  Sum_probs=75.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .....++|+|.|||+...+-||+.+|.+||.|.+|.|+.+.  ++||+||.|++++||++|..+|||..+.||+|.|+.+
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            44556789999999999999999999999999999999864  5899999999999999999999999999999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      +.+.
T Consensus       172 TarV  175 (376)
T KOG0125|consen  172 TARV  175 (376)
T ss_pred             chhh
Confidence            7664

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=3.6e-16  Score=123.44  Aligned_cols=149  Identities=28%  Similarity=0.470  Sum_probs=127.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC----
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS----  132 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~----  132 (335)
                      ..|||++||+.+.+.+|..+|..||.+..+.+    ..||+||+|.+..+|..|+..||+..+.|..+.+.|+...    
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m----k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~   77 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM----KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGR   77 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee----ecccceeccCchhhhhcccchhcCceecceeeeeeccccccccc
Confidence            35999999999999999999999999988866    3368999999999999999999999999998999988742    


Q ss_pred             --CCc-----------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHH
Q 019811          133 --GQR-----------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA  199 (335)
Q Consensus       133 --~~~-----------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  199 (335)
                        +..           ......+.+.+.+++..+.+.+|.+.|..+|.+.....        ..+++||+|...++|.+|
T Consensus        78 g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra  149 (216)
T KOG0106|consen   78 GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRA  149 (216)
T ss_pred             CCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhc
Confidence              111           11233567899999999999999999999999844433        245799999999999999


Q ss_pred             HHHhCCceeCCeeeEEEE
Q 019811          200 INDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       200 ~~~l~~~~~~g~~l~v~~  217 (335)
                      +..|++..+.++.|.+..
T Consensus       150 ~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  150 LEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             chhccchhhcCceeeecc
Confidence            999999999999999943

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=7.8e-16  Score=114.80  Aligned_cols=79  Identities=28%  Similarity=0.510  Sum_probs=72.9

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQ  134 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~  134 (335)
                      -.+.|||+||+..+++.||...|..||++.+|||...+ .|||||+|+++.+|+.|+..|+|..|.|..|+|+++.....
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            35779999999999999999999999999999998854 48999999999999999999999999999999999976554

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.64  E-value=2.8e-15  Score=101.66  Aligned_cols=84  Identities=18%  Similarity=0.252  Sum_probs=75.7

Q ss_pred             CCCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           48 PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        48 ~~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ++..++...+-|||+|||+++|.+++.++|.+||.|..|++-..+ .+|.|||.|++..+|++|++.|+|..+.++.+.|
T Consensus        10 ~~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~v   89 (124)
T KOG0114|consen   10 NIRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVV   89 (124)
T ss_pred             CCCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEE
Confidence            444456778889999999999999999999999999999997766 4699999999999999999999999999999999


Q ss_pred             eeecc
Q 019811          127 NWAYA  131 (335)
Q Consensus       127 ~~~~~  131 (335)
                      .+..+
T Consensus        90 lyyq~   94 (124)
T KOG0114|consen   90 LYYQP   94 (124)
T ss_pred             EecCH
Confidence            88754

>PF00076 RRM_1: RNA recognition motif

Probab=99.61  E-value=2.2e-15  Score=100.74  Aligned_cols=67  Identities=34%  Similarity=0.652  Sum_probs=62.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      |||+|||.++|+++|+++|+.||.|..+++..+   ..+++|||+|.+.++|.+|++.++|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999885   2358999999999999999999999999999885

(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 ....

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

Probab=99.61  E-value=4.2e-15  Score=116.81  Aligned_cols=84  Identities=27%  Similarity=0.477  Sum_probs=80.2

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+..+|.|.||+.+++|++|.++|.+||.|.++.+.+|+.+|.++|||||.|.+.++|.+|++.|+|.-+++-.|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            34667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      ++++
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9874

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.60  E-value=3.1e-14  Score=122.78  Aligned_cols=164  Identities=19%  Similarity=0.272  Sum_probs=119.7

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .....|.+.+||.++|++||.++|+.+ .|..+.+.+  .+|++.|-|||+|.+++++.+|++ .+...+..+.|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            344678899999999999999999988 466665554  478999999999999999999997 5888899999999877


Q ss_pred             cCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEe-
Q 019811          219 TKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ-  297 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~-  297 (335)
                      .........+...                        +........|.+++||+.+|++||.++|+..-.+.. -+.+. 
T Consensus        84 ~~~e~d~~~~~~g------------------------~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~-gi~l~~  138 (510)
T KOG4211|consen   84 GGAEADWVMRPGG------------------------PNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPD-GILLPM  138 (510)
T ss_pred             CCccccccccCCC------------------------CCCCCCCceEEecCCCccCcHHHHHHHhcCCccccc-ceeeec
Confidence            6544322111000                        000022367999999999999999999996531111 22222 


Q ss_pred             ----cccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          298 ----RDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       298 ----~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                          +..|-|||.|++.+.|.+|+..- ..   .|+-|-|.|
T Consensus       139 d~rgR~tGEAfVqF~sqe~ae~Al~rh-re---~iGhRYIEv  176 (510)
T KOG4211|consen  139 DQRGRPTGEAFVQFESQESAEIALGRH-RE---NIGHRYIEV  176 (510)
T ss_pred             cCCCCcccceEEEecCHHHHHHHHHHH-HH---hhccceEEe
Confidence                23588999999999999999653 33   466665543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.60  E-value=5.1e-14  Score=119.43  Aligned_cols=188  Identities=19%  Similarity=0.293  Sum_probs=132.4

Q ss_pred             cceEEECCCCccccHHHHHHHh-ccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          141 HFNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f-~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+.+||+|||++..+.+|+++| ++.|+|..|.++.| .+|+++|.|.|+|++++.+++|++.|+...+.||+|.|+-..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            4569999999999999999999 56799999999999 578999999999999999999999999999999999998654


Q ss_pred             CCCCCCCCCC-----------------------------Ccccc-cchhccCCCCcCCc--------------------C
Q 019811          220 KGAGNNEDKQ-----------------------------SSDAK-SVVELTNGSSEDGK--------------------E  249 (335)
Q Consensus       220 ~~~~~~~~~~-----------------------------~~~~~-~~~~~~~~~~~~~~--------------------~  249 (335)
                      ......-...                             ..... +..+....+.....                    .
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence            4211000000                             00000 00000000000000                    0


Q ss_pred             CCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE--ec---ccceEEEEeCCHHHHHHHHHhhcCCC
Q 019811          250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV--QR---DKGFGFVRYSTHAEAALAIQMGNTTQ  324 (335)
Q Consensus       250 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~--~~---~~g~afV~f~~~~~a~~A~~~l~g~~  324 (335)
                      ...+......+....+||.||.+.+..+.|++.|.-.|.  +..+.+  .+   ++|+|.++|+++-+|..|+..+++. 
T Consensus       203 Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGk--v~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~-  279 (608)
T KOG4212|consen  203 FLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGK--VQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQ-  279 (608)
T ss_pred             hhhhccCCCCCccceeeeeccccccchHHHHHHhcccee--eeeeceeeccccccCCeeEEEecchHHHHHHHHhhccC-
Confidence            000001112334467999999999999999999999884  555544  33   3799999999999999999999976 


Q ss_pred             cccccCcccc
Q 019811          325 SSYLFGKQMK  334 (335)
Q Consensus       325 ~~~~~g~~l~  334 (335)
                        .+.+++++
T Consensus       280 --g~~~~~~~  287 (608)
T KOG4212|consen  280 --GLFDRRMT  287 (608)
T ss_pred             --CCccccce
Confidence              55555543

>PF00076 RRM_1: RNA recognition motif

Probab=99.60  E-value=7.5e-15  Score=98.16  Aligned_cols=70  Identities=37%  Similarity=0.769  Sum_probs=66.8

Q ss_pred             EEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       144 l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      |||+|||.++++++|+++|+.||.+..+.+..+ .++..+++|||+|.+.++|.+|++.+++..+.|++|+
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            799999999999999999999999999999987 6788999999999999999999999999999999885

(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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.59  E-value=9.9e-15  Score=118.49  Aligned_cols=77  Identities=26%  Similarity=0.415  Sum_probs=71.3

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      .++|||+|||+.+|+++|+++|+.||.|.+|.|..++ .+|||||+|.+.++|..|+. |+|..|.|+.|+|.++....
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            5789999999999999999999999999999999886 46999999999999999995 99999999999999986543

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

Probab=99.56  E-value=1.2e-14  Score=102.63  Aligned_cols=78  Identities=27%  Similarity=0.489  Sum_probs=71.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      -..+++|||+||...++|+.|+++|+++|+|..|.+-.++.    .|||||+|.+.++|..|++-++|..+..+.|++.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            34678999999999999999999999999999988876654    39999999999999999999999999999999988


Q ss_pred             ec
Q 019811          129 AY  130 (335)
Q Consensus       129 ~~  130 (335)
                      -.
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            64

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.54  E-value=3.4e-14  Score=94.90  Aligned_cols=67  Identities=31%  Similarity=0.600  Sum_probs=60.9

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      |||+|||.++++++|+++|+.||.|..+.+..++.   +|+|||+|.+.++|.+|+..+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999998763   68999999999999999999999999999874

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 ....

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

Probab=99.53  E-value=1.3e-13  Score=108.62  Aligned_cols=81  Identities=28%  Similarity=0.460  Sum_probs=75.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|.|.||+.+++|++|.++|.+||.|.+|.+.+++.    +|||||.|.+.++|.+|+..|||.-+.+--|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            345677899999999999999999999999999999999874    5899999999999999999999999999999999


Q ss_pred             eeccC
Q 019811          128 WAYAS  132 (335)
Q Consensus       128 ~~~~~  132 (335)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99864

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.52  E-value=1.1e-13  Score=92.40  Aligned_cols=70  Identities=33%  Similarity=0.671  Sum_probs=64.3

Q ss_pred             EEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       144 l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      |+|+|||+++++++|.++|+.||.|..+.+..++. +..+++|||+|.+.++|.+|+..+++..++|+.|+
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            78999999999999999999999999999998866 88999999999999999999999999999999874

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 ....

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=3e-13  Score=119.70  Aligned_cols=169  Identities=20%  Similarity=0.337  Sum_probs=131.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +-....++|++||..++++.+.++...||++....++.+.    ++||||.+|.++.....|+..|||..++++.|.|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            3445679999999999999999999999999998888765    469999999999999999999999999999999987


Q ss_pred             eccCCCccC---------------------CCCcceEEECCCCc--c-cc-------HHHHHHHhccCCCceeeEEeecC
Q 019811          129 AYASGQRED---------------------TSGHFNIFVGDLSP--E-VT-------DATLFACFSVYPSCSDARVMWDQ  177 (335)
Q Consensus       129 ~~~~~~~~~---------------------~~~~~~l~v~nlp~--~-~t-------~~~l~~~f~~~g~v~~~~~~~~~  177 (335)
                      +........                     ..++..|.+.|+=.  + ..       .++++..|.+||.|.+|.+.++-
T Consensus       366 A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~  445 (500)
T KOG0120|consen  366 AIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPY  445 (500)
T ss_pred             hhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCC
Confidence            654322111                     11223333333311  1 11       14566677899999999998772


Q ss_pred             C---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          178 K---TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       178 ~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      .   .....|-.||+|.+.+++.+|++.|+|..|.|+++...|....
T Consensus       446 ~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  446 PDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             CCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            1   1234567899999999999999999999999999999997653

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

Probab=99.50  E-value=6.8e-14  Score=98.85  Aligned_cols=81  Identities=26%  Similarity=0.458  Sum_probs=76.2

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+++|||+||+..++|+.|.++|+.+|+|..|.+-.|+.+..+-|||||+|-+.++|..|+..+++..++.+.|++.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            34799999999999999999999999999999998898888899999999999999999999999999999999999874


Q ss_pred             C
Q 019811          220 K  220 (335)
Q Consensus       220 ~  220 (335)
                      -
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            4

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.50  E-value=5.7e-14  Score=110.14  Aligned_cols=80  Identities=38%  Similarity=0.622  Sum_probs=74.1

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ++|||+||+..+..++|++.|+.||+|.+..++.|+.+|+++||+||+|+|.++|.+|++. .+-.|+||+..|+.+...
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~lg   91 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASLG   91 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhhc
Confidence            5899999999999999999999999999999999999999999999999999999999974 456789999999998774


Q ss_pred             C
Q 019811          222 A  222 (335)
Q Consensus       222 ~  222 (335)
                      .
T Consensus        92 ~   92 (247)
T KOG0149|consen   92 G   92 (247)
T ss_pred             C
Confidence            3

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.48  E-value=1.8e-13  Score=112.21  Aligned_cols=103  Identities=29%  Similarity=0.433  Sum_probs=86.9

Q ss_pred             CCccccCceeEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHH
Q 019811          115 NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ  194 (335)
Q Consensus       115 ~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~  194 (335)
                      ++....|..+....+...+   .....+.|+|+|||+...+-||+.+|.+||.|.+|.|+.+.  ..+|||+||+|++.+
T Consensus        73 ~~~~t~g~~~~~~~st~s~---s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~  147 (376)
T KOG0125|consen   73 NGAPTDGQPIQTQPSTNSS---SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPA  147 (376)
T ss_pred             CCCCCCCCccccCCCCcCC---CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChh
Confidence            4555666666665543332   34455789999999999999999999999999999999873  468999999999999


Q ss_pred             HHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          195 DAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       195 ~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      +|++|.++|+|..+.||+|.|+.+..+-
T Consensus       148 dadRARa~LHgt~VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  148 DADRARAELHGTVVEGRKIEVNNATARV  175 (376)
T ss_pred             hHHHHHHHhhcceeeceEEEEeccchhh
Confidence            9999999999999999999999987763

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.48  E-value=3.3e-13  Score=91.70  Aligned_cols=82  Identities=18%  Similarity=0.313  Sum_probs=73.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .+.-++.|||.|||+++|.+++.++|.+||.|..+++-..   ...+|.|||.|++..+|.+|++.|+|..+.++.+.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~---k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT---KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc---cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            3455679999999999999999999999999999998744   4568999999999999999999999999999999999


Q ss_pred             EccCC
Q 019811          217 WATKG  221 (335)
Q Consensus       217 ~~~~~  221 (335)
                      |....
T Consensus        91 yyq~~   95 (124)
T KOG0114|consen   91 YYQPE   95 (124)
T ss_pred             ecCHH
Confidence            87653

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.48  E-value=5e-15  Score=111.05  Aligned_cols=83  Identities=29%  Similarity=0.550  Sum_probs=77.7

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ++.-|||+|||+.+||.+|.-.|+.||.+..|.++||+.+|+++||||+.|++..+...|+..|||..+.||.|+|....
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            34579999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      ...
T Consensus       114 ~Yk  116 (219)
T KOG0126|consen  114 NYK  116 (219)
T ss_pred             ccc
Confidence            443

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=1.1e-13  Score=103.38  Aligned_cols=79  Identities=30%  Similarity=0.488  Sum_probs=72.2

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..+.|||+||+..+++.||..+|..||.+..|+|-+     .+.|||||+|++..+|+.|+..|+|..|+|..|+|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr-----nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEee-----cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            357899999999999999999999999999998875     457899999999999999999999999999999999986


Q ss_pred             CCCC
Q 019811          220 KGAG  223 (335)
Q Consensus       220 ~~~~  223 (335)
                      -...
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            6543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.47  E-value=1.8e-13  Score=118.02  Aligned_cols=77  Identities=21%  Similarity=0.321  Sum_probs=71.6

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCH--HHHHHHHHHhCCccccCceeEEeeecc
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDR--RSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~--~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ...+||||||++.+++++|...|..||.|.+|.|++...+|||||+|.+.  .++.+|+..|||..|.|+.|+|..+.+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            34679999999999999999999999999999999887899999999987  789999999999999999999998754

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.47  E-value=8.4e-13  Score=113.68  Aligned_cols=121  Identities=28%  Similarity=0.437  Sum_probs=102.9

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec-
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY-  130 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~-  130 (335)
                      .++|||+|||.++++++|+++|..||.|..+.+..++    .+|+|||.|.+.++|..|+..++|..|.|+.|.|.+.. 
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            6889999999999999999999999999999998764    46999999999999999999999999999999999954 


Q ss_pred             ---cCCCcc-----------------CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeec
Q 019811          131 ---ASGQRE-----------------DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWD  176 (335)
Q Consensus       131 ---~~~~~~-----------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~  176 (335)
                         ......                 .......+++.+++..++..++...|..+|.+....+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence               211111                 1223467899999999999999999999999966665543

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

Probab=99.46  E-value=4.4e-13  Score=108.56  Aligned_cols=83  Identities=23%  Similarity=0.429  Sum_probs=78.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      .++-++|||+-|+.+++|++|++.|+.||.|+.|.+++|..+|+++|||||+|+++.+...|....+|..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            35667999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccC
Q 019811          218 ATK  220 (335)
Q Consensus       218 ~~~  220 (335)
                      ...
T Consensus       178 ERg  180 (335)
T KOG0113|consen  178 ERG  180 (335)
T ss_pred             ccc
Confidence            644

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.46  E-value=1.3e-13  Score=105.74  Aligned_cols=87  Identities=30%  Similarity=0.496  Sum_probs=80.4

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      .+..+-..|.|.||-+.++.++|..+|++||.|.+|.|++|+.++.++|||||.|.+..+|+.|+++|+|..++|+.|.|
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            34456678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 019811          216 NWATKGA  222 (335)
Q Consensus       216 ~~~~~~~  222 (335)
                      .++.-..
T Consensus        88 q~arygr   94 (256)
T KOG4207|consen   88 QMARYGR   94 (256)
T ss_pred             hhhhcCC
Confidence            8775543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.45  E-value=2.1e-12  Score=113.39  Aligned_cols=161  Identities=20%  Similarity=0.199  Sum_probs=108.2

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      .....++|+|-|||..+++++|+.+|+.||+|..|+....+ .|.+||+|.|..+|++|+++|++..+.|+.++-.....
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~-~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~  149 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK-RGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGAR  149 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc-CceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccc
Confidence            45567889999999999999999999999999997665443 48999999999999999999999999999888211111


Q ss_pred             CCC----------------ccCCC---CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCC
Q 019811          132 SGQ----------------REDTS---GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN  192 (335)
Q Consensus       132 ~~~----------------~~~~~---~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~  192 (335)
                      ...                .....   ....+++ .|++..+..-++.++.-+|.+.. +-     ++.-...-|+.|.+
T Consensus       150 ~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~-----~~~~~hq~~~~~~~  222 (549)
T KOG4660|consen  150 RAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-MLSPTRSSILLEHISSVDGSSPG-RE-----TPLLNHQRFVEFAD  222 (549)
T ss_pred             ccchhcccchhhhhccchhhcCCCCCCcCCccee-eeccchhhhhhhcchhccCcccc-cc-----ccchhhhhhhhhcc
Confidence            000                00001   1123333 38887777666666666666544 21     12222246777877


Q ss_pred             HHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          193 QQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       193 ~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ..++..+.... |..+.+....+.++...
T Consensus       223 ~~s~a~~~~~~-G~~~s~~~~v~t~S~~~  250 (549)
T KOG4660|consen  223 NRSYAFSEPRG-GFLISNSSGVITFSGPG  250 (549)
T ss_pred             ccchhhcccCC-ceecCCCCceEEecCCC
Confidence            77775555432 55666666666665543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.45  E-value=7.4e-13  Score=105.84  Aligned_cols=76  Identities=20%  Similarity=0.300  Sum_probs=69.7

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ...+|||+||++.+|+++|+++|+.||.|.+|+|.+++. +++|||+|.++++|+.|+ .|+|..|.+++|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            457899999999999999999999999999999998864 479999999999999998 6999999999999987654

>smart00362 RRM_2 RNA recognition motif

Probab=99.45  E-value=7.2e-13  Score=88.72  Aligned_cols=70  Identities=36%  Similarity=0.668  Sum_probs=64.5

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      +|+|+|||..++.++|+++|+.||.|..+.+..++  .+|+|||+|.+.++|.+|+..+++..+.|+.+.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999888765  46899999999999999999999999999998763

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.45  E-value=6.8e-13  Score=107.87  Aligned_cols=77  Identities=17%  Similarity=0.218  Sum_probs=70.7

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||+.+++++|+++|+.||.|.++.++++.   .++|||||+|.+.++|..|+. |+|..+.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            4689999999999999999999999999999999874   357899999999999999995 999999999999999765


Q ss_pred             C
Q 019811          221 G  221 (335)
Q Consensus       221 ~  221 (335)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.42  E-value=4.1e-12  Score=109.37  Aligned_cols=144  Identities=28%  Similarity=0.422  Sum_probs=110.3

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||..+++++|.++|..||.+..+.+..++.++.++|+|||+|.+.++|..|+..+++..+.|+.|.|.+...
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            58999999999999999999999999999999999988899999999999999999999999999999999999999754


Q ss_pred             -CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec
Q 019811          221 -GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR  298 (335)
Q Consensus       221 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~  298 (335)
                       ..........            ......................+++.+++..++..++...|..+|.  +....+..
T Consensus       195 ~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~  259 (306)
T COG0724         195 ASQPRSELSNN------------LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGD--IVRASLPP  259 (306)
T ss_pred             ccccccccccc------------cchhhhccccccccccccccceeeccccccccchhHHHHhcccccc--ceeeeccC
Confidence             1111110000            0000000001222233445578999999999999999999999994  54444443

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.42  E-value=1.9e-13  Score=105.80  Aligned_cols=85  Identities=33%  Similarity=0.518  Sum_probs=80.5

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||++|...+++.-|...|-+||+|..+.++.|-.+++++||+||+|...++|..|+..||+.++.||+|+|+++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 019811          220 KGAGN  224 (335)
Q Consensus       220 ~~~~~  224 (335)
                      +.+..
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            86643

>PF13893 RRM_5: RNA recognition motif

Probab=99.40  E-value=1.7e-12  Score=82.33  Aligned_cols=56  Identities=36%  Similarity=0.650  Sum_probs=51.5

Q ss_pred             HHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           73 LQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        73 l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      |+++|++||.|.++.+..++ +++|||+|.+.++|..|++.|||..+.|++|+|.|+
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            68899999999999997776 689999999999999999999999999999999986

(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 ....

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.38  E-value=1.9e-12  Score=114.10  Aligned_cols=83  Identities=30%  Similarity=0.611  Sum_probs=79.8

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      +.+||+|+|+++++++|.++|+..|.|.+++++.|+.+|.++||+|++|.+.++|..|++.|+|.++.|++|+|.|+...
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            78999999999999999999999999999999999999999999999999999999999999999999999999998776


Q ss_pred             CCC
Q 019811          222 AGN  224 (335)
Q Consensus       222 ~~~  224 (335)
                      +..
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            653

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.38  E-value=1.4e-12  Score=102.36  Aligned_cols=78  Identities=21%  Similarity=0.338  Sum_probs=68.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +..-.+|||+||+..+..++|+++|++||+|.+..++.|+    ++||+||.|+|.++|.+|++.. .-.|+||+..++.
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccch
Confidence            4556789999999999999999999999999999999876    4699999999999999999764 5688999988887


Q ss_pred             ecc
Q 019811          129 AYA  131 (335)
Q Consensus       129 ~~~  131 (335)
                      +.-
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            644

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.37  E-value=9e-13  Score=101.13  Aligned_cols=76  Identities=25%  Similarity=0.408  Sum_probs=70.3

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ...+|.|-||.+-++.++|+.+|++||.|-+|.|.+++    .+|||||.|.+..+|+.|+++|+|..+.|+.|+|.++.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            44679999999999999999999999999999998876    36999999999999999999999999999999998763

>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=99.37  E-value=5.6e-12  Score=84.79  Aligned_cols=71  Identities=35%  Similarity=0.703  Sum_probs=65.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+..   +++|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999999988763   68999999999999999999999999999998864

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).

>smart00362 RRM_2 RNA recognition motif

Probab=99.37  E-value=5e-12  Score=84.56  Aligned_cols=72  Identities=39%  Similarity=0.735  Sum_probs=66.4

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      +|+|+|||..+++++|+++|..||.+..+.+.+++  +.++++|||+|.+.++|.+|+..+++..+.|+.+.|+
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            48999999999999999999999999999888775  6788999999999999999999999999999988763

>smart00360 RRM RNA recognition motif

Probab=99.35  E-value=4.8e-12  Score=84.35  Aligned_cols=67  Identities=37%  Similarity=0.681  Sum_probs=61.7

Q ss_pred             EeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           61 VGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        61 v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      |+|||..+++++|+++|+.||.|..+++..++.    +|+|||+|.+.++|.+|+..+++..+.|+.++|.
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            579999999999999999999999999988654    6899999999999999999999999999998873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.35  E-value=3.7e-12  Score=109.99  Aligned_cols=78  Identities=19%  Similarity=0.342  Sum_probs=71.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCceeCCeeeEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ--QDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~--~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....|||+||++.+++++|...|..||.|.++.|++.  +|  +|||||+|.+.  .++.+|+..|+|..|.|+.|+|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            34578999999999999999999999999999999944  55  99999999987  68999999999999999999999


Q ss_pred             EccC
Q 019811          217 WATK  220 (335)
Q Consensus       217 ~~~~  220 (335)
                      .+++
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            8755

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.35  E-value=2.9e-11  Score=105.46  Aligned_cols=151  Identities=21%  Similarity=0.272  Sum_probs=113.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC------CCC---eEEEEEcCHHHHHHHHHHhCC----cc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD------KSS---YGFIHYFDRRSAAMAILSLNG----RH  118 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~------~~g---~afv~f~~~~~A~~a~~~l~~----~~  118 (335)
                      .+.-++.||||+||.+++|+.|...|..||.+.-=+-.+..      .+|   |+|+.|+++.++..-+.++.-    ..
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~y  334 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYY  334 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceE
Confidence            45567889999999999999999999999987433332211      235   999999999998776654321    11


Q ss_pred             c-------cCceeEEeeecc-C-----CCccCCCCcceEEECCCCccccHHHHHHHhc-cCCCceeeEEeecCCCCCcce
Q 019811          119 L-------FGQPIKVNWAYA-S-----GQREDTSGHFNIFVGDLSPEVTDATLFACFS-VYPSCSDARVMWDQKTGRSRG  184 (335)
Q Consensus       119 ~-------~g~~l~v~~~~~-~-----~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~g~v~~~~~~~~~~~~~~~g  184 (335)
                      |       ..+.+.|..-.. .     .....-++.++|||++||..++.++|..+|+ -||.|..+.|-.|++-+-++|
T Consensus       335 f~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkG  414 (520)
T KOG0129|consen  335 FKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKG  414 (520)
T ss_pred             EEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCC
Confidence            1       122233322110 0     1123345678999999999999999999997 799999999999988888999


Q ss_pred             EEEEEeCCHHHHHHHHHH
Q 019811          185 FGFVSFRNQQDAQSAIND  202 (335)
Q Consensus       185 ~afv~f~~~~~a~~a~~~  202 (335)
                      -|=|+|.+..+-.+||.+
T Consensus       415 aGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  415 AGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cceeeecccHHHHHHHhh
Confidence            999999999999999974

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.34  E-value=2.9e-12  Score=91.47  Aligned_cols=87  Identities=23%  Similarity=0.452  Sum_probs=80.2

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ..+.....|||+++...+++++|.+.|..||+|+.+.+-.|+.+|-.+|||+|+|++.+.|.+|+..+||..+.|..|.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            33445689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 019811          216 NWATKGA  222 (335)
Q Consensus       216 ~~~~~~~  222 (335)
                      .|.-.+.
T Consensus       147 Dw~Fv~g  153 (170)
T KOG0130|consen  147 DWCFVKG  153 (170)
T ss_pred             EEEEecC
Confidence            9975543

>smart00360 RRM RNA recognition motif

Probab=99.34  E-value=6.6e-12  Score=83.66  Aligned_cols=71  Identities=38%  Similarity=0.713  Sum_probs=66.0

Q ss_pred             ECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          146 VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       146 v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      |+|||..+++++|+++|..||.|..+.+..++.++.++++|||+|.+.++|..|+..+++..+.|+.+.|+
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            57999999999999999999999999999887778899999999999999999999999999999988763

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

Probab=99.33  E-value=8.5e-12  Score=101.20  Aligned_cols=78  Identities=23%  Similarity=0.439  Sum_probs=72.2

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+-+||||+-|+++++|..|+..|+.||+|+.|.|++++    ++|||||+|++..+...|.+..+|..|.|+.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            45677999999999999999999999999999999999874    57999999999999999999999999999999987


Q ss_pred             ee
Q 019811          128 WA  129 (335)
Q Consensus       128 ~~  129 (335)
                      +-
T Consensus       177 vE  178 (335)
T KOG0113|consen  177 VE  178 (335)
T ss_pred             ec
Confidence            54

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.33  E-value=1.8e-13  Score=102.75  Aligned_cols=79  Identities=29%  Similarity=0.516  Sum_probs=72.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..+.-|||+|||++.||.+|.-.|++||.|..|.+++++    ++||||+.|++..+...|+..|||..|.||+|+|.+.
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            455679999999999999999999999999999999986    4689999999999999999999999999999999876


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      ...
T Consensus       113 ~~Y  115 (219)
T KOG0126|consen  113 SNY  115 (219)
T ss_pred             ccc
Confidence            443

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.32  E-value=1.1e-11  Score=99.12  Aligned_cols=77  Identities=17%  Similarity=0.305  Sum_probs=69.9

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|+|+||++.+|+++|+++|+.||.|.++.++++.   ..+++|||+|++.+++..|+ .|+|..|.++.|.|....
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            34799999999999999999999999999999999873   55689999999999999999 599999999999998765


Q ss_pred             C
Q 019811          220 K  220 (335)
Q Consensus       220 ~  220 (335)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            4

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.30  E-value=2.9e-12  Score=99.26  Aligned_cols=81  Identities=30%  Similarity=0.527  Sum_probs=74.5

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec----CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~----~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||++|..++++.-|...|-+||.|..|.+..+    +++||+||+|...++|..|+..||+..+.|++|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45689999999999999999999999999999998765    46899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          130 YASGQ  134 (335)
Q Consensus       130 ~~~~~  134 (335)
                      .+...
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            76553

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.29  E-value=8.3e-13  Score=121.11  Aligned_cols=145  Identities=14%  Similarity=0.211  Sum_probs=122.1

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEe----ecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~----~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ...++||+||+..+.+.+|...|..+|.+..+.+.    .++-+|+||+.|..+++|.+|+...++..++          
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g----------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG----------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh----------
Confidence            34578999999999999999999999987666554    2334699999999999999999766665554          


Q ss_pred             cCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       131 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                                ...++|.|.|+..|.++++.+++.+|.+.+++++.. ..|+++|.++|.|.++.++.++....+...+..
T Consensus       736 ----------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE  804 (881)
T KOG0128|consen  736 ----------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRE  804 (881)
T ss_pred             ----------hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhh
Confidence                      236899999999999999999999999999987755 468999999999999999999998888777777


Q ss_pred             eeeEEEEccC
Q 019811          211 RQIRCNWATK  220 (335)
Q Consensus       211 ~~l~v~~~~~  220 (335)
                      +.+.+..+++
T Consensus       805 ~~~~v~vsnp  814 (881)
T KOG0128|consen  805 NNGEVQVSNP  814 (881)
T ss_pred             cCccccccCC
Confidence            7777777655

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.29  E-value=8.5e-12  Score=104.46  Aligned_cols=162  Identities=17%  Similarity=0.200  Sum_probs=117.8

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhc---c-CCceeEEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSS---T-GPVEGCKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~---~-G~v~~v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ---|.+++||+++++.++.+||..   . |.++.|..++.   +-+|-|||.|..+++|..|+.. |...++-|.|.+-.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            345788999999999999999963   2 23445555443   3479999999999999999965 33344333333221


Q ss_pred             ecc----------------------------CCCccCCCCcceEEECCCCccccHHHHHHHhccCC-Ccee--eEEeecC
Q 019811          129 AYA----------------------------SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYP-SCSD--ARVMWDQ  177 (335)
Q Consensus       129 ~~~----------------------------~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~--~~~~~~~  177 (335)
                      ++.                            ...........+|.+++||+..+.++|.++|..|. .|..  +.++.+ 
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-  318 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-  318 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-
Confidence            110                            00011223356899999999999999999999885 3433  566656 


Q ss_pred             CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          178 KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       178 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..|.+.|-|||+|.+.++|..|....++...++|.|.|-...
T Consensus       319 ~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  319 GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            468899999999999999999999888888888988887653

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=1.8e-11  Score=87.50  Aligned_cols=82  Identities=26%  Similarity=0.524  Sum_probs=73.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .-....|||.++-..++|++|.+.|..||+|+.+.+..++.    +|||+|+|++.+.|..|+..+||..+.|..|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34556799999999999999999999999999999988765    58999999999999999999999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.-+.+
T Consensus       149 ~Fv~gp  154 (170)
T KOG0130|consen  149 CFVKGP  154 (170)
T ss_pred             EEecCC
Confidence            865443

>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=99.27  E-value=5.5e-11  Score=79.86  Aligned_cols=74  Identities=39%  Similarity=0.773  Sum_probs=67.7

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      +|+|+|||..+++++|.++|..+|.+..+.+..++.+ .++++|||+|.+.++|..|+..+++..+.|+.+.|.+
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            4789999999999999999999999999999877543 6789999999999999999999999999999998864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.26  E-value=1.2e-10  Score=104.72  Aligned_cols=187  Identities=12%  Similarity=0.040  Sum_probs=118.5

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      +.+-+.+++++.++.+++++|... .+.+..+..+...+...|.++|.|....++.+|+.. +...+-+|.+.+.-....
T Consensus       312 ~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~~  389 (944)
T KOG4307|consen  312 YYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGNL  389 (944)
T ss_pred             heeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCcc
Confidence            446678899999999999999653 355555555555555578899999999999999874 444555565555433222


Q ss_pred             CCCCCCCCCcccc-cchhcc---CCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEE-EEE
Q 019811          222 AGNNEDKQSSDAK-SVVELT---NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE-VRV  296 (335)
Q Consensus       222 ~~~~~~~~~~~~~-~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~-v~~  296 (335)
                      .......-..... ......   +....++..+.....+.......+|||..||..++..++.++|...-  .|++ |.+
T Consensus       390 ~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~--~Ved~I~l  467 (944)
T KOG4307|consen  390 GRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAA--AVEDFIEL  467 (944)
T ss_pred             ccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhh--hhhheeEe
Confidence            1110000000000 000000   01111122222222334445568999999999999999999999654  2444 554


Q ss_pred             ecc-----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          297 QRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       297 ~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      -+.     ++.|||.|..+.++.+|...-+..   .++.|.|+|
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~---y~G~r~irv  508 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVKTKF---YPGHRIIRV  508 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhccccc---ccCceEEEe
Confidence            332     689999999999999998777777   788887765

>PF13893 RRM_5: RNA recognition motif

Probab=99.25  E-value=4.3e-11  Score=75.75  Aligned_cols=56  Identities=32%  Similarity=0.657  Sum_probs=50.2

Q ss_pred             HHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       158 l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      |.++|++||.|..+.+..+.     +++|||+|.+.++|..|++.|++..+.|+.|+|.|+
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            67899999999999887442     589999999999999999999999999999999986

(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 ....

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.24  E-value=3.2e-10  Score=99.10  Aligned_cols=163  Identities=21%  Similarity=0.261  Sum_probs=106.1

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCC-C--CCcce---EEEEEeCCHHHHHHHHHHhCCceeCCee
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK-T--GRSRG---FGFVSFRNQQDAQSAINDLTGKWLGSRQ  212 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~-~--~~~~g---~afv~f~~~~~a~~a~~~l~~~~~~g~~  212 (335)
                      .-++.|||++||.+++|+.|...|..||.+.. .+.+... .  -.++|   |+|+.|+++......+.++.-   ....
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~  332 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKV-DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGN  332 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEe-ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccc
Confidence            34578999999999999999999999997643 2332111 1  13566   999999999998877765543   3333


Q ss_pred             eEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhh-hcCCeee
Q 019811          213 IRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFH-SLGAGVI  291 (335)
Q Consensus       213 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~~~i  291 (335)
                      +.+..+.+.-....   ............-..         .......+.+||||++||-.++.++|..+|+ .||.  |
T Consensus       333 ~yf~vss~~~k~k~---VQIrPW~laDs~fv~---------d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGg--V  398 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKE---VQIRPWVLADSDFVL---------DHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGG--V  398 (520)
T ss_pred             eEEEEecCcccccc---eeEEeeEeccchhhh---------ccCcccCccceEEecCCCCcchHHHHHHHHHHhcCc--e
Confidence            33333322211110   000000000000000         0122333459999999999999999999999 8996  5


Q ss_pred             EEEEEecc------cceEEEEeCCHHHHHHHHHh
Q 019811          292 EEVRVQRD------KGFGFVRYSTHAEAALAIQM  319 (335)
Q Consensus       292 ~~v~~~~~------~g~afV~f~~~~~a~~A~~~  319 (335)
                      ..+-|+-|      +|.|-|+|.+..+-.+|+++
T Consensus       399 ~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  399 LYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             EEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            55555443      79999999999999999965

>smart00361 RRM_1 RNA recognition motif

Probab=99.23  E-value=5.4e-11  Score=78.96  Aligned_cols=61  Identities=25%  Similarity=0.479  Sum_probs=54.1

Q ss_pred             HHHHHHHhc----cCCCceeeE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          155 DATLFACFS----VYPSCSDAR-VMWDQKT--GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       155 ~~~l~~~f~----~~g~v~~~~-~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      +++|+++|+    .||.|.++. ++.++.+  +.++|+|||+|.+.++|.+|+..|+|..+.|+.|.+
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            567778887    999999995 6666656  889999999999999999999999999999999876

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.22  E-value=2.7e-11  Score=106.96  Aligned_cols=77  Identities=35%  Similarity=0.591  Sum_probs=72.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      +.|||||+|+++++++|.++|+..|.|.++++..|+.    +||||++|.+.++|.+|++.|||..+.|++|+|.|+...
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            7899999999999999999999999999999998764    689999999999999999999999999999999998654


Q ss_pred             C
Q 019811          133 G  133 (335)
Q Consensus       133 ~  133 (335)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.19  E-value=5.3e-10  Score=100.63  Aligned_cols=77  Identities=14%  Similarity=0.058  Sum_probs=62.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCcee-EEEee---cCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG-CKLIR---KDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~-v~~~~---~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ......|||..||..+++.++.++|...-.|++ |.+..   ++.++-|||.|..++.+..|...-+...++.+-|+|..
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            344567999999999999999999988766666 66654   34468999999999999999887777788888888865


Q ss_pred             e
Q 019811          129 A  129 (335)
Q Consensus       129 ~  129 (335)
                      .
T Consensus       511 i  511 (944)
T KOG4307|consen  511 I  511 (944)
T ss_pred             h
Confidence            4

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=2e-11  Score=94.70  Aligned_cols=146  Identities=24%  Similarity=0.356  Sum_probs=120.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC--CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~--~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      +...+||||.|+-..++|+.|.++|-+-|+|..|.|..++.  ..||||.|.++-+..-|++-+||..+.+..+.+.+-.
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            34568899999999999999999999999999999877553  3599999999999999999999999999999887543


Q ss_pred             cCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       131 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      ....            .-|...++++.+.+.|+..|.+..+++..+. +|.++.++|+.+....+.-.++....+....-
T Consensus        86 G~sh------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~  152 (267)
T KOG4454|consen   86 GNSH------------APLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQ  152 (267)
T ss_pred             CCCc------------chhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCC
Confidence            2211            1255678899999999999999999998774 47888899999988888888887766655443


Q ss_pred             e
Q 019811          211 R  211 (335)
Q Consensus       211 ~  211 (335)
                      +
T Consensus       153 ~  153 (267)
T KOG4454|consen  153 K  153 (267)
T ss_pred             C
Confidence            3

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.11  E-value=6.5e-12  Score=115.35  Aligned_cols=219  Identities=20%  Similarity=0.224  Sum_probs=168.1

Q ss_pred             cceEEEeCCCCCCCHH-HHHHHHhccCCceeEEEeecC---C-CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           56 CRSVYVGNIHTQVTEP-LLQEVFSSTGPVEGCKLIRKD---K-SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~-~l~~~f~~~G~v~~v~~~~~~---~-~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      .+..++.++-+..... ..+..|+.+|.|+.|++-..+   . ..++++.+....+++.|. ...+..+.++...+..+.
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat-~pa~~~~a~~~~av~~ad  649 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESAT-VPAGGALANRSAAVGLAD  649 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcc-cccccccCCccccCCCCC
Confidence            3446677776665554 678899999999998876522   1 248899999999998886 467888888888888776


Q ss_pred             cCCCccCC-------CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 019811          131 ASGQREDT-------SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL  203 (335)
Q Consensus       131 ~~~~~~~~-------~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  203 (335)
                      ++......       ....++|++||+..+.+++|...|..+|.+..+.+......+..+|+||+.|...+.+.+|+...
T Consensus       650 ~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~  729 (881)
T KOG0128|consen  650 AEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR  729 (881)
T ss_pred             chhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhh
Confidence            55432211       12256899999999999999999999998877766644456788999999999999999999865


Q ss_pred             CCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHh
Q 019811          204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHF  283 (335)
Q Consensus       204 ~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f  283 (335)
                      +++.++.                                                    ..|+|.|.|+..|.++++.++
T Consensus       730 d~~~~gK----------------------------------------------------~~v~i~g~pf~gt~e~~k~l~  757 (881)
T KOG0128|consen  730 DSCFFGK----------------------------------------------------ISVAISGPPFQGTKEELKSLA  757 (881)
T ss_pred             hhhhhhh----------------------------------------------------hhhheeCCCCCCchHHHHhhc
Confidence            5544441                                                    459999999999999999999


Q ss_pred             hhcCCeeeEEEEEe-----cccceEEEEeCCHHHHHHHHHhhcCCCcccccCcc
Q 019811          284 HSLGAGVIEEVRVQ-----RDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ  332 (335)
Q Consensus       284 ~~~G~~~i~~v~~~-----~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~  332 (335)
                      .++|.  +.++++.     +.+|.|+|.|.+..++.++...+++.   .+..+.
T Consensus       758 ~~~gn--~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~---~~rE~~  806 (881)
T KOG0128|consen  758 SKTGN--VTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVA---GKRENN  806 (881)
T ss_pred             cccCC--ccccchhhhhccccccceeccCCCcchhhhhcccchhh---hhhhcC
Confidence            99994  4444332     34799999999999999988777766   554433

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.11  E-value=6.1e-11  Score=98.42  Aligned_cols=84  Identities=25%  Similarity=0.417  Sum_probs=79.2

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      -..+.+.|||..|.+-++.++|.-+|+.||.|.++.+++|+.+|.+.-||||+|++.+++++|.-.|++..|+.+.|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccC
Q 019811          217 WATK  220 (335)
Q Consensus       217 ~~~~  220 (335)
                      |+..
T Consensus       315 FSQS  318 (479)
T KOG0415|consen  315 FSQS  318 (479)
T ss_pred             hhhh
Confidence            8744

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.10  E-value=2.2e-10  Score=104.34  Aligned_cols=106  Identities=25%  Similarity=0.379  Sum_probs=84.7

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR  135 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~  135 (335)
                      ++|||||+|+..+++.+|.++|+.||.|.+|.++..+  |+|||.+....+|.+|+..|++..+.++.|+|.|+..+..+
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R--~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR--GCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPK  498 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC--ceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcc
Confidence            6899999999999999999999999999999887655  69999999999999999999999999999999999877765


Q ss_pred             cCCCC--cceEEECCCCccccHHHHHHHhc
Q 019811          136 EDTSG--HFNIFVGDLSPEVTDATLFACFS  163 (335)
Q Consensus       136 ~~~~~--~~~l~v~nlp~~~t~~~l~~~f~  163 (335)
                      .+-..  ...+=|+-||...-.+++..++.
T Consensus       499 se~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  499 SEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             hhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            52111  12233445566544444555554

>smart00361 RRM_1 RNA recognition motif

Probab=99.08  E-value=5.1e-10  Score=74.23  Aligned_cols=57  Identities=28%  Similarity=0.371  Sum_probs=49.3

Q ss_pred             HHHHHHHHh----ccCCceeEE-Eeec------CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           70 EPLLQEVFS----STGPVEGCK-LIRK------DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        70 ~~~l~~~f~----~~G~v~~v~-~~~~------~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      +++|+++|+    +||.|.+|. +..+      .++|+|||.|.+.++|.+|+..|||..+.|+.|++
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            577888888    999999985 4433      24799999999999999999999999999999876

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.04  E-value=1.5e-10  Score=107.08  Aligned_cols=160  Identities=19%  Similarity=0.350  Sum_probs=137.2

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +...+++||++||+..+++.+|+..|..+|.|.+|.|-...   ...|+||.|.+...+-.|...+.+..|..-.+++.+
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            56678899999999999999999999999999998875442   235999999999999999999999999877777776


Q ss_pred             eccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       129 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      ...     ....++.+++++|+..+....+...|..||.|..|.+-      ....|++|.|.+...+..|+..+.|..+
T Consensus       448 G~~-----kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~~~aq~a~~~~rgap~  516 (975)
T KOG0112|consen  448 GQP-----KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESPPAAQAATHDMRGAPL  516 (975)
T ss_pred             ccc-----ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccCccchhhHHHHhcCcC
Confidence            644     33456789999999999999999999999999988665      3345999999999999999999999999


Q ss_pred             CC--eeeEEEEccCCC
Q 019811          209 GS--RQIRCNWATKGA  222 (335)
Q Consensus       209 ~g--~~l~v~~~~~~~  222 (335)
                      +|  +.++|.|+....
T Consensus       517 G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  517 GGPPRRLRVDLASPPG  532 (975)
T ss_pred             CCCCcccccccccCCC
Confidence            75  678888886644

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.01  E-value=1.2e-09  Score=86.99  Aligned_cols=162  Identities=29%  Similarity=0.443  Sum_probs=124.4

Q ss_pred             EEEeCCCCCCCHHH-H--HHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           59 VYVGNIHTQVTEPL-L--QEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        59 v~v~nlp~~~t~~~-l--~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      .+++++-..+..+- |  ...|+.|-.+...+++++.   .++++|+.|.....-.++-..-++..++-..+++.-....
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtsw  178 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSW  178 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecccccc
Confidence            45555555544433 2  5666666666555555543   4589999998887777776666677776666776544322


Q ss_pred             C---CccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          133 G---QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       133 ~---~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      .   ..+-....+.||.+.|..+++.+-|...|.+|-.....++++|+.+|+++||+||.|.+..++..|+..++|..++
T Consensus       179 edPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVg  258 (290)
T KOG0226|consen  179 EDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVG  258 (290)
T ss_pred             CCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccc
Confidence            2   2233456689999999999999999999999998888899999999999999999999999999999999999999


Q ss_pred             CeeeEEEEccC
Q 019811          210 SRQIRCNWATK  220 (335)
Q Consensus       210 g~~l~v~~~~~  220 (335)
                      .+.|+++-+.-
T Consensus       259 srpiklRkS~w  269 (290)
T KOG0226|consen  259 SRPIKLRKSEW  269 (290)
T ss_pred             cchhHhhhhhH
Confidence            99998875543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.01  E-value=1.1e-09  Score=91.04  Aligned_cols=78  Identities=18%  Similarity=0.465  Sum_probs=70.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHH-hCCccccCceeEEeeec
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILS-LNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~-l~~~~~~g~~l~v~~~~  130 (335)
                      .+....+|||+||-..+++.+|++.|-+||+|.++.+...+  ++|||+|.+.++|+.|.+. ++...|.|++|+|.|+.
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~--~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK--GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc--ccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            45677899999999999999999999999999999987765  4999999999999998865 57778899999999998


Q ss_pred             c
Q 019811          131 A  131 (335)
Q Consensus       131 ~  131 (335)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            7

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.97  E-value=2.1e-09  Score=97.09  Aligned_cols=79  Identities=27%  Similarity=0.548  Sum_probs=72.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      ....++|||+||++.++++.|...|..||+|.+|+|+..++       +.++||.|-+..+|++|+..|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            45567799999999999999999999999999999998643       46999999999999999999999999999999


Q ss_pred             Eeeecc
Q 019811          126 VNWAYA  131 (335)
Q Consensus       126 v~~~~~  131 (335)
                      +.|+..
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999843

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.92  E-value=3.2e-09  Score=96.99  Aligned_cols=79  Identities=22%  Similarity=0.430  Sum_probs=73.3

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      +++|||++|+.++++.+|..+|+.||+|.+|.++      .++++|||.+....+|.+|+.+|++..+.++.|+|.|+..
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 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI------PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec------cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            5899999999999999999999999999999887      6688999999999999999999999999999999999987


Q ss_pred             CCCCC
Q 019811          221 GAGNN  225 (335)
Q Consensus       221 ~~~~~  225 (335)
                      +....
T Consensus       495 ~G~ks  499 (894)
T KOG0132|consen  495 KGPKS  499 (894)
T ss_pred             CCcch
Confidence            66544

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.92  E-value=5.1e-09  Score=81.04  Aligned_cols=81  Identities=17%  Similarity=0.384  Sum_probs=74.7

Q ss_pred             cceEEECCCCccccHHHHHHHhccC-CCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVY-PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~-g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ...+++..+|..+.+.++..+|..| |.+..+++-|++.+|.++|||||+|++.+.|.-|-+.||+-.+.++-|.|.+-.
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            3578999999999999999999998 677888888999999999999999999999999999999999999999999976


Q ss_pred             CC
Q 019811          220 KG  221 (335)
Q Consensus       220 ~~  221 (335)
                      +.
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            65

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.91  E-value=3.7e-09  Score=88.04  Aligned_cols=80  Identities=21%  Similarity=0.423  Sum_probs=73.0

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCC----eEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g----~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+-..|||..|.+-+|.++|.-+|+.||.|.++.++++..+|    ||||+|.+.+++++|.-.|++..|..++|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            34445679999999999999999999999999999999998764    99999999999999999999999999999999


Q ss_pred             eecc
Q 019811          128 WAYA  131 (335)
Q Consensus       128 ~~~~  131 (335)
                      ++..
T Consensus       315 FSQS  318 (479)
T KOG0415|consen  315 FSQS  318 (479)
T ss_pred             hhhh
Confidence            8754

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.81  E-value=1.6e-08  Score=78.27  Aligned_cols=78  Identities=21%  Similarity=0.290  Sum_probs=68.2

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcc-CCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSST-GPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~-G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ....++++.+|..+.+.++..+|.++ |.|..+++.+++    ++|||||+|++.+.|.-|.+.||+..+.|+.|.+.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34458999999999999999999998 788888887765    4689999999999999999999999999999998876


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      .+.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.79  E-value=1.2e-08  Score=84.97  Aligned_cols=73  Identities=29%  Similarity=0.499  Sum_probs=64.1

Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .....+|||++|-..+++.+|++.|.+||  .+.++++...+++|||+|.+..+|..|...+-+. + .|+|.+|+|
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyG--eirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~-l-vI~G~Rl~i  297 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYG--EIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNK-L-VINGFRLKI  297 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcC--CeeeEEeecccccceeeehhhHHHHHHHHhhcce-e-eecceEEEE
Confidence            33458999999999999999999999999  6999999999999999999999999998776553 1 789998875

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.79  E-value=8.1e-09  Score=87.27  Aligned_cols=167  Identities=20%  Similarity=0.272  Sum_probs=131.2

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEee----cCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~----~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++.|++++-..+.+.+...++..+|.+.......    ..++|++++.|...+.+..|+.........++.+..-...
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            567899999999999999999999999665554443    2356899999999999999996543335555444433222


Q ss_pred             cCC-------CccCCCCcceEE-ECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 019811          131 ASG-------QREDTSGHFNIF-VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND  202 (335)
Q Consensus       131 ~~~-------~~~~~~~~~~l~-v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  202 (335)
                      ...       .+.......+++ +++++..+++++|...|..+|.|..+++..++.++..++++++.|.....+..++..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            211       122223334455 999999999999999999999999999999999999999999999999999999987


Q ss_pred             hCCceeCCeeeEEEEccCCC
Q 019811          203 LTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       203 l~~~~~~g~~l~v~~~~~~~  222 (335)
                       ....+.++.+.+.+.....
T Consensus       247 -~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  247 -QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             -ccCcccCcccccccCCCCc
Confidence             7889999999999887654

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

Probab=98.76  E-value=2.5e-08  Score=88.18  Aligned_cols=82  Identities=26%  Similarity=0.358  Sum_probs=75.5

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||.+|...+-..+|+.+|++||.|.-.+++.+..+...+.|+||++.+..+|.+||..|+...+.|+.|.|..++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            47899999999999999999999999999999998877777889999999999999999999999999999999998765


Q ss_pred             CC
Q 019811          221 GA  222 (335)
Q Consensus       221 ~~  222 (335)
                      ..
T Consensus       485 Ep  486 (940)
T KOG4661|consen  485 EP  486 (940)
T ss_pred             Cc
Confidence            43

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.74  E-value=1.1e-08  Score=90.44  Aligned_cols=165  Identities=19%  Similarity=0.236  Sum_probs=103.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ...+..+|+|.|||..+++++|.++|+.||+|+.++.-     ...+|.+||+|-|..+|++|++.|++..+.|+.|...
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~  145 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRP  145 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCC
Confidence            34566799999999999999999999999999996543     3557899999999999999999999999999998822


Q ss_pred             EccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      ......    ...... ...+.....       +.....+..... ..++.- |++..+..-++..+.-+|.  +..-..
T Consensus       146 ~~~~~~----~~~~~~-~~~~~~~~~-------p~a~s~pgg~~~-~~~~g~-l~P~~s~~~~~~~~~~~~~--~~~~~~  209 (549)
T KOG4660|consen  146 GGARRA----MGLQSG-TSFLNHFGS-------PLANSPPGGWPR-GQLFGM-LSPTRSSILLEHISSVDGS--SPGRET  209 (549)
T ss_pred             Cccccc----chhccc-chhhhhccc-------hhhcCCCCCCcC-Ccceee-eccchhhhhhhcchhccCc--cccccc
Confidence            211111    111111 111111111       111111111111 223333 8888877666677777774  322222


Q ss_pred             ecccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          297 QRDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       297 ~~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      ..-+..-+++|.+..++..+...+ |.
T Consensus       210 ~~~~hq~~~~~~~~~s~a~~~~~~-G~  235 (549)
T KOG4660|consen  210 PLLNHQRFVEFADNRSYAFSEPRG-GF  235 (549)
T ss_pred             cchhhhhhhhhccccchhhcccCC-ce
Confidence            222346778888888885555433 44

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.71  E-value=1.2e-07  Score=65.84  Aligned_cols=79  Identities=16%  Similarity=0.194  Sum_probs=68.0

Q ss_pred             ceEEECCCCccccHHHHHHHhccC--CCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC----CeeeEE
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG----SRQIRC  215 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~----g~~l~v  215 (335)
                      ++|+|.|+|...|.++|.+++...  |...-+.++.|..++.+.|||||.|.+.+.|.+-.+.++|..+.    .+...|
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            689999999999999999998653  67788889999888999999999999999999999999998774    455666


Q ss_pred             EEccC
Q 019811          216 NWATK  220 (335)
Q Consensus       216 ~~~~~  220 (335)
                      .|+..
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            66654

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.70  E-value=4.1e-09  Score=82.07  Aligned_cols=137  Identities=21%  Similarity=0.259  Sum_probs=101.3

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||.|+-..++|+-|.++|-..|+|..+.|..++ .++.+ ||||.|+++....-|++.+||..+.++.+.+.+-
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 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            345799999999999999999999999999999888664 45556 9999999999999999999999999988877654


Q ss_pred             cCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec
Q 019811          219 TKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~  298 (335)
                      .-....                                            -|...++++.+...|+.-|.  +..+++..
T Consensus        85 ~G~sha--------------------------------------------pld~r~~~ei~~~v~s~a~p--~~~~R~~~  118 (267)
T KOG4454|consen   85 CGNSHA--------------------------------------------PLDERVTEEILYEVFSQAGP--IEGVRIPT  118 (267)
T ss_pred             cCCCcc--------------------------------------------hhhhhcchhhheeeecccCC--CCCccccc
Confidence            321100                                            13445677777777777763  55555543


Q ss_pred             -----ccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          299 -----DKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       299 -----~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                           ++.+.|+++--.-+.-.++....+.
T Consensus       119 ~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l  148 (267)
T KOG4454|consen  119 DNDGRNRNFGFVTYQRLCAVPFALDLYQGL  148 (267)
T ss_pred             cccCCccCccchhhhhhhcCcHHhhhhccc
Confidence                 3567777765555555555555444

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.69  E-value=1.3e-08  Score=94.55  Aligned_cols=149  Identities=19%  Similarity=0.304  Sum_probs=124.1

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+.+||++||+..+++.+|+..|..+|.+..|.|-+.+ .+...-|+||.|.+...+-.|+..+.+..|..-.+++.+..
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            45789999999999999999999999999999886542 23445689999999999999999898888876655555543


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~  299 (335)
                      .+                                     ....+.+++++|+.-+....|..+|..||+  +..|.+...
T Consensus       450 ~k-------------------------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGp--ir~Idy~hg  490 (975)
T KOG0112|consen  450 PK-------------------------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGP--IRIIDYRHG  490 (975)
T ss_pred             cc-------------------------------------cccceeeccCCCCCCChHHHHHHHhhccCc--ceeeecccC
Confidence            21                                     112367999999999999999999999995  777777777


Q ss_pred             cceEEEEeCCHHHHHHHHHhhcCCCcccccCc
Q 019811          300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGK  331 (335)
Q Consensus       300 ~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~  331 (335)
                      ..+|||.|.+...|..|+..|.|.   .|+|-
T Consensus       491 q~yayi~yes~~~aq~a~~~~rga---p~G~P  519 (975)
T KOG0112|consen  491 QPYAYIQYESPPAAQAATHDMRGA---PLGGP  519 (975)
T ss_pred             CcceeeecccCccchhhHHHHhcC---cCCCC
Confidence            789999999999999999999999   78764

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

Probab=98.64  E-value=1.8e-07  Score=82.96  Aligned_cols=80  Identities=25%  Similarity=0.411  Sum_probs=72.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..-+++|||.+|...+...+|+.+|++||.|...+++.+..    +-|+||.+.+.++|.+||+.|+-+.+.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            44568899999999999999999999999999999988753    35999999999999999999999999999999998


Q ss_pred             eccC
Q 019811          129 AYAS  132 (335)
Q Consensus       129 ~~~~  132 (335)
                      +++.
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            7654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.64  E-value=1.2e-07  Score=83.56  Aligned_cols=79  Identities=19%  Similarity=0.323  Sum_probs=65.5

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec----CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~----~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      .......+|||+|||.++++++|.++|..||+|+...|...    +...||||+|.+.+++..|+.+ +-..+++++|.|
T Consensus       283 ~~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~V  361 (419)
T KOG0116|consen  283 EPRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNV  361 (419)
T ss_pred             ceeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEE
Confidence            34445566999999999999999999999999988777542    3337999999999999999976 477888999999


Q ss_pred             eeec
Q 019811          127 NWAY  130 (335)
Q Consensus       127 ~~~~  130 (335)
                      +--.
T Consensus       362 eek~  365 (419)
T KOG0116|consen  362 EEKR  365 (419)
T ss_pred             Eecc
Confidence            7543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.60  E-value=2.1e-07  Score=75.86  Aligned_cols=83  Identities=27%  Similarity=0.376  Sum_probs=75.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .....|+|.|||..++.++|+++|..||.+..+.+.++ ..|.+.|.|-|.|...++|.+|++.+++..++|+.+.+...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            34468999999999999999999999999999988888 46889999999999999999999999999999999998876


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      ....
T Consensus       160 ~~~~  163 (243)
T KOG0533|consen  160 SSPS  163 (243)
T ss_pred             cCcc
Confidence            5544

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.59  E-value=4e-07  Score=60.07  Aligned_cols=69  Identities=19%  Similarity=0.347  Sum_probs=47.5

Q ss_pred             eEEEeCCCCCCCHHHH----HHHHhccC-CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           58 SVYVGNIHTQVTEPLL----QEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l----~~~f~~~G-~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      .|+|.|||.+.+...|    +.++..+| .|.+|      ..+.|.|.|.+.+.|.+|.+.|+|..+.|.+|.|.+....
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE--------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            5899999999887655    55666787 56665      2357999999999999999999999999999999988543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.57  E-value=3.4e-07  Score=74.66  Aligned_cols=80  Identities=21%  Similarity=0.289  Sum_probs=70.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .....+|+|.|||+.+++++|.++|..||.+..+-+..++.   .|.|-|.|...++|.+|++.++|..+.|+.+++...
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            34446799999999999999999999999988888877664   489999999999999999999999999999998876


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      ...
T Consensus       160 ~~~  162 (243)
T KOG0533|consen  160 SSP  162 (243)
T ss_pred             cCc
Confidence            443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.57  E-value=8.3e-08  Score=81.20  Aligned_cols=165  Identities=25%  Similarity=0.303  Sum_probs=120.9

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ...++|++++...+.+.+...++..+|......+.........++++++.|...+.+..|+.........++.+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            34678999999998888888889999987777666655667889999999999999999998544445666655555444


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeE-EEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTV-YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~  298 (335)
                      .........                        ....... ...++ ++.++++++++++|+..|..+|  .+..++++.
T Consensus       167 ~~~~~~~n~------------------------~~~~~~~-~s~~~~~~~~~~f~~~~d~~~~~~~~~~--~i~~~r~~~  219 (285)
T KOG4210|consen  167 RRGLRPKNK------------------------LSRLSSG-PSDTIFFVGELDFSLTRDDLKEHFVSSG--EITSVRLPT  219 (285)
T ss_pred             cccccccch------------------------hcccccC-ccccceeecccccccchHHHhhhccCcC--cceeeccCC
Confidence            333111100                        0001111 22345 4999999999999999999998  577777764


Q ss_pred             c------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          299 D------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       299 ~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .      +|+|||.|.+...+..++.. .+.   .++++.+.+
T Consensus       220 ~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~---~~~~~~~~~  258 (285)
T KOG4210|consen  220 DEESGDSKGFAYVDFSAGNSKKLALND-QTR---SIGGRPLRL  258 (285)
T ss_pred             CCCccchhhhhhhhhhhchhHHHHhhc-ccC---cccCccccc
Confidence            3      68999999999999999976 666   788877653

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.44  E-value=6e-07  Score=71.86  Aligned_cols=143  Identities=26%  Similarity=0.362  Sum_probs=100.0

Q ss_pred             HHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchh
Q 019811          159 FACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVE  238 (335)
Q Consensus       159 ~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~  238 (335)
                      ...|+.+-.+....++++. -+.-.+++|+.|+......++-..-+++.++...+++.-...-..               
T Consensus       117 ~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswed---------------  180 (290)
T KOG0226|consen  117 PVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWED---------------  180 (290)
T ss_pred             hhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCC---------------
Confidence            4456666666666666663 356678999999888777777665566666666544432211000               


Q ss_pred             ccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcC----CeeeEEEEEecccceEEEEeCCHHHHH
Q 019811          239 LTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAA  314 (335)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G----~~~i~~v~~~~~~g~afV~f~~~~~a~  314 (335)
                                    ....+-......||-+.|...++++-|-..|.+|-    ...+.+-+..+.+|++||.|.+..++.
T Consensus       181 --------------Psl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~  246 (290)
T KOG0226|consen  181 --------------PSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYV  246 (290)
T ss_pred             --------------cccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHH
Confidence                          00011112236799999999999999999999874    223444455566899999999999999


Q ss_pred             HHHHhhcCCCcccccCcccc
Q 019811          315 LAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       315 ~A~~~l~g~~~~~~~g~~l~  334 (335)
                      .|+..|+|.   .++.|.|+
T Consensus       247 rAmrem~gk---yVgsrpik  263 (290)
T KOG0226|consen  247 RAMREMNGK---YVGSRPIK  263 (290)
T ss_pred             HHHHhhccc---ccccchhH
Confidence            999999999   99999876

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.44  E-value=1.5e-07  Score=79.61  Aligned_cols=146  Identities=17%  Similarity=0.131  Sum_probs=115.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-------CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-------KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-------~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      .|.|.||.+.+|.+.++.+|...|.|..+.++.+-       ....|||.|.|...+..| ..|.+++|-++.|.|.++.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va-QhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA-QHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHH-hhhccceeeeeeEEEEecC
Confidence            69999999999999999999999999999998742       136899999999999877 4788999999988887663


Q ss_pred             cCCCccC-----------------------------------------------------CCCcceEEECCCCccccHHH
Q 019811          131 ASGQRED-----------------------------------------------------TSGHFNIFVGDLSPEVTDAT  157 (335)
Q Consensus       131 ~~~~~~~-----------------------------------------------------~~~~~~l~v~nlp~~~t~~~  157 (335)
                      ....+..                                                     ..-.+++++.+|+..+...+
T Consensus        88 ~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e  167 (479)
T KOG4676|consen   88 DEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPE  167 (479)
T ss_pred             CCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchh
Confidence            3221000                                                     00126688999999999999


Q ss_pred             HHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       158 l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      +.+.|..+|+|....+-    .+....+|.+.|........|+. .+|..+.
T Consensus       168 ~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            99999999999777654    44566789999988888888886 4666554

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.42  E-value=1.6e-06  Score=60.30  Aligned_cols=71  Identities=20%  Similarity=0.189  Sum_probs=54.9

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec------ccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR------DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~------~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      +||.|+|+|...|.++|.+++..........+-++-      +.|+|||.|.+++.|.+-.+.++|++|..+..+++
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kv   78 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKV   78 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcE
Confidence            689999999999999999988754333343343332      27999999999999999999999997644554443

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.41  E-value=3.5e-07  Score=77.47  Aligned_cols=180  Identities=13%  Similarity=0.062  Sum_probs=111.4

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK---TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..|.|.||.++++.+.+..+|...|.|..+.++....   -......|||.|.|...+..|.. |.+..+-++.|.|-..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            3799999999999999999999999999998875321   22356789999999988887764 7777776777666544


Q ss_pred             cCCCCCCCCCC----Ccccc-------cchhccCCCCcCCcCCCCCCC-CCC---------CCCCCeEEEcCCCcccCHH
Q 019811          219 TKGAGNNEDKQ----SSDAK-------SVVELTNGSSEDGKETTNTEA-PEN---------NPQYTTVYVGNLAPEVTQL  277 (335)
Q Consensus       219 ~~~~~~~~~~~----~~~~~-------~~~~~~~~~~~~~~~~~~~~~-~~~---------~~~~~~l~v~nlp~~~t~~  277 (335)
                      ...........    ..++.       ............+..+...-. +..         ..-.++++|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            33222111000    00000       000000000011111100000 111         1112789999999999999


Q ss_pred             HHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          278 DLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       278 ~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      ++.+.|..+|.+......-.....+|.++|........|+. ++|.
T Consensus       167 e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gr  211 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGR  211 (479)
T ss_pred             hhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcch
Confidence            99999999995333333333445677799988888888874 4565

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.41  E-value=6.1e-07  Score=79.21  Aligned_cols=79  Identities=28%  Similarity=0.476  Sum_probs=67.6

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ..|||.|||.+++.++|.++|..||.|+...|......+....||||+|.+.+.+..|+.+ +...++++++.|+-....
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            4599999999999999999999999999988876543344449999999999999999985 578899999999876553

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.37  E-value=1.8e-06  Score=56.99  Aligned_cols=65  Identities=22%  Similarity=0.318  Sum_probs=44.9

Q ss_pred             CeEEEcCCCcccCHHH----HHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          263 TTVYVGNLAPEVTQLD----LHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~----l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..|+|.|||.+.....    |+.++..||+ .+..|.    .+.|+|.|.+.+.|.+|.+.|+|.   .+.|++|.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGG-kVl~v~----~~tAilrF~~~~~A~RA~KRmegE---dVfG~kI~v   71 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGG-KVLSVS----GGTAILRFPNQEFAERAQKRMEGE---DVFGNKISV   71 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT---EEE------TT-EEEEESSHHHHHHHHHHHTT-----SSSS--EE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCC-EEEEEe----CCEEEEEeCCHHHHHHHHHhhccc---ccccceEEE
Confidence            3589999999877655    5667779994 666662    579999999999999999999999   888888864

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.37  E-value=8.8e-07  Score=72.48  Aligned_cols=83  Identities=19%  Similarity=0.264  Sum_probs=76.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+...+||+|+...++.+++...|+.||.+..+.++.|+..+.++||+||+|.+.+.+..++. |++..+.|+.+.+.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            4455789999999999999999999999999999999998888899999999999999999998 999999999999998


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      ....
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            7654

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.30  E-value=2.8e-07  Score=78.87  Aligned_cols=154  Identities=24%  Similarity=0.376  Sum_probs=119.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCc-cccCceeEEeeeccCCCcc
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR-HLFGQPIKVNWAYASGQRE  136 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~-~~~g~~l~v~~~~~~~~~~  136 (335)
                      .+|++||.+.++.++|..+|...-.-.+-.++.  ..||+||.+.+..-|.+|++.++|. .+.|+++.+.++-++..+ 
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~--k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqr-   79 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV--KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQR-   79 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee--ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHH-
Confidence            489999999999999999997531100000111  2479999999999999999999985 567999999888665432 


Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                          ++.+-|.|+|+...++-+..++..||.+..+..+.   +....-..-|+|...+.+..|+..+++..+.+..+.+.
T Consensus        80 ----srk~Qirnippql~wevld~Ll~qyg~ve~~eqvn---t~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~  152 (584)
T KOG2193|consen   80 ----SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVN---TDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVG  152 (584)
T ss_pred             ----hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhc---cchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcc
Confidence                24588999999999999999999999998886641   11222234567888999999999999999999999998


Q ss_pred             EccCC
Q 019811          217 WATKG  221 (335)
Q Consensus       217 ~~~~~  221 (335)
                      |-...
T Consensus       153 YiPde  157 (584)
T KOG2193|consen  153 YIPDE  157 (584)
T ss_pred             cCchh
Confidence            86543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.25  E-value=1.6e-07  Score=80.35  Aligned_cols=145  Identities=23%  Similarity=0.340  Sum_probs=111.6

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeeeEEEEccC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK-WLGSRQIRCNWATK  220 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~-~~~g~~l~v~~~~~  220 (335)
                      +.+|++||.+..+.+++..+|...-.-.+-.++      ...||+||.+.+...|.+|++.++++ .+.|..+.+.++..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl------~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee------eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            368999999999999999999754211111222      23579999999999999999999986 68999999998876


Q ss_pred             CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE-ecc
Q 019811          221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV-QRD  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~-~~~  299 (335)
                      +....                                     +.+-|+|+|+..-++-|..+...||.  +..|.. ..+
T Consensus        76 kkqrs-------------------------------------rk~Qirnippql~wevld~Ll~qyg~--ve~~eqvnt~  116 (584)
T KOG2193|consen   76 KKQRS-------------------------------------RKIQIRNIPPQLQWEVLDSLLAQYGT--VENCEQVNTD  116 (584)
T ss_pred             HHHHh-------------------------------------hhhhHhcCCHHHHHHHHHHHHhccCC--HhHhhhhccc
Confidence            54322                                     55889999999999999999999994  444432 222


Q ss_pred             --cceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          300 --KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       300 --~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                        .-..-|+|.+.+.+.-|+..|+|.   .+.+..++
T Consensus       117 ~etavvnvty~~~~~~~~ai~kl~g~---Q~en~~~k  150 (584)
T KOG2193|consen  117 SETAVVNVTYSAQQQHRQAIHKLNGP---QLENQHLK  150 (584)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcch---Hhhhhhhh
Confidence              234457899999999999999998   67665554

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.23  E-value=4.2e-06  Score=76.39  Aligned_cols=72  Identities=32%  Similarity=0.547  Sum_probs=62.5

Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec---------ccceEEEEeCCHHHHHHHHHhhcCCCccccc
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR---------DKGFGFVRYSTHAEAALAIQMGNTTQSSYLF  329 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~---------~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~  329 (335)
                      .+..+.|||+||++.++++.|...|..||+  +..++++-         ++.|+||-|.+..+|.+|++.|+|.   .+.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgP--lasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~---iv~  245 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGP--LASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGI---IVM  245 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCc--ccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcce---eee
Confidence            344578999999999999999999999995  77777752         3679999999999999999999999   888


Q ss_pred             CccccC
Q 019811          330 GKQMKV  335 (335)
Q Consensus       330 g~~l~v  335 (335)
                      +..|++
T Consensus       246 ~~e~K~  251 (877)
T KOG0151|consen  246 EYEMKL  251 (877)
T ss_pred             eeeeee
Confidence            887764

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.18  E-value=3.2e-06  Score=69.24  Aligned_cols=80  Identities=20%  Similarity=0.324  Sum_probs=70.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.+.+||+|+.+.+|.+++...|+.||.|..+.+..++.    +||+||+|.+.+.+..|+. |+|..+.|+.+.+.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            345567899999999999999999999999998888877653    5799999999999999998 99999999999998


Q ss_pred             eeccC
Q 019811          128 WAYAS  132 (335)
Q Consensus       128 ~~~~~  132 (335)
                      +..-.
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            76543

>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=98.14  E-value=7.1e-06  Score=58.58  Aligned_cols=57  Identities=21%  Similarity=0.335  Sum_probs=39.9

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      ..|+|.+++..++.++|++.|+.||  .|.+|.+.+....|||.|.+.+.|.+|+..+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g--~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFG--EVAYVDFSRGDTEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS----EEEEE--TT-SEEEEEESS---HHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcC--CcceEEecCCCCEEEEEECCcchHHHHHHHHH
Confidence            5689999999999999999999999  69999999999999999999999999988764

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.04  E-value=1.3e-05  Score=57.20  Aligned_cols=57  Identities=19%  Similarity=0.283  Sum_probs=38.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN  115 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~  115 (335)
                      +.|.|.|++.+++.++|++.|+.||.|..|.+.....  .|||.|.++++|..|+..+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~--~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT--EGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S--EEEEEESS---HHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC--EEEEEECCcchHHHHHHHHH
Confidence            4689999999999999999999999999888766543  79999999999999998764

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.92  E-value=1.1e-05  Score=67.25  Aligned_cols=80  Identities=18%  Similarity=0.355  Sum_probs=62.8

Q ss_pred             ceEEECCCCccccHHHH------HHHhccCCCceeeEEeecCCCC-CcceE--EEEEeCCHHHHHHHHHHhCCceeCCee
Q 019811          142 FNIFVGDLSPEVTDATL------FACFSVYPSCSDARVMWDQKTG-RSRGF--GFVSFRNQQDAQSAINDLTGKWLGSRQ  212 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l------~~~f~~~g~v~~~~~~~~~~~~-~~~g~--afv~f~~~~~a~~a~~~l~~~~~~g~~  212 (335)
                      +-+||-+||+.+..++.      .++|..||.|..+.+-+...+. ...+.  .||+|.+.++|.+|++..+|..++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            56899999988766652      3789999999998776543221 11222  499999999999999999999999999


Q ss_pred             eEEEEccCC
Q 019811          213 IRCNWATKG  221 (335)
Q Consensus       213 l~v~~~~~~  221 (335)
                      |+..|...+
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            999998664

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.88  E-value=1.7e-05  Score=66.18  Aligned_cols=105  Identities=21%  Similarity=0.301  Sum_probs=73.3

Q ss_pred             eEEEeCCCCCCCHHHH------HHHHhccCCceeEEEeecCC-----CCe--EEEEEcCHHHHHHHHHHhCCccccCcee
Q 019811           58 SVYVGNIHTQVTEPLL------QEVFSSTGPVEGCKLIRKDK-----SSY--GFIHYFDRRSAAMAILSLNGRHLFGQPI  124 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l------~~~f~~~G~v~~v~~~~~~~-----~g~--afv~f~~~~~A~~a~~~l~~~~~~g~~l  124 (335)
                      -+||-+||+.+..+++      .++|.+||.|..|.+-+..+     .+.  .||.|.+.++|.+|+...+|..++|+-|
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            4799999988877663      46899999999887765431     132  3999999999999999999999999999


Q ss_pred             EEeeeccCC-----CccCCCCcceEEECCCCc---cccHHHHHHHh
Q 019811          125 KVNWAYASG-----QREDTSGHFNIFVGDLSP---EVTDATLFACF  162 (335)
Q Consensus       125 ~v~~~~~~~-----~~~~~~~~~~l~v~nlp~---~~t~~~l~~~f  162 (335)
                      +..|...+-     +...-....+.|+.---+   ..+.++|...=
T Consensus       196 katYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~q  241 (480)
T COG5175         196 KATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQ  241 (480)
T ss_pred             eeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhhh
Confidence            998875431     111112224566533222   35667766543

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.79  E-value=7.4e-05  Score=60.27  Aligned_cols=90  Identities=22%  Similarity=0.324  Sum_probs=78.0

Q ss_pred             HHHHHHHHHhCCccccCceeEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcce
Q 019811          105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRG  184 (335)
Q Consensus       105 ~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g  184 (335)
                      .-|..|...|++....|+.++|.|+..          ..|+|.||...++.+.+...|+.||++....+..| ..++..+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~----------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~   73 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH----------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTR   73 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc----------ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccc
Confidence            346677778999999999999999964          26999999999999999999999999988877766 4567888


Q ss_pred             EEEEEeCCHHHHHHHHHHhCC
Q 019811          185 FGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       185 ~afv~f~~~~~a~~a~~~l~~  205 (335)
                      -++|.|...-.|.+|...+..
T Consensus        74 eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   74 EGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             cchhhhhcchhHHHHHHHhcc
Confidence            899999999999999987743

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.74  E-value=8.9e-05  Score=45.65  Aligned_cols=52  Identities=17%  Similarity=0.313  Sum_probs=42.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHH
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI  111 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~  111 (335)
                      +.|-|.|.|.+.. +++...|..||.|..+.+-  ......+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~--~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP--ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC--CCCcEEEEEECCHHHHHhhC
Confidence            5688999998775 5566688889999987774  33458999999999999985

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.71  E-value=0.00012  Score=45.14  Aligned_cols=52  Identities=23%  Similarity=0.500  Sum_probs=43.9

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHH
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAI  317 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~  317 (335)
                      +.|-|.+.+....+. +...|..||  .|..+.+......++|+|.+..+|.+|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fG--eI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFG--EIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcC--CEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            568889999776654 556888999  6999999977889999999999999985

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.64  E-value=3.1e-05  Score=62.38  Aligned_cols=73  Identities=15%  Similarity=0.252  Sum_probs=61.1

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCC--------CCc----ceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKT--------GRS----RGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~--------~~~----~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      ....||+++||+.+....|+++|+.||.|-.|.+-....+        |.+    ..-|+|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3458999999999999999999999999999988654333        222    2247999999999999999999999


Q ss_pred             eCCee
Q 019811          208 LGSRQ  212 (335)
Q Consensus       208 ~~g~~  212 (335)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99874

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.63  E-value=3.4e-05  Score=62.10  Aligned_cols=69  Identities=28%  Similarity=0.365  Sum_probs=59.5

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCC----------------CeEEEEEcCHHHHHHHHHHhCCcc
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----------------SYGFIHYFDRRSAAMAILSLNGRH  118 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~----------------g~afv~f~~~~~A~~a~~~l~~~~  118 (335)
                      ..-.||+++||+.+...-|+++|+.||.|-.|.+-.....                .-|+|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3457999999999999999999999999999888653211                257899999999999999999999


Q ss_pred             ccCce
Q 019811          119 LFGQP  123 (335)
Q Consensus       119 ~~g~~  123 (335)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.57  E-value=0.00016  Score=61.28  Aligned_cols=82  Identities=23%  Similarity=0.277  Sum_probs=69.6

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCcee--------EEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG--------CKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHL  119 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~  119 (335)
                      ..+...+|||-+||..+++++|.++|.++|.|..        |++.+++    .++-|.|.|.+...|..|+..+++..|
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            4566678999999999999999999999998743        4454544    358999999999999999999999999


Q ss_pred             cCceeEEeeeccCC
Q 019811          120 FGQPIKVNWAYASG  133 (335)
Q Consensus       120 ~g~~l~v~~~~~~~  133 (335)
                      .+.+|+|..+..+.
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999998876544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.54  E-value=9e-05  Score=62.82  Aligned_cols=85  Identities=24%  Similarity=0.295  Sum_probs=75.7

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCce--------eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCS--------DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      ....++||-+||..+++.+|.+.|..+|.|.        .+.+.++++++.+++-|.|.|.+...|..|+.-+++..+.+
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            3446899999999999999999999998774        46777888999999999999999999999999999999999


Q ss_pred             eeeEEEEccCCCC
Q 019811          211 RQIRCNWATKGAG  223 (335)
Q Consensus       211 ~~l~v~~~~~~~~  223 (335)
                      .+|+|..+.....
T Consensus       144 n~ikvs~a~~r~~  156 (351)
T KOG1995|consen  144 NTIKVSLAERRTG  156 (351)
T ss_pred             CCchhhhhhhccC
Confidence            9999988876653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.51  E-value=0.00013  Score=63.18  Aligned_cols=64  Identities=22%  Similarity=0.308  Sum_probs=55.7

Q ss_pred             CCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-------------------cceEEEEeCCHHHHHHHHH
Q 019811          258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-------------------KGFGFVRYSTHAEAALAIQ  318 (335)
Q Consensus       258 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-------------------~g~afV~f~~~~~a~~A~~  318 (335)
                      ...++++|.+.|||.+-.-+.|.++|..+|  .|..|+|.+.                   +-+|+|+|++.+.|.+|.+
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G--~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVG--SIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhccc--ceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            344669999999999999999999999999  6899998754                   4589999999999999998


Q ss_pred             hhcCC
Q 019811          319 MGNTT  323 (335)
Q Consensus       319 ~l~g~  323 (335)
                      .|+..
T Consensus       305 ~~~~e  309 (484)
T KOG1855|consen  305 LLNPE  309 (484)
T ss_pred             hhchh
Confidence            88655

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.50  E-value=0.00049  Score=45.68  Aligned_cols=59  Identities=17%  Similarity=0.255  Sum_probs=42.7

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG  116 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~  116 (335)
                      |+.....+|+ .|..+...||.++|+.||.| .|.-+.+.   .|||...+.+.|..++..++.
T Consensus         6 P~RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT---SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    6 PSRDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT---SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             -SGCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT---EEEEEECCCHHHHHHHHHHTT
T ss_pred             CCcceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC---cEEEEeecHHHHHHHHHHhcc
Confidence            3344445666 99999999999999999999 44444554   599999999999999887753

; 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.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.45  E-value=0.00076  Score=47.41  Aligned_cols=72  Identities=21%  Similarity=0.127  Sum_probs=51.3

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEE-Ee----------ecCCCCeEEEEEcCHHHHHHHHHHhCCccccCce-
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCK-LI----------RKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQP-  123 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~-~~----------~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~-  123 (335)
                      .+.|.|-|.|.. ....|.+.|++||.|.+.. +.          .....+...|.|.++.+|.+||. .||..+.|.- 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456999999998 5788999999999987764 10          11234699999999999999995 6999998754 


Q ss_pred             eEEeee
Q 019811          124 IKVNWA  129 (335)
Q Consensus       124 l~v~~~  129 (335)
                      +-|.+.
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence            445555

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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.42  E-value=0.00047  Score=56.74  Aligned_cols=61  Identities=21%  Similarity=0.233  Sum_probs=52.5

Q ss_pred             HHHHHHHHhccCCceeEEEeecCCC-----CeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           70 EPLLQEVFSSTGPVEGCKLIRKDKS-----SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        70 ~~~l~~~f~~~G~v~~v~~~~~~~~-----g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ++++.+-|++||.|..|.|+-..+.     --.||+|...++|.+|+-.|||.+|+|+.++..+..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            5778889999999999888765432     357999999999999999999999999999988763

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.36  E-value=0.0006  Score=56.14  Aligned_cols=68  Identities=16%  Similarity=0.203  Sum_probs=56.2

Q ss_pred             HHHHHHHhccCCCceeeEEeecCCCCCc-ceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          155 DATLFACFSVYPSCSDARVMWDQKTGRS-RGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       155 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~-~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      ++++.+.+.+||.|..|.|..++..... ..-.||+|...+.|.+|+-.|||+.|+|+.++..|.+..+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ek  368 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEK  368 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHh
Confidence            6788899999999999988766433222 2347999999999999999999999999999998876543

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.36  E-value=0.00071  Score=54.76  Aligned_cols=85  Identities=22%  Similarity=0.298  Sum_probs=69.7

Q ss_pred             HHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCccc
Q 019811          195 DAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEV  274 (335)
Q Consensus       195 ~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~  274 (335)
                      -|..|...|++....|+.++|.|+..                                          ..|+|.||...+
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~------------------------------------------a~l~V~nl~~~~   43 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH------------------------------------------AELYVVNLMQGA   43 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc------------------------------------------ceEEEEecchhh
Confidence            46677788999999999999999976                                          459999999999


Q ss_pred             CHHHHHHHhhhcCCeeeEEEEEec---ccceEEEEeCCHHHHHHHHHhhc
Q 019811          275 TQLDLHRHFHSLGAGVIEEVRVQR---DKGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       275 t~~~l~~~f~~~G~~~i~~v~~~~---~~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      +-+.+...|+.||.++..-+.+..   ..+-++|+|.....|.+|+..++
T Consensus        44 sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   44 SNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             hhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            999999999999963333333332   24678999999999999998773

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.35  E-value=0.00013  Score=59.06  Aligned_cols=60  Identities=17%  Similarity=0.224  Sum_probs=50.5

Q ss_pred             HHHHHHHh-ccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           71 PLLQEVFS-STGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        71 ~~l~~~f~-~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ++|...|+ +||.|+++++..+..   .|-+||.|...++|++|+..||+.++.|++|...++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            45555555 899999987766542   5789999999999999999999999999999988763

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.28  E-value=0.00034  Score=63.10  Aligned_cols=77  Identities=16%  Similarity=0.176  Sum_probs=63.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHh-ccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc---CceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFS-STGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF---GQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~-~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~---g~~l~v~  127 (335)
                      ....+..|+|.||-...|...|+.++. ..|.|.+.||  ++-+..|||.|.+.++|...+.+|||..|.   ++.|.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            455677899999999999999999998 5667888866  444457999999999999999999998875   4666666


Q ss_pred             eec
Q 019811          128 WAY  130 (335)
Q Consensus       128 ~~~  130 (335)
                      |..
T Consensus       518 f~~  520 (718)
T KOG2416|consen  518 FVR  520 (718)
T ss_pred             ecc
Confidence            653

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.27  E-value=0.001  Score=59.73  Aligned_cols=78  Identities=19%  Similarity=0.201  Sum_probs=62.9

Q ss_pred             CcceEEECCCCccc------cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCee
Q 019811          140 GHFNIFVGDLSPEV------TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL-GSRQ  212 (335)
Q Consensus       140 ~~~~l~v~nlp~~~------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~-~g~~  212 (335)
                      -...|+|.|+|.--      -..-|..+|+++|.+....++.+..+ ..+||.|++|.+..+|..|++.|||..+ .+++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~g-gtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEG-GTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccC-CeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            34689999998631      23456688999999999999988655 4999999999999999999999999887 4677


Q ss_pred             eEEEEc
Q 019811          213 IRCNWA  218 (335)
Q Consensus       213 l~v~~~  218 (335)
                      ..|..-
T Consensus       136 f~v~~f  141 (698)
T KOG2314|consen  136 FFVRLF  141 (698)
T ss_pred             EEeehh
Confidence            777643

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.24  E-value=0.0026  Score=40.13  Aligned_cols=53  Identities=21%  Similarity=0.357  Sum_probs=44.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhcc----CCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSST----GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL  114 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~----G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l  114 (335)
                      ..|+|+|+. +++.++|..+|..|    ++. .|.-+.+.+   |=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~-~IEWIdDtS---cNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPF-RIEWIDDTS---CNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCc-eEEEecCCc---EEEEECCHHHHHHHHHcC
Confidence            359999985 48899999999999    544 676677765   999999999999999764

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.16  E-value=0.0022  Score=45.07  Aligned_cols=64  Identities=28%  Similarity=0.327  Sum_probs=47.1

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEE-------------EecccceEEEEeCCHHHHHHHHHhhcCCCccccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-------------VQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLF  329 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~-------------~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~  329 (335)
                      ..|.|-+.|+. ....|.+.|+.||  .|.+..             ......+..|+|++..+|.+|+ .-||.   .|+
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G--~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~---i~~   79 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFG--TILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGT---IFS   79 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS---EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTE---EET
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcc--eEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCe---EEc
Confidence            56888899988 5667889999999  465553             4555779999999999999999 45888   787


Q ss_pred             Cccc
Q 019811          330 GKQM  333 (335)
Q Consensus       330 g~~l  333 (335)
                      |.-|
T Consensus        80 g~~m   83 (100)
T PF05172_consen   80 GSLM   83 (100)
T ss_dssp             TCEE
T ss_pred             CcEE
Confidence            7544

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.12  E-value=0.0024  Score=42.46  Aligned_cols=55  Identities=18%  Similarity=0.297  Sum_probs=40.4

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      ...+++ +|..|...||.++|++||.| .|.++-|.       .|||...+.+.|..++..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            455564 99999999999999999987 44455331       499999999999999987753

; 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.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.02  E-value=0.0053  Score=53.51  Aligned_cols=69  Identities=16%  Similarity=0.158  Sum_probs=56.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeec---CCC--CCc--------ceEEEEEeCCHHHHHHHHHHhC
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWD---QKT--GRS--------RGFGFVSFRNQQDAQSAINDLT  204 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~---~~~--~~~--------~g~afv~f~~~~~a~~a~~~l~  204 (335)
                      ..+.++|.+.|||.+-.-+.|.++|..+|.|..|+|...   +.+  +..        +-.|+|+|+..+.|.+|.+.++
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            356789999999999999999999999999999999855   222  112        3468999999999999999875


Q ss_pred             Cc
Q 019811          205 GK  206 (335)
Q Consensus       205 ~~  206 (335)
                      ..
T Consensus       308 ~e  309 (484)
T KOG1855|consen  308 PE  309 (484)
T ss_pred             hh
Confidence            54

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.00  E-value=0.0011  Score=55.90  Aligned_cols=76  Identities=17%  Similarity=0.320  Sum_probs=66.7

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCC--CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYP--SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ...++||+||-..+|.+||.+.+...|  .+..+++..++.+|.++|||+|...+..+.++.++.|..+.+.|..-.|
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            346899999999999999999998876  5777888888889999999999999999999999999999998865554

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.97  E-value=0.00035  Score=56.62  Aligned_cols=53  Identities=23%  Similarity=0.406  Sum_probs=45.7

Q ss_pred             HHHHHHhh-hcCCeeeEEEEEecc-----cceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          277 LDLHRHFH-SLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       277 ~~l~~~f~-~~G~~~i~~v~~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                      |||...|+ +||  ++..+.+..+     .|.+||.|...++|.+|+..|||.   +|.|++|.
T Consensus        83 Ed~f~E~~~kyg--Eiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnR---w~~G~pi~  141 (260)
T KOG2202|consen   83 EDVFTELEDKYG--EIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNR---WYNGRPIH  141 (260)
T ss_pred             HHHHHHHHHHhh--hhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCc---cccCCcce
Confidence            56666666 899  6888877655     689999999999999999999999   99999985

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.85  E-value=0.0034  Score=46.90  Aligned_cols=69  Identities=20%  Similarity=0.216  Sum_probs=48.5

Q ss_pred             CCCCCeEEEcCCC-----cccCHH----HHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCccccc
Q 019811          259 NPQYTTVYVGNLA-----PEVTQL----DLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLF  329 (335)
Q Consensus       259 ~~~~~~l~v~nlp-----~~~t~~----~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~  329 (335)
                      +|+..||.|.=+.     .....+    +|.+.|..||  .+.-+++..  +..+|+|.+-..|.+|+ .++|.   .++
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~G--evvLvRfv~--~~mwVTF~dg~sALaal-s~dg~---~v~   95 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYG--EVVLVRFVG--DTMWVTFRDGQSALAAL-SLDGI---QVN   95 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS---ECEEEEET--TCEEEEESSCHHHHHHH-HGCCS---EET
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCC--ceEEEEEeC--CeEEEEECccHHHHHHH-ccCCc---EEC
Confidence            3444677666554     112232    6777889999  466667765  49999999999999998 67999   999


Q ss_pred             CccccC
Q 019811          330 GKQMKV  335 (335)
Q Consensus       330 g~~l~v  335 (335)
                      |+.|+|
T Consensus        96 g~~l~i  101 (146)
T PF08952_consen   96 GRTLKI  101 (146)
T ss_dssp             TEEEEE
T ss_pred             CEEEEE
Confidence            999875

; PDB: 1UFW_A 2DNR_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.78  E-value=0.0061  Score=45.59  Aligned_cols=56  Identities=23%  Similarity=0.354  Sum_probs=44.5

Q ss_pred             HHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           71 PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        71 ~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      .+|.+.|..||.+.=|++..+    .-+|.|.+.++|.+|+ .++|..+.|+.|+|..-.+
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~----~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD----TMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT----CEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeCC----eEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCCc
Confidence            467888899998877766553    5999999999999998 5899999999999987643

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.63  E-value=0.015  Score=36.73  Aligned_cols=53  Identities=19%  Similarity=0.152  Sum_probs=42.6

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhc----CCeeeEEEEEecccceEEEEeCCHHHHHHHHHhh
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSL----GAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG  320 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~----G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l  320 (335)
                      ..|+|+++. +++.+||+.+|..|    +   ...|....+ ..|-|-|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~---~~~IEWIdD-tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEG---PFRIEWIDD-TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCC---CceEEEecC-CcEEEEECCHHHHHHHHHcC
Confidence            579999985 58899999999999    5   455555543 46778899999999999765

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.62  E-value=0.0059  Score=54.96  Aligned_cols=69  Identities=9%  Similarity=0.117  Sum_probs=54.9

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      +.|.|+-||..+..|+|+.+|+.-....+++|.+.-+ ...||+|++..+|..|.+.|.... .+|.|+.|
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-~nWyITfesd~DAQqAykylreev-k~fqgKpI  244 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-DNWYITFESDTDAQQAYKYLREEV-KTFQGKPI  244 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-CceEEEeecchhHHHHHHHHHHHH-HhhcCcch
Confidence            6789999999999999999999533236777777643 367999999999999998886652 26888776

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.60  E-value=0.002  Score=58.39  Aligned_cols=77  Identities=22%  Similarity=0.223  Sum_probs=61.3

Q ss_pred             CCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       256 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      +..+..++.|+|.||--.+|.-.|+.++..-|. .|.+.=|.+-+..|||.|.+.++|.....+|||..|=.-+++.|
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg-~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGG-NVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccC-chHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            445667789999999999999999999995542 56666444557899999999999999999999997633455544

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.37  E-value=0.019  Score=51.99  Aligned_cols=75  Identities=25%  Similarity=0.286  Sum_probs=58.0

Q ss_pred             CCcceEEEeCCCCCC--C----HHHHHHHHhccCCceeEEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCcccc-Cce
Q 019811           54 STCRSVYVGNIHTQV--T----EPLLQEVFSSTGPVEGCKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLF-GQP  123 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~--t----~~~l~~~f~~~G~v~~v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~-g~~  123 (335)
                      .-...|.|.|+|---  .    ..-|..+|+++|.+..+.+..+   +.+||.|++|.+..+|..|+..|||..+. .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            444569999999432  2    2346678999999988877643   35699999999999999999999998886 567


Q ss_pred             eEEee
Q 019811          124 IKVNW  128 (335)
Q Consensus       124 l~v~~  128 (335)
                      ..|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            76653

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.15  E-value=0.019  Score=42.38  Aligned_cols=73  Identities=15%  Similarity=0.283  Sum_probs=54.3

Q ss_pred             CCCcceEEEeCCCCCCCH----HHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTE----PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~----~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+-.||.|+=|..++..    ..+...++.||+|.+|.+.-..   .|.|.|.|..+|-+|+.++.. ...|..+...|
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq---savVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ---SAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc---eEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            444567888877766643    3455566889999998764433   599999999999999998865 56677777766


Q ss_pred             e
Q 019811          129 A  129 (335)
Q Consensus       129 ~  129 (335)
                      -
T Consensus       159 q  159 (166)
T PF15023_consen  159 Q  159 (166)
T ss_pred             c
Confidence            5

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=95.86  E-value=0.63  Score=39.09  Aligned_cols=158  Identities=14%  Similarity=0.215  Sum_probs=103.9

Q ss_pred             CCCCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----------CCCeEEEEEcCHHHHHHHHH---
Q 019811           47 LPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----------KSSYGFIHYFDRRSAAMAIL---  112 (335)
Q Consensus        47 ~~~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----------~~g~afv~f~~~~~A~~a~~---  112 (335)
                      .|.|.+.-.+|.|...|+..+++-..+...|-+||+|++|.++.+.           ......+.|-+.+.+-....   
T Consensus         6 LPkGdD~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvL   85 (309)
T PF10567_consen    6 LPKGDDEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVL   85 (309)
T ss_pred             cCCCCccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHH
Confidence            4667778889999999999999999999999999999999998765           12478999999998866543   


Q ss_pred             -HhCC--ccccCceeEEeeecc---------CC--------------CccCCCCcceEEECCCCccccHHHHHH----Hh
Q 019811          113 -SLNG--RHLFGQPIKVNWAYA---------SG--------------QREDTSGHFNIFVGDLSPEVTDATLFA----CF  162 (335)
Q Consensus       113 -~l~~--~~~~g~~l~v~~~~~---------~~--------------~~~~~~~~~~l~v~nlp~~~t~~~l~~----~f  162 (335)
                       +|+.  ..+....|.+.+..-         ..              .-.....++.|.|. +...+..+++.+    ++
T Consensus        86 QrLsEfK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL  164 (309)
T PF10567_consen   86 QRLSEFKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFL  164 (309)
T ss_pred             HHHHHHHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhh
Confidence             2222  234455666666531         00              00123445666663 223343333322    22


Q ss_pred             ccCCC----ceeeEEeecC--CCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          163 SVYPS----CSDARVMWDQ--KTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       163 ~~~g~----v~~~~~~~~~--~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      ..-+.    ++++.++...  ...-+..||.+.|-+..-|.+.+..+..
T Consensus       165 ~~~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~  213 (309)
T PF10567_consen  165 KNSNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKS  213 (309)
T ss_pred             ccCCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHh
Confidence            22232    5666666322  2234678999999999999999887764

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

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

Probab=95.81  E-value=0.0066  Score=55.91  Aligned_cols=69  Identities=22%  Similarity=0.311  Sum_probs=60.6

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +.-+|||+|+-..+..+-+......+|.|.+++...     |+|..|.....+.+|+..++...+.|..+.+..
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-----fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-----FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-----hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            445699999999999999999999999998776544     999999999999999999999999888877754

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.63  E-value=0.019  Score=48.70  Aligned_cols=67  Identities=22%  Similarity=0.371  Sum_probs=56.5

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec------ccceEEEEeCCHHHHHHHHHhhcCCCcccccCcc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR------DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ  332 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~------~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~  332 (335)
                      .++||+||-+-+|++||.+.+..-|--.+.++++..      ++|+|+|-..+..+.++.|+.|-.+   +|+|..
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k---~iHGQ~  153 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTK---TIHGQS  153 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccc---eecCCC
Confidence            679999999999999999988877744566666654      3799999999999999999999888   888864

>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=95.61  E-value=0.16  Score=36.45  Aligned_cols=65  Identities=15%  Similarity=0.177  Sum_probs=47.0

Q ss_pred             eEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      .+.+...|...+.++|..+...+- .|..++++++.  ..++-.++++|.+..+|..-...+||+.+.
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            344444444455566665555553 57788888773  246778999999999999999999998874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.58  E-value=0.013  Score=46.16  Aligned_cols=68  Identities=12%  Similarity=0.032  Sum_probs=45.2

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhc-cCCc---eeEEEeecC------CCCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSS-TGPV---EGCKLIRKD------KSSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~-~G~v---~~v~~~~~~------~~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      .....|-||+||+.+|++++++.++. ++.-   ..+.-..+.      ...-|||.|.+.+++......++|..|.+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            34567999999999999999997776 5554   222211111      12479999999999999999999987764

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.

>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=95.39  E-value=0.024  Score=44.68  Aligned_cols=81  Identities=14%  Similarity=0.229  Sum_probs=50.2

Q ss_pred             CcceEEECCCCccccHHHHHHHhcc-CCCc---eeeEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceeCC---
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSV-YPSC---SDARVMWDQKT--GRSRGFGFVSFRNQQDAQSAINDLTGKWLGS---  210 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~-~g~v---~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g---  210 (335)
                      ....|.|++||+++|++++.+.++. ++..   ..+.-......  ......|||.|.+.+++..-...++|..|.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3458999999999999999998887 6655   33321122111  1234569999999999999999999977632   


Q ss_pred             --eeeEEEEccC
Q 019811          211 --RQIRCNWATK  220 (335)
Q Consensus       211 --~~l~v~~~~~  220 (335)
                        ....|+++.-
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              2344555544

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.36  E-value=0.043  Score=43.44  Aligned_cols=61  Identities=20%  Similarity=0.212  Sum_probs=46.2

Q ss_pred             CHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC--CccccCceeEEeeecc
Q 019811           69 TEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN--GRHLFGQPIKVNWAYA  131 (335)
Q Consensus        69 t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~--~~~~~g~~l~v~~~~~  131 (335)
                      ..+.|+++|..|+.+..+..++.-.  -..|.|.+.+.|.+|...|+  +..+.|..+++.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr--Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR--RIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT--EEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC--EEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            4588999999999988877766554  59999999999999999999  9999999999988843

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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.06  E-value=0.01  Score=50.42  Aligned_cols=81  Identities=16%  Similarity=0.278  Sum_probs=61.3

Q ss_pred             ceEEECCCCccccHHHHH---HHhccCCCceeeEEeecCC--CC-CcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          142 FNIFVGDLSPEVTDATLF---ACFSVYPSCSDARVMWDQK--TG-RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~---~~f~~~g~v~~~~~~~~~~--~~-~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      +-+|+-+|+.....+++.   +.|..||.|..+.+.++..  .+ ...--++|+|...++|..|+...+|..++|+.++.
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            457888888776555444   5678889999998877652  11 11223899999999999999999999999999888


Q ss_pred             EEccCCC
Q 019811          216 NWATKGA  222 (335)
Q Consensus       216 ~~~~~~~  222 (335)
                      .+...+.
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            8776544

>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=94.97  E-value=0.3  Score=35.09  Aligned_cols=63  Identities=14%  Similarity=0.018  Sum_probs=46.5

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc----cceEEEEeCCHHHHHHHHHhhcCCCccccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMGNTTQSSYLF  329 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~  329 (335)
                      ..+.+...|.-++.++|..+.+.+- ..+..+++.++    +-.+.++|.+...|.+-...+||+   .|+
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~-~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk---~Fn   80 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFR-EDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGK---PFN   80 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhccc-ccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCC---ccC
Confidence            3344444455566677776666665 36778888876    447899999999999999999999   554

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.96  E-value=0.018  Score=54.59  Aligned_cols=71  Identities=23%  Similarity=0.332  Sum_probs=61.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc--CceeEEeeecc
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF--GQPIKVNWAYA  131 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~~~~  131 (335)
                      .++.|.+-..+...|..+|..||.|.+.|..++-+  .|.|+|...+.|..|+.+|+|....  |.+.+|.+++.
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N--~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN--MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccccc--chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            45567777788899999999999999999988776  8999999999999999999997664  78888887754

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.75  E-value=0.11  Score=41.07  Aligned_cols=63  Identities=22%  Similarity=0.194  Sum_probs=47.0

Q ss_pred             cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeeeEEEEccCCC
Q 019811          154 TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT--GKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       154 t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~g~~l~v~~~~~~~  222 (335)
                      ..+.|+++|..++.+.....+      ++.+-..|.|.+.++|.+|...|+  +..+.|..+++.|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L------~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPL------KSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEE------TTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEc------CCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            468899999999999888777      334559999999999999999999  899999999999985443

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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.62  E-value=0.015  Score=49.35  Aligned_cols=76  Identities=17%  Similarity=0.227  Sum_probs=60.1

Q ss_pred             ceEEEeCCCCCCCHHHHH---HHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           57 RSVYVGNIHTQVTEPLLQ---EVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~---~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      .-+||-+|+.....+.+.   ++|.+||.|.+|.+.++.+       .--++|.|...++|..||...+|....|+.++.
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            447888898776554443   4888999999998877552       125799999999999999999999999999888


Q ss_pred             eeeccC
Q 019811          127 NWAYAS  132 (335)
Q Consensus       127 ~~~~~~  132 (335)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            776543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.36  E-value=0.19  Score=44.52  Aligned_cols=69  Identities=14%  Similarity=0.176  Sum_probs=59.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccC-CceeEEEeecCC--CCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G-~v~~v~~~~~~~--~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      +.+++.|.|=.+|..++..||..|+..+- .|..+++++++.  +-.+++.|.+.++|....+.+||..|..
T Consensus        71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   71 ASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            33478899999999999999999998765 588999999764  3478999999999999999999988853

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.33  E-value=0.35  Score=40.63  Aligned_cols=71  Identities=23%  Similarity=0.167  Sum_probs=53.2

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCce-eEEeeec
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQP-IKVNWAY  130 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~-l~v~~~~  130 (335)
                      ..-|-|-+.|+.- -..|...|++||.|.+...-  .+..+-+|.|.+..+|.+||. .||..|.|.. |-|....
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~--~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP--SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC--CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            3447788888765 56788899999999765443  445699999999999999995 6888887753 3454433

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.12  E-value=0.27  Score=43.61  Aligned_cols=67  Identities=21%  Similarity=0.319  Sum_probs=58.4

Q ss_pred             cceEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      ++.|.|-.+|..++-.||..++..+- .|.+++++||..  .++-.++++|.+..+|......+||+.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            67899999999999999999998764 688999998742  55677999999999999999999998874

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.01  E-value=0.16  Score=46.19  Aligned_cols=95  Identities=14%  Similarity=0.119  Sum_probs=66.3

Q ss_pred             HHHHHHHhCCccccCceeEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhcc--CCCceeeEEeecCCCCCcce
Q 019811          107 AAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSV--YPSCSDARVMWDQKTGRSRG  184 (335)
Q Consensus       107 A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~--~g~v~~~~~~~~~~~~~~~g  184 (335)
                      -..+++..-+..++.+-.+|...         ...+.|.|+-||.+.-+|+++.+|+.  +-.+.+|.+-.+.       
T Consensus       150 I~Evlresp~VqvDekgekVrp~---------~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------  213 (684)
T KOG2591|consen  150 IVEVLRESPNVQVDEKGEKVRPN---------HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------  213 (684)
T ss_pred             HHHHHhcCCCceeccCccccccC---------cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------
Confidence            34455554555555555555433         23357888999999999999999964  6678888776441       


Q ss_pred             EEEEEeCCHHHHHHHHHHhCC--ceeCCeeeEEEE
Q 019811          185 FGFVSFRNQQDAQSAINDLTG--KWLGSRQIRCNW  217 (335)
Q Consensus       185 ~afv~f~~~~~a~~a~~~l~~--~~~~g~~l~v~~  217 (335)
                      -=||+|++..||..|...|..  +.|.|+.|..++
T Consensus       214 nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  214 NWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            169999999999999887754  457777766544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.00  E-value=0.2  Score=37.22  Aligned_cols=71  Identities=18%  Similarity=0.297  Sum_probs=51.0

Q ss_pred             cceEEECCCCcc----ccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          141 HFNIFVGDLSPE----VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       141 ~~~l~v~nlp~~----~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      -.+|.|.=|..+    -+...+...++.||+|.++...     |  +-.|.|.|+|..+|-.|+.++.. ..-|..+.+.
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            346666544444    3344556667889999999775     2  33599999999999999998776 5566777777


Q ss_pred             Ecc
Q 019811          217 WAT  219 (335)
Q Consensus       217 ~~~  219 (335)
                      |-.
T Consensus       158 Wqq  160 (166)
T PF15023_consen  158 WQQ  160 (166)
T ss_pred             ccc
Confidence            754

>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=93.93  E-value=0.36  Score=31.03  Aligned_cols=56  Identities=13%  Similarity=0.137  Sum_probs=44.4

Q ss_pred             CCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           66 TQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        66 ~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ..++-++++..+..|+-.   +|..++. | -||.|.+..+|+++....+|..+.+..+.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~~---~I~~d~t-G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRWD---RIRDDRT-G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCcc---eEEecCC-E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            357889999999999855   3444544 3 479999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=93.55  E-value=0.16  Score=42.07  Aligned_cols=59  Identities=12%  Similarity=0.202  Sum_probs=45.9

Q ss_pred             CCCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHH
Q 019811           48 PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA  107 (335)
Q Consensus        48 ~~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A  107 (335)
                      +++....-...|+++|||.++.-.||+..+.+.|.+ -..+.+....|-||+.|.+...|
T Consensus       322 ~~g~~a~~~~di~~~nl~rd~rv~dlk~~lr~~~~~-pm~iswkg~~~k~flh~~~~~~~  380 (396)
T KOG4410|consen  322 QSGVEAGAKTDIKLTNLSRDIRVKDLKSELRKRECT-PMSISWKGHFGKCFLHFGNRKGV  380 (396)
T ss_pred             CCcccCccccceeeccCccccchHHHHHHHHhcCCC-ceeEeeecCCcceeEecCCccCC
Confidence            334344445669999999999999999999988865 45667777888999999876543

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=93.36  E-value=0.13  Score=35.08  Aligned_cols=73  Identities=15%  Similarity=0.155  Sum_probs=46.1

Q ss_pred             EEEEeCCHHHHHHHHHHhC-CceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCe
Q 019811          186 GFVSFRNQQDAQSAINDLT-GKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTT  264 (335)
Q Consensus       186 afv~f~~~~~a~~a~~~l~-~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (335)
                      |+|+|.+..-|.+.++.-. ...+++..+.|.-..-..........                          ......++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv--------------------------~~~vs~rt   54 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQV--------------------------FSGVSKRT   54 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEE--------------------------EEcccCCE
Confidence            6899999999999987322 23466777766654322111111000                          01112278


Q ss_pred             EEEcCCCcccCHHHHHHHhh
Q 019811          265 VYVGNLAPEVTQLDLHRHFH  284 (335)
Q Consensus       265 l~v~nlp~~~t~~~l~~~f~  284 (335)
                      |.|.|||..+.+++|++.++
T Consensus        55 Vlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   55 VLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             EEEeCCCCCCChhhheeeEE
Confidence            99999999999999987655

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.17  E-value=0.062  Score=47.73  Aligned_cols=77  Identities=19%  Similarity=0.181  Sum_probs=62.6

Q ss_pred             CCcceEEEeCCCCCC-CHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           54 STCRSVYVGNIHTQV-TEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~-t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ...+.|-+.-.|+.. +.++|...|.+||.|..|.+-..  .-.|.|.|.+..+|-+|. +.++..|.++.|+|.|..+.
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~--~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS--SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc--hhhheeeeeccccccchh-ccccceecCceeEEEEecCC
Confidence            344556777777775 46899999999999999988555  236999999999998886 46899999999999998765


Q ss_pred             C
Q 019811          133 G  133 (335)
Q Consensus       133 ~  133 (335)
                      +
T Consensus       447 ~  447 (526)
T KOG2135|consen  447 P  447 (526)
T ss_pred             c
Confidence            4

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=93.11  E-value=3.9  Score=34.52  Aligned_cols=175  Identities=9%  Similarity=0.124  Sum_probs=100.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecC-------CCCCcceEEEEEeCCHHHHHHH----HHHhCC
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ-------KTGRSRGFGFVSFRNQQDAQSA----INDLTG  205 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~-------~~~~~~g~afv~f~~~~~a~~a----~~~l~~  205 (335)
                      +.-.++.|.+.|+..+++--.+...|.+||+|+++.++.+.       .......-+.+-|-+.+.+-.-    ++.|..
T Consensus        11 D~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsE   90 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSE   90 (309)
T ss_pred             ccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHH
Confidence            34445788999999999999999999999999999998653       0112345688899988887553    333332


Q ss_pred             --ceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHH-HHHH
Q 019811          206 --KWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLD-LHRH  282 (335)
Q Consensus       206 --~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~-l~~~  282 (335)
                        ..+....|.+.|..-............ ...........        .-.-......+.|.|.-- ..+..++ +.+.
T Consensus        91 fK~~L~S~~L~lsFV~l~y~~~~~~~~~~-~~~~~~~~~~L--------~~~i~~~gATRSl~IeF~-~~~~~~dl~~~k  160 (309)
T PF10567_consen   91 FKTKLKSESLTLSFVSLNYQKKTDPNDEE-ADFSDYLVASL--------QYNIINRGATRSLAIEFK-DPVDKDDLIEKK  160 (309)
T ss_pred             HHHhcCCcceeEEEEEEeccccccccccc-cchhhHHhhhh--------hheeecCCcceEEEEEec-CccchhHHHHHh
Confidence              346778888888765433322211100 00000000000        000000111266766433 4443333 3332


Q ss_pred             h---hhcC--CeeeEEEEEec--------ccceEEEEeCCHHHHHHHHHhhc
Q 019811          283 F---HSLG--AGVIEEVRVQR--------DKGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       283 f---~~~G--~~~i~~v~~~~--------~~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      +   ..-+  .-.+++|.+..        +..+|.++|-+..=|.+.+..+.
T Consensus       161 L~fL~~~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  161 LPFLKNSNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             hhhhccCCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            2   2111  11456665543        25799999999999999887775

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.73  E-value=0.22  Score=41.79  Aligned_cols=64  Identities=23%  Similarity=0.242  Sum_probs=49.4

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      .=|.|-++|+... .-|...|+.||  .|.+....++..+.+|.|.+..+|.+|+.. +|+   .|+|..+
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG--~Vvkhv~~~ngNwMhirYssr~~A~KALsk-ng~---ii~g~vm  261 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCG--EVVKHVTPSNGNWMHIRYSSRTHAQKALSK-NGT---IIDGDVM  261 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhC--eeeeeecCCCCceEEEEecchhHHHHhhhh-cCe---eeccceE
Confidence            3455667776533 44778899999  688887777778999999999999999965 788   7877654

>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=92.50  E-value=0.55  Score=30.20  Aligned_cols=53  Identities=17%  Similarity=0.275  Sum_probs=43.0

Q ss_pred             ccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          273 EVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       273 ~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      .++-++++..+.+|+   -..|...  +-.-||.|.+..+|.+.....+|.   .+.+.+|
T Consensus        11 ~~~v~d~K~~Lr~y~---~~~I~~d--~tGfYIvF~~~~Ea~rC~~~~~~~---~~f~y~m   63 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR---WDRIRDD--RTGFYIVFNDSKEAERCFRAEDGT---LFFTYRM   63 (66)
T ss_pred             CccHHHHHHHHhcCC---cceEEec--CCEEEEEECChHHHHHHHHhcCCC---EEEEEEE
Confidence            578899999999997   5555544  446789999999999999999999   7766554

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=92.21  E-value=0.16  Score=47.27  Aligned_cols=69  Identities=20%  Similarity=0.269  Sum_probs=57.6

Q ss_pred             CCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       258 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                      ..++..++||+|+...+..+-++.+...+|.  |.+.....   |+|+.|..+..+..|+..++-.   .++|.++.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~--v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~---~~~~~kl~  104 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGF--VPSWKRDK---FGFCEFLKHIGDLRASRLLTEL---NIDDQKLI  104 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCc--chhhhhhh---hcccchhhHHHHHHHHHHhccc---CCCcchhh
Confidence            3445588999999999999999999999995  44443333   9999999999999999999888   88888764

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=91.95  E-value=0.29  Score=33.44  Aligned_cols=67  Identities=9%  Similarity=0.013  Sum_probs=43.6

Q ss_pred             EEEEEcCHHHHHHHHHHh-CCccccCceeEEe--eeccCCC----ccCCCCcceEEECCCCccccHHHHHHHhc
Q 019811           97 GFIHYFDRRSAAMAILSL-NGRHLFGQPIKVN--WAYASGQ----REDTSGHFNIFVGDLSPEVTDATLFACFS  163 (335)
Q Consensus        97 afv~f~~~~~A~~a~~~l-~~~~~~g~~l~v~--~~~~~~~----~~~~~~~~~l~v~nlp~~~t~~~l~~~f~  163 (335)
                      |+|.|.+..-|.+.++.- +...+.+..+.|.  +......    -......++|.++|||...++++|++.++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            689999999999988642 1233445544443  3322211    12334557899999999999999986543

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.09  E-value=0.12  Score=46.12  Aligned_cols=70  Identities=24%  Similarity=0.300  Sum_probs=57.3

Q ss_pred             CCCCeEEEcCCCccc-CHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          260 PQYTTVYVGNLAPEV-TQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       260 ~~~~~l~v~nlp~~~-t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ...+.|-+.-.|..+ +-++|...|.+||  .|..|.+..+--.|.|+|.+..+|.+|. ..++.   .|+||.|+|
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG--~i~n~qv~~~~~~a~vTF~t~aeag~a~-~s~~a---vlnnr~iKl  440 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFG--EIENIQVDYSSLHAVVTFKTRAEAGEAY-ASHGA---VLNNRFIKL  440 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcC--ccccccccCchhhheeeeeccccccchh-ccccc---eecCceeEE
Confidence            344667777778766 5688999999999  6888888877778999999999998886 56788   899998875

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=91.08  E-value=1.1  Score=37.35  Aligned_cols=47  Identities=15%  Similarity=0.230  Sum_probs=41.4

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCH
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTH  310 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~  310 (335)
                      .-|+++||+.++.-.||+..+.+.| ....++.+.-..|.||++|.+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~-~~pm~iswkg~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRE-CTPMSISWKGHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcC-CCceeEeeecCCcceeEecCCc
Confidence            5699999999999999999999988 3667788888899999999765

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.88  E-value=0.18  Score=48.23  Aligned_cols=59  Identities=20%  Similarity=0.218  Sum_probs=51.0

Q ss_pred             EEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCc
Q 019811          265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQS  325 (335)
Q Consensus       265 l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~  325 (335)
                      ..+.|.+-..+-..|..+|..||  .+.+....++-..|.|+|.+.+.|..|+.+|+|+++
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg--~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkev  359 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYG--SVASAWTLRDLNMALVSFSSVESAILALDALQGKEV  359 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhc--chhhheecccccchhhhhHHHHHHHHhhhhhcCCcc
Confidence            44445555667778999999999  699999999999999999999999999999999965

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=89.53  E-value=1.1  Score=29.70  Aligned_cols=58  Identities=19%  Similarity=0.248  Sum_probs=34.6

Q ss_pred             cccCHHHHHHHhhhcC---CeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          272 PEVTQLDLHRHFHSLG---AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       272 ~~~t~~~l~~~f~~~G---~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..++..+|..++...+   ...|-.|.+..+  ++||+-. .+.|..++..|++.   .+.|++++|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--~S~vev~-~~~a~~v~~~l~~~---~~~gk~v~v   71 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--FSFVEVP-EEVAEKVLEALNGK---KIKGKKVRV   71 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---EEEEE--TT-HHHHHHHHTT-----SSS----E
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--EEEEEEC-HHHHHHHHHHhcCC---CCCCeeEEE
Confidence            3578888888887653   234666777755  8888874 45888899999999   999999875

; PDB: 2G0C_A 3MOJ_B.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=88.00  E-value=1.1  Score=29.56  Aligned_cols=59  Identities=15%  Similarity=0.314  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHHHhccCCc-----eeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           66 TQVTEPLLQEVFSSTGPV-----EGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        66 ~~~t~~~l~~~f~~~G~v-----~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..++..+|..++...+.|     -.|.+..    .|+||+-... .|..++..|++..+.|++++|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~----~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD----NFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S----S-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee----eEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            457788888888776544     3444422    3788887654 678999999999999999999753

; PDB: 2G0C_A 3MOJ_B.

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]

Probab=84.64  E-value=1.8  Score=43.60  Aligned_cols=23  Identities=13%  Similarity=0.300  Sum_probs=10.3

Q ss_pred             EEEcCCCcccCHHHHHHHhhhcC
Q 019811          265 VYVGNLAPEVTQLDLHRHFHSLG  287 (335)
Q Consensus       265 l~v~nlp~~~t~~~l~~~f~~~G  287 (335)
                      .-++|.....+...-...+..||
T Consensus      2065 ~~~~n~~s~~n~s~~qq~~~~~~ 2087 (2131)
T KOG4369|consen 2065 SSLGNASSTTNPSRTQQMYQQYG 2087 (2131)
T ss_pred             chhcccCCCCCccHHHHHHHHhc
Confidence            34455544443333344444554

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=84.02  E-value=2  Score=32.94  Aligned_cols=114  Identities=9%  Similarity=-0.016  Sum_probs=72.0

Q ss_pred             EEEeCCC--CCCCHHHHHHHHhc-cCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCc
Q 019811           59 VYVGNIH--TQVTEPLLQEVFSS-TGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR  135 (335)
Q Consensus        59 v~v~nlp--~~~t~~~l~~~f~~-~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~  135 (335)
                      ..|+.+.  .+.+-..|...+.. ++....+.+..= ..++..+.|.+.+++.+++. .....+.|..+.+..-.+....
T Consensus        18 ~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l-~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~   95 (153)
T PF14111_consen   18 CLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL-GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNP   95 (153)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe-CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcccccc
Confidence            4455442  34566666666644 343333333221 33689999999999999885 3456677777777655433222


Q ss_pred             cCCC---CcceEEECCCCcc-ccHHHHHHHhccCCCceeeEEe
Q 019811          136 EDTS---GHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVM  174 (335)
Q Consensus       136 ~~~~---~~~~l~v~nlp~~-~t~~~l~~~f~~~g~v~~~~~~  174 (335)
                      ....   ...=|.|.|||.. ++++-+..+.+.+|.+..+...
T Consensus        96 ~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen   96 SEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             cccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence            1111   1223667899987 7788889999999999887554

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.70  E-value=11  Score=35.15  Aligned_cols=130  Identities=12%  Similarity=0.155  Sum_probs=73.5

Q ss_pred             CCCcceEEEeCCCCC-CCHHHHHHHHhcc----CCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           53 PSTCRSVYVGNIHTQ-VTEPLLQEVFSST----GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~-~t~~~l~~~f~~~----G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+++|=|-|+..+ +...+|.-+|+.|    |.|.+|.|....        |-..        .|.-..+.|-++.+-
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSe--------FGke--------RM~eEeV~GP~~el~  234 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSE--------FGKE--------RMKEEEVHGPPKELF  234 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhh--------hhHH--------HhhhhcccCChhhhc
Confidence            456778999999976 7889999988765    478899886643        1111        122223333322221


Q ss_pred             eeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          128 WAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       128 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      -....... .     .     .....-++-.+.-+..|+ +..+..          -||.|+|.+...|......|+|..
T Consensus       235 ~~~e~~~~-s-----~-----sD~ee~~~~~~~kLR~Yq-~~rLkY----------YyAVvecDsi~tA~~vYe~CDG~E  292 (650)
T KOG2318|consen  235 KPVEEYKE-S-----E-----SDDEEEEDVDREKLRQYQ-LNRLKY----------YYAVVECDSIETAKAVYEECDGIE  292 (650)
T ss_pred             cccccCcc-c-----c-----cchhhhhhHHHHHHHHHH-hhhhee----------EEEEEEecCchHHHHHHHhcCcce
Confidence            11000000 0     0     001111112233444442 222222          279999999999999999999998


Q ss_pred             eC--CeeeEEEEccC
Q 019811          208 LG--SRQIRCNWATK  220 (335)
Q Consensus       208 ~~--g~~l~v~~~~~  220 (335)
                      +.  +..+.++|...
T Consensus       293 fEsS~~~~DLRFIPD  307 (650)
T KOG2318|consen  293 FESSANKLDLRFIPD  307 (650)
T ss_pred             eccccceeeeeecCC
Confidence            85  55666666543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	335
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		9e-34
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		1e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		7e-26
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-25
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		8e-19
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		7e-18
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-08
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		8e-18
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-17
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		4e-17
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-16
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-15
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-08
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-15
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-08
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-13
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-11
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		8e-13
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		1e-09
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		3e-12
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		7e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-12
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-11
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-11
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-05
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		2e-11
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-10
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		7e-10
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-08
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-08
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-08
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-08
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-08
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		9e-07
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		5e-08
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		6e-08
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-08
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		6e-08
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-08
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		7e-08
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		7e-08
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		7e-08
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		7e-08
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		8e-08
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		9e-08
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		1e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		1e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		1e-07
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-07
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		2e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-07
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-07
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		3e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		3e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-07
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		4e-07
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		4e-07
2khc_A	118	Bruno Rrm3+ Length = 118		5e-07
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		6e-07
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		7e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		9e-07
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		1e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		2e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		3e-06
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		4e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		5e-06
2adc_A	229	Solution Structure Of Polypyrimidine Tract Binding		7e-06
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		8e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-05
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-05
1qm9_A	198	Nmr, Representative Structure Length = 198		1e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		1e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		2e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		2e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		2e-05
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-05
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-05
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-05
2cpd_A	99	Solution Structure Of The Rna Recognition Motif Of		3e-05
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		3e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		9e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		4e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		4e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		4e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		4e-05
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		9e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		9e-05
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		1e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		1e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		1e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-04
1fj7_A	101	Solution Structure Of Nucleolin Rbd1 Length = 101		2e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		2e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		2e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		3e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		3e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		3e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-04
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		6e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		6e-04
2dk2_A	97	Solution Structure Of Rrm Domain In Heterogeneous N		6e-04

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score =  140 bits (353), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 68/167 (40%), Positives = 104/167 (62%), Gaps = 4/167 (2%)
Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKS-SYGFIHYFDRRSAAMAILS 113
           R +YVGN+   +TE +L++ F   GP+   K++  + +K+ +Y F+ Y     A +A+ +
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 114 LNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV 173
           LNG+ +    +K+NWA+ S Q+  +   FN+FVGDL+  V D TL   F  +PS     V
Sbjct: 61  LNGKQIENNIVKINWAFQS-QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           MWD +TG SRG+GFVSF +Q DAQ+A++ + G+ L  R +R NWA K
Sbjct: 120 MWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/196 (21%), Positives = 84/196 (42%), Gaps = 41/196 (20%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+L   +T+  L   F V    ++ ++M D K  ++  + FV +    DA  A+  L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
            GK + +  ++ NWA +       +QSS                 +T N           
Sbjct: 62  NGKQIENNIVKINWAFQS------QQSS---------------SDDTFN----------- 89
Query: 264 TVYVGNLAPEVTQLDLHRHFHS----LGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
            ++VG+L   V    L   F      L   V+ +++    +G+GFV +++  +A  A+  
Sbjct: 90  -LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM-- 146
Query: 320 GNTTQSSYLFGKQMKV 335
            ++ Q   L G+ +++
Sbjct: 147 -DSMQGQDLNGRPLRI 161

>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 =  114 bits (285), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 51/90 (56%), Positives = 70/90 (77%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SGQ++DTS HF++FVGDLSPE+T   + A F+ +   SDARV+ D  TG+S+G+GFVSF
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N+ DA++AI  + G+WLG RQIR NWAT+
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATR 94

>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 = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 54/101 (53%), Gaps = 18/101 (17%)
Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVR 295
           ++GSS   K+T+N         +  V+VG+L+PE+T  D+   F   G    A V++++ 
Sbjct: 2   SSGSSGQKKDTSN---------HFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA 52
Query: 296 VQRDKGFGFVRYSTHAEAALAI-QMGNTTQSSYLFGKQMKV 335
             + KG+GFV +    +A  AI QMG      +L G+Q++ 
Sbjct: 53  TGKSKGYGFVSFFNKWDAENAIQQMGG----QWLGGRQIRT 89

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score =  113 bits (282), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 50/90 (55%), Positives = 70/90 (77%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SGQ++DTS HF++FVGDLSPE+T   + + F+ +   SDARV+ D  TG+S+G+GFVSF
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N+ DA++AI  + G+WLG RQIR NWAT+
Sbjct: 65  YNKLDAENAIVHMGGQWLGGRQIRTNWATR 94

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/101 (30%), Positives = 53/101 (52%), Gaps = 18/101 (17%)
Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVR 295
           ++GSS   K+T+N         +  V+VG+L+PE+T  D+   F   G    A V++++ 
Sbjct: 2   SSGSSGQKKDTSN---------HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMA 52
Query: 296 VQRDKGFGFVRYSTHAEAALAI-QMGNTTQSSYLFGKQMKV 335
             + KG+GFV +    +A  AI  MG      +L G+Q++ 
Sbjct: 53  TGKSKGYGFVSFYNKLDAENAIVHMGG----QWLGGRQIRT 89

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 90.9 bits (224), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 46/80 (57%), Positives = 62/80 (77%)
Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
           HF++FVGDLSPE+T A + A F+ +   SDARV+ D  TG+S+G+GFVSF N+ DA++AI
Sbjct: 6   HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65
Query: 201 NDLTGKWLGSRQIRCNWATK 220
             + G+WLG RQIR NWAT+
Sbjct: 66  QQMGGQWLGGRQIRTNWATR 85

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 87.8 bits (216), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 93/178 (52%), Gaps = 13/178 (7%)
Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGF 98
           P G++ P        S+YVG++H  VTE +L E FS  GP+   ++ R    +    Y +
Sbjct: 2   PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDT---SGHFNIFVGDLSPEVTD 155
           +++     A  A+ ++N   + G+P+++ W+    QR+ +   SG  NIF+ +L   + +
Sbjct: 62  VNFQQPADAERALDTMNFDVIKGKPVRIMWS----QRDPSLRKSGVGNIFIKNLDKSIDN 117
Query: 156 ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
             L+  FS + +    +V+ D+    S+G+GFV F  Q+ A+ AI  + G  L  R++
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 76/181 (41%), Gaps = 35/181 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++VGDL P+VT+A L+  FS        RV  D  T RS G+ +V+F+   DA+ A++ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           +    +  + +R  W+         +  S  KS V                         
Sbjct: 77  MNFDVIKGKPVRIMWSQ--------RDPSLRKSGV------------------------- 103
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--KGFGFVRYSTHAEAALAIQMG 320
             +++ NL   +    L+  F + G  +  +V    +  KG+GFV + T   A  AI+  
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 163
Query: 321 N 321
           N
Sbjct: 164 N 164

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 87.8 bits (216), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 41/79 (51%), Positives = 53/79 (67%)
Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           FN+FVGDL+  V D TL   F  +PS     VMWD +TG SRG+GFVSF +Q DAQ+A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 202 DLTGKWLGSRQIRCNWATK 220
            + G+ L  R +R NWA K
Sbjct: 62  SMQGQDLNGRPLRINWAAK 80

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 85.5 bits (210), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 52/144 (36%), Positives = 78/144 (54%), Gaps = 9/144 (6%)
Query: 68  VTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQ 122
           +T+   + +F S G +E CKL+R DK +     YGF++Y D + A  AI +LNG  L  +
Sbjct: 14  MTQEEFRSLFGSIGEIESCKLVR-DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72
Query: 123 PIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRS 182
            IKV++A  S     +    N++V  L   +T   L   FS Y     +R++ DQ TG S
Sbjct: 73  TIKVSYARPSSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVS 129
Query: 183 RGFGFVSFRNQQDAQSAINDLTGK 206
           RG GF+ F  + +A+ AI  L G+
Sbjct: 130 RGVGFIRFDKRIEAEEAIKGLNGQ 153

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 41/180 (22%), Positives = 73/180 (40%), Gaps = 39/180 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ + +DA+ AIN 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           L G  L ++ I+ ++A   + +  D                                   
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRD----------------------------------- 88
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAALAIQ 318
             +YV  L   +TQ +L + F   G  +   + V +     +G GF+R+    EA  AI+
Sbjct: 89  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 85.5 bits (210), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 48/163 (29%), Positives = 88/163 (53%), Gaps = 13/163 (7%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAILS 113
           S+YVG++H  VTE +L E FS  GP+   ++ R    +    Y ++++     A  A+ +
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 114 LNGRHLFGQPIKVNWAYASGQREDT---SGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
           +N   + G+P+++ W+    QR+ +   SG  NIF+ +L   + +  L+  FS + +   
Sbjct: 72  MNFDVIKGKPVRIMWS----QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
            +V+ D+    S+G+GFV F  Q+ A+ AI  + G  L  R++
Sbjct: 128 CKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 76/181 (41%), Gaps = 35/181 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++VGDL P+VT+A L+  FS        RV  D  T RS G+ +V+F+   DA+ A++ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           +    +  + +R  W+         +  S  KS V                         
Sbjct: 72  MNFDVIKGKPVRIMWSQ--------RDPSLRKSGV------------------------- 98
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--KGFGFVRYSTHAEAALAIQMG 320
             +++ NL   +    L+  F + G  +  +V    +  KG+GFV + T   A  AI+  
Sbjct: 99  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 158
Query: 321 N 321
           N
Sbjct: 159 N 159

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 81.6 bits (200), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 54/159 (33%), Positives = 84/159 (52%), Gaps = 10/159 (6%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           ++ V  +   +T+   + +F S G +E CKL+R DK +     YGF++Y D   A  AI 
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVR-DKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
           +LNG  L  + IKV++A  S     +    N++V  L   ++   +   FS Y     +R
Sbjct: 65  TLNGLKLQTKTIKVSYARPSSA---SIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG-KWLGS 210
           ++ DQ TG SRG GF+ F  + +A+ AI  L G K LG+
Sbjct: 122 ILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGA 160

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 38/180 (21%), Positives = 71/180 (39%), Gaps = 39/180 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ +  DA  AIN 
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           L G  L ++ I+ ++A   + +  D                                   
Sbjct: 66  LNGLKLQTKTIKVSYARPSSASIRD----------------------------------- 90
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAALAIQ 318
             +YV  L   ++Q ++ + F   G  +   + + +     +G GF+R+    EA  AI+
Sbjct: 91  ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/153 (33%), Positives = 80/153 (52%), Gaps = 9/153 (5%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           ++ V  +   +T+  L+ +FSS G VE  KLIR DK +     YGF++Y   + A  AI 
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
           +LNG  L  + IKV++A  S +        N+++  L   +T   +   FS +    ++R
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSE---VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSR 119
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           V+ DQ TG SRG  F+ F  + +A+ AI    G
Sbjct: 120 VLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 74/182 (40%), Gaps = 39/182 (21%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           G  N+ V  L   +T   L + FS       A+++ D+  G S G+GFV++   +DA+ A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 200 INDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENN 259
           IN L G  L S+ I+ ++A                        SSE  K+          
Sbjct: 61  INTLNGLRLQSKTIKVSYARP----------------------SSEVIKD---------- 88
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAAL 315
                +Y+  L   +TQ D+   F   G  +   V V +     +G  F+R+   +EA  
Sbjct: 89  ---ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 316 AI 317
           AI
Sbjct: 146 AI 147

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/153 (33%), Positives = 80/153 (52%), Gaps = 9/153 (5%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           ++ V  +   +T+  L+ +FSS G VE  KLIR DK +     YGF++Y   + A  AI 
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIR-DKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
           +LNG  L  + IKV++A  S +        N+++  L   +T   +   FS +    ++R
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSE---VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSR 119
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           V+ DQ TG SRG  F+ F  + +A+ AI    G
Sbjct: 120 VLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 74/182 (40%), Gaps = 39/182 (21%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           G  N+ V  L   +T   L + FS       A+++ D+  G S G+GFV++   +DA+ A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 200 INDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENN 259
           IN L G  L S+ I+ ++A                        SSE  K+          
Sbjct: 61  INTLNGLRLQSKTIKVSYARP----------------------SSEVIKD---------- 88
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAAL 315
                +Y+  L   +TQ D+   F   G  +   V V +     +G  F+R+   +EA  
Sbjct: 89  ---ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEE 145
Query: 316 AI 317
           AI
Sbjct: 146 AI 147

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 72.0 bits (175), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 78/151 (51%), Gaps = 9/151 (5%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILS 113
           ++ V  +   +T+  L  +F + GP+  C+++R  K+ Y     F+ +     +  AI  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 114 LNGRHLFGQPIKVNWAYASGQR-EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
           LNG  +  + +KV++A   G+  +DT    N++V +L   +TD  L   F  Y S     
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++ D+ TGR RG  FV +  +++AQ AI+ L
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 65.1 bits (157), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 48/183 (26%), Positives = 76/183 (41%), Gaps = 39/183 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L  ++TD  L+A F      +  R+M D KTG S G+ FV F ++ D+Q AI  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           L G  + +++++ ++A  G  + +D                                   
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKD----------------------------------- 89
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           T +YV NL   +T   L   F   G+     ++ +    R +G  FVRY+   EA  AI 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 319 MGN 321
             N
Sbjct: 150 ALN 152

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 71.2 bits (173), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 47/158 (29%), Positives = 78/158 (49%), Gaps = 10/158 (6%)
Query: 52  DPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRS 106
           DP    +  + N   Q  T+  L  +F + GP+  C++ R  K+ Y     F+ +     
Sbjct: 9   DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQR-EDTSGHFNIFVGDLSPEVTDATLFACFSVY 165
           +  AI  LNG  +  + +KV++A   G+  +DT    N++V +L   +TD  L   F  Y
Sbjct: 69  SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKY 124
Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
            S     ++ D+ TGR RG  FV +  +++AQ AI+ L
Sbjct: 125 GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 74/183 (40%), Gaps = 39/183 (21%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L  + TD  L+A F      +  R+  D KTG S G+ FV F ++ D+Q AI  
Sbjct: 16  NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           L G  + +++++ ++A  G  + +D                                   
Sbjct: 76  LNGITVRNKRLKVSYARPGGESIKD----------------------------------- 100
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGA----GVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           T +YV NL   +T   L   F   G+     ++ +    R +G  FVRY+   EA  AI 
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 319 MGN 321
             N
Sbjct: 161 ALN 163

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 52/75 (69%), Gaps = 2/75 (2%)
Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           R++YVGN+   VTE L+ ++FS  GP + CK+I +  S+  Y F+ +++ R AA A+ ++
Sbjct: 16  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 115 NGRHLFGQPIKVNWA 129
           NGR + G+ +KVNWA
Sbjct: 76  NGRKILGKEVKVNWA 90

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  ED      ++VG+LS +VT+  +   FS    C   +++ +  +     + FV F
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEF 62
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
              +DA +A+  + G+ +  ++++ NWAT
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWAT 91

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 68.2 bits (165), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 50/81 (61%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG LS +  + +L   FS Y   S+  V+ D++T RSRGFGFV+F N  DA+ A+  +
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 204 TGKWLGSRQIRCNWATKGAGN 224
            GK +  RQIR + A K + N
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDN 95

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 85/179 (47%), Gaps = 19/179 (10%)
Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAI 111
           CR VYVG+I+ ++ E  +++ F+  GP++   +    +      + F+ Y    +A +A+
Sbjct: 14  CR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 112 LSLNGRHLFGQPIKVNWAYASGQR--------EDTSGHFNIFVGDLSPEVTD---ATLFA 160
             +N   L G+ IKV      GQ         E+      I+V  +  +++D    ++F 
Sbjct: 73  EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 132
Query: 161 CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            F    SC+ AR   D  TG+ +G+GF+ +   Q +Q A++ +    LG + +R   A 
Sbjct: 133 AFGKIKSCTLAR---DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/170 (21%), Positives = 71/170 (41%), Gaps = 32/170 (18%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG +  E+ + T+   F+ +       + WD  T + +GF FV +   + AQ A+  +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
               LG R I+      G  +N       A+ +++               +  E    + 
Sbjct: 76  NSVMLGGRNIKV-----GRPSN----IGQAQPIID---------------QLAEEARAFN 111
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRY 307
            +YV ++  +++  D+   F + G   I+   + RD      KG+GF+ Y
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGK--IKSCTLARDPTTGKHKGYGFIEY 159

>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/173 (23%), Positives = 83/173 (47%), Gaps = 12/173 (6%)
Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAILSL 114
           VYVG+I+ ++ E  +++ F+  GP++   +    +      + F+ Y    +A +A+  +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 115 NGRHLFGQPIKVNWAYASGQRE-------DTSGHFN-IFVGDLSPEVTDATLFACFSVYP 166
           N   L G+ IKV      GQ +       + +  FN I+V  +  +++D  + + F  + 
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 167 SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
               A +  D  TG+ +G+GF+ +   Q +Q A++ +    LG + +R   A 
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/170 (20%), Positives = 69/170 (40%), Gaps = 32/170 (18%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG +  E+ + T+   F+ +       + WD  T + +GF FV +   + AQ A+  +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
               LG R I+    +             A+ +++               +  E    + 
Sbjct: 91  NSVMLGGRNIKVGRPSN---------IGQAQPIID---------------QLAEEARAFN 126
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRY 307
            +YV ++  +++  D+   F + G   I+   + RD      KG+GF+ Y
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGK--IKSATLARDPTTGKHKGYGFIEY 174

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 53/84 (63%), Gaps = 3/84 (3%)
Query: 141 HFNIFVGDLSPEVTDATLFACF-SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
            +++FVGDL+P+V D  L+  F  VYPSC   +V+ DQ TG S+G+GFV F ++ + + A
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRA 67
Query: 200 INDLTGK-WLGSRQIRCNWATKGA 222
           + +  G   LGS+ +R + A   A
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKA 91

>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 = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 82/173 (47%), Gaps = 24/173 (13%)
Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----IRKDKSSYGFIHYFDRRSAAMAI 111
           CR VYVG+I+ ++ E  +++ F+  GP++        +      + F+ Y    +A +A+
Sbjct: 13  CR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 112 LSLNGRHLFGQPIKVNWAYASGQR--------EDTSGHFNIFVGDLSPEVTD---ATLFA 160
              N   L G+ IKV      GQ         E+      I+V  +  +++D    ++F 
Sbjct: 72  EQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 131
Query: 161 CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN-----DLTGKWL 208
            F    SC+ AR   D  TG+ +G+GF+ +   Q +Q A++     DL G++L
Sbjct: 132 AFGKIKSCTLAR---DPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181

>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 = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/184 (19%), Positives = 72/184 (39%), Gaps = 32/184 (17%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG +  E+ + T+   F+ +         WD  T + +GF FV +   + AQ A+   
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
               LG R I+              + S+      + +  +E+ +             + 
Sbjct: 75  NSVXLGGRNIKVG------------RPSNIGQAQPIIDQLAEEARA------------FN 110
Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            +YV ++  +++  D+   F + G   I+   + RD      KG+GF+ Y     +  A+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGK--IKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 318 QMGN 321
              N
Sbjct: 169 SSXN 172

>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 = 61.6 bits (148), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 54/93 (58%), Gaps = 5/93 (5%)
Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDR 104
           P  D S  RSV+VGNI  + TE  L+++FS  GPV   +L+   ++     YGF  Y D+
Sbjct: 2   PAVDRS-LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQRED 137
            +A  A+ +LNGR   G+ ++V+ A +   +E+
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 48/86 (55%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++FVG++  E T+  L   FS        R+++D++TG+ +G+GF  +++Q+ A SA+ +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDK 228
           L G+    R +R + A       E K
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELK 95

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/142 (28%), Positives = 75/142 (52%), Gaps = 12/142 (8%)
Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAM 109
            +C+ +++G ++   TE  L+E F   G V   K+++   +     +GF+  F++ S+  
Sbjct: 2   ESCK-MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLS-FEKPSSVD 59
Query: 110 AILSLNGRHLF-GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
            ++    +H+  G+ I    A    +++ T     IFVG + P+V        FS + + 
Sbjct: 60  EVVKT--QHILDGKVIDPKRAIPRDEQDKTG---KIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 169 SDARVMWDQKTGRSRGFGFVSF 190
            DA++M D+ TG+SRGFGFV++
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTY 136

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/173 (24%), Positives = 70/173 (40%), Gaps = 45/173 (26%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G L+ + T+  L   F  Y + +D ++M D  TGRSRGFGF+SF            
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF------------ 52
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
                                    ++ S    VV+  +    DGK      A   + Q 
Sbjct: 53  -------------------------EKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQD 85
Query: 263 TT--VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYST 309
            T  ++VG + P+V   +    F   G  +  ++ + +D    +GFGFV Y +
Sbjct: 86  KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 77/157 (49%), Gaps = 15/157 (9%)
Query: 47  LPPGFDPSTCR-SVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDR 104
           L PG    T R  ++VGN+ T +TE   + +F   G P E    I +D+  +GFI    R
Sbjct: 12  LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEV--FINRDRG-FGFIRLESR 68
Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSV 164
             A +A   L+G  L  +P+++ +A        T G   + V +LSP V++  L   FS 
Sbjct: 69  TLAEIAKAELDGTILKSRPLRIRFA--------THGA-ALTVKNLSPVVSNELLEQAFSQ 119
Query: 165 YPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           +     A V+ D + GR+ G GFV F  +  A+ A+ 
Sbjct: 120 FGPVEKAVVVVDDR-GRATGKGFVEFAAKPPARKALE 155

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FVG+L  ++T+      F  Y   S+  +       R RGFGF+   ++  A+ A  +
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 203 LTGKWLGSRQIRCNWATKGAG 223
           L G  L SR +R  +AT GA 
Sbjct: 78  LDGTILKSRPLRIRFATHGAA 98

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           Q   ++VGNL  ++T+ D  R F   G     EV + RD+GFGF+R  +   A +A
Sbjct: 21  QRCRLFVGNLPTDITEEDFKRLFERYGEP--SEVFINRDRGFGFIRLESRTLAEIA 74

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G L+ E  +  L A F  +   S+  ++ D +T +SRGF F++F N  DA++A  D+
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 204 TGKWLGSRQIRCNWATK 220
            GK L  + I+   A K
Sbjct: 69  NGKSLHGKAIKVEQAKK 85

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 47/154 (30%), Positives = 75/154 (48%), Gaps = 13/154 (8%)
Query: 49  PGFDPSTCRS-VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA 107
           PG    T RS ++VGN+   +TE  ++++F   G   G   I KDK  +GFI    R  A
Sbjct: 14  PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA-GEVFIHKDK-GFGFIRLETRTLA 71
Query: 108 AMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPS 167
            +A + L+   L G+ ++V +A  S          ++ V +L   V++  L   FSV+  
Sbjct: 72  EIAKVELDNMPLRGKQLRVRFACHSA---------SLTVRNLPQYVSNELLEEAFSVFGQ 122
Query: 168 CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
              A V+ D + GR  G G V F  +  A+ A++
Sbjct: 123 VERAVVIVDDR-GRPSGKGIVEFSGKPAARKALD 155

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 9/77 (11%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLG-AGVIEEVRVQRDKGFGFVRYSTHAEAALA-IQ 318
           Q + ++VGNL P++T+ ++ + F   G AG   EV + +DKGFGF+R  T   A +A ++
Sbjct: 21  QRSRLFVGNLPPDITEEEMRKLFEKYGKAG---EVFIHKDKGFGFIRLETRTLAEIAKVE 77
Query: 319 MGNTTQSSYLFGKQMKV 335
           + N      L GKQ++V
Sbjct: 78  LDNMP----LRGKQLRV 90

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 204 TGKWLGSRQIRCNWA 218
               L  R IR N A
Sbjct: 126 NESELFGRTIRVNLA 140

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N 
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
              K  G                          VVE     S +     +++ P  +   
Sbjct: 76  RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 105
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
             ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 157

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N 
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
              K  G                          VVE     S +     +++ P  +   
Sbjct: 75  RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 104
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
             ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N 
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
              K  G                          VVE     S +     +++ P  +   
Sbjct: 74  RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 103
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
             ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 155

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N 
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
              K  G                          VVE     S +     +++ P  +   
Sbjct: 73  RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 102
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
             ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 154

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N 
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
              K  G                          VVE     S +     +++ P  +   
Sbjct: 75  RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 104
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
             ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 204 TGKWLGSRQIRCNWA 218
               L  R IR N A
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 204 TGKWLGSRQIRCNWA 218
               L  R IR N A
Sbjct: 70  NESELFGRTIRVNLA 84

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 204 TGKWLGSRQIRCNWA 218
               L  R IR N A
Sbjct: 68  NESELFGRTIRVNLA 82

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 34/172 (19%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
              K  G                          VVE     S +     +++ P  +   
Sbjct: 68  RPHKVDG-------------------------RVVEPKRAVSRE-----DSQRPGAHLTV 97
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTH 310
             ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149

>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 = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 50/77 (64%), Gaps = 2/77 (2%)
Query: 144 IFVGDLSPEVTDATLF-ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++G +  + T+  +   C +V P   + ++M+D +TGRS+G+ F+ FR+ + + SA+ +
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 203 LTGKWLGSRQIRCNWAT 219
           L G  LGSR ++C +++
Sbjct: 66  LNGYQLGSRFLKCGYSS 82

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 50/77 (64%), Gaps = 2/77 (2%)
Query: 144 IFVGDLSPEVTDATLF-ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++G +  + T+  +   C +V P   + ++M+D +TGRS+G+ F+ FR+ + + SA+ +
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 203 LTGKWLGSRQIRCNWAT 219
           L G  LGSR ++C +++
Sbjct: 65  LNGYQLGSRFLKCGYSS 81

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 45/79 (56%), Gaps = 6/79 (7%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           +VYVG +  +V+EPLL E+F   GPV    +  KD+ +     YGF+ +     A  AI 
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHM-PKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 113 SLNGRHLFGQPIKVNWAYA 131
            ++   L+G+PI+VN A A
Sbjct: 76  IMDMIKLYGKPIRVNKASA 94

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L  +V++  L+  F       +  +  D+ TG+ +G+GFV F +++DA  AI  +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 204 TGKWLGSRQIRCNWAT 219
               L  + IR N A+
Sbjct: 78  DMIKLYGKPIRVNKAS 93

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 27/80 (33%), Positives = 45/80 (56%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L  ++TD  L+A F      +  R+M D KTG S G+ FV F ++ D+Q AI  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 203 LTGKWLGSRQIRCNWATKGA 222
           L G  + +++++ ++A  G 
Sbjct: 65  LNGITVRNKRLKVSYARPGG 84

>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 = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/88 (35%), Positives = 47/88 (53%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG R +   +  + V  LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F
Sbjct: 5   SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            N  DA+ A     G  L  R+IR +++
Sbjct: 65  ENVDDAKEAKERANGMELDGRRIRVDFS 92

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/91 (31%), Positives = 53/91 (58%), Gaps = 5/91 (5%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSC-SDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           +SG   IF+G+L PE+ +  L+  FS +       ++M D  TG S+G+ F++F +   +
Sbjct: 2   SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 197 QSAINDLTGKWLGSRQIRCNWA----TKGAG 223
            +AI  + G++L +R I  ++A    +KG+G
Sbjct: 62  DAAIEAMNGQYLCNRPITVSYAFKKDSKGSG 92

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 204 TGKWLGSRQIRCNWA 218
               L  R IR N A
Sbjct: 75  NESELFGRTIRVNLA 89

>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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 43/79 (54%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           G  N+ V  L   +T   L + FS       A+++ D+  G S G+GFV++   +DA+ A
Sbjct: 3   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 200 INDLTGKWLGSRQIRCNWA 218
           IN L G  L S+ I+ ++A
Sbjct: 63  INTLNGLRLQSKTIKVSYA 81

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 47/91 (51%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG R +   +  + V  LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F
Sbjct: 5   SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
            N  DA+ A     G  L  R+IR +  + G
Sbjct: 65  ENVDDAKEAKERANGMELDGRRIRVSGPSSG 95

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 54/103 (52%), Gaps = 6/103 (5%)
Query: 42  IPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS--YG 97
           IP   + P  +P   R++ V  I T V E  L+++F   GP+E  K++  R+ + S  YG
Sbjct: 30  IPPTQMNP--EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87
Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           F+ +    SA  AI  LNG ++  + +KV  A +  QR   +G
Sbjct: 88  FVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAG 130

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  +   V +  L   F  Y      +++ D++T +SRG+GFV F++   AQ AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 203 LTGKWLGSRQIRCNWATKG 221
           L G  + +++++   A  G
Sbjct: 104 LNGFNILNKRLKVALAASG 122

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 47/76 (61%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++G +  + T+  +    S      + ++M+D +TGRS+G+ F+ FR+ + + SA+ +L
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 204 TGKWLGSRQIRCNWAT 219
            G  LGSR ++C +++
Sbjct: 65  NGYQLGSRFLKCGYSS 80

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 43/85 (50%)
Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           D  G  ++ V +L+   +  TL   F  Y    D  +  D+ T  SRGF FV F +++DA
Sbjct: 43  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 197 QSAINDLTGKWLGSRQIRCNWATKG 221
           + A++ + G  L  R++R   A  G
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYG 127

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 39/70 (55%)
Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F N  DA+ A     G  L
Sbjct: 54  LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 209 GSRQIRCNWA 218
             R+IR +++
Sbjct: 114 DGRRIRVDFS 123

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGP---VEGCKLIRKDKSSYGFIHYFDRRSAAMAILS 113
           R+V+VGN+  +V E +L E+F   GP   V  CK       S+GF+ +    S + AI  
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 114 LNGRHLFGQPIKVN 127
           LNG  L+G+PI V+
Sbjct: 77  LNGIRLYGRPINVS 90

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 39/70 (55%)
Query: 149 LSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL 208
           LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F N  DA+ A     G  L
Sbjct: 20  LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 209 GSRQIRCNWA 218
             R+IR +++
Sbjct: 80  DGRRIRVDFS 89

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+F+  L  E TD  L + F  + +   A+V  D++T  S+ FGFVSF N   AQ AI  
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 203 LTGKWLGSRQIR 214
           + G  +G+++++
Sbjct: 102 MNGFQVGTKRLK 113

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 43/85 (50%)
Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           D  G  ++ V +L+   +  TL   F  Y    D  +  D+ T  SRGF FV F +++DA
Sbjct: 66  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 197 QSAINDLTGKWLGSRQIRCNWATKG 221
           + A++ + G  L  R++R   A  G
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYG 150

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 52  DPSTCRS-VYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAM 109
           DP +  S V++GN++T  V +  ++ +FS  G V GC + +     Y F+ Y + R A  
Sbjct: 22  DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK----GYAFVQYSNERHARA 77
Query: 110 AILSLNGRHLFGQPIKVNWA 129
           A+L  NGR L GQ + +N A
Sbjct: 78  AVLGENGRVLAGQTLDINMA 97

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 47/86 (54%)
Query: 135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
           ++ ++G   ++VG L   +T+  L   F  +      ++M D +TGRS+G+GF++F + +
Sbjct: 20  QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 195 DAQSAINDLTGKWLGSRQIRCNWATK 220
            A+ A+  L G  L  R ++    T+
Sbjct: 80  CAKKALEQLNGFELAGRPMKVGHVTE 105

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/100 (29%), Positives = 54/100 (54%), Gaps = 6/100 (6%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG R       N++V +L   + D  L   FS + + + A+VM +   GRS+GFGFV F
Sbjct: 5   SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCF 62
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
            + ++A  A+ ++ G+ + ++ +    A +     E++QS
Sbjct: 63  SSPEEATKAVTEMNGRIVATKPLYVALAQR----KEERQS 98

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           A  Q+E   G  N+F+  L  E  D  L   F  + +   A+V  D++T  S+ FGFVS+
Sbjct: 16  AGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNW 217
            N   AQ+AI  + G  +G ++++   
Sbjct: 75  DNPVSAQAAIQSMNGFQIGMKRLKVQL 101

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  LS + T+ TL   F        AR++ D++TG S+GFGFV F +++DA++A   +
Sbjct: 18  LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 204 TGKWLGSRQIRCNWA 218
               +   ++  +WA
Sbjct: 75  EDGEIDGNKVTLDWA 89

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/83 (31%), Positives = 44/83 (53%)
Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   ++VG L   +T+  L   F  +    +  +M D  TGRS+G+GF++F + + A+
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 198 SAINDLTGKWLGSRQIRCNWATK 220
            A+  L G  L  R +R    T+
Sbjct: 62  RALEQLNGFELAGRPMRVGHVTE 84

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            IFVG L    TDA+L   F  +    +A V+ D++TG+SRG+GFV+  ++  A+ A  D
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 203 LTGKWLGSRQIRCNWATKGA 222
                +  R+   N A  GA
Sbjct: 79  -PNPIIDGRKANVNLAYLGA 97

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 7/76 (9%)
Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA-IQM 319
           Q + ++VGNL P++T+ ++ + F   G     EV + +DKGFGF+R  T   A +A +++
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKA--GEVFIHKDKGFGFIRLETRTLAEIAKVEL 71
Query: 320 GNTTQSSYLFGKQMKV 335
            N      L GKQ++V
Sbjct: 72  DNMP----LRGKQLRV 83

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           G  NIF+ +L   + +  L+  FS + +    +V+ D+    S+G+GFV F  Q+ A+ A
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 61
Query: 200 INDLTGKWLGSRQI 213
           I  + G  L  R++
Sbjct: 62  IEKMNGMLLNDRKV 75

>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein Rbd34 Complexed With Cucucu Rna Length = 229

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 42/181 (23%), Positives = 78/181 (43%), Gaps = 8/181 (4%)
Query: 139 SGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +G+  + V +L+PE VT  +LF  F VY      ++++++K         V   +   AQ
Sbjct: 32  AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQ 86
Query: 198 SAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPE 257
            A++ L G  L  + IR   +         +   D     +  N      K+  +     
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146
Query: 258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-VQRDKGFGFVRYSTHAEAALA 316
             P   T+++ N+ P V++ DL   F S G GV++  +  Q+D+    ++  +  EA  A
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFSSNG-GVVKGFKFFQKDRKMALIQMGSVEEAVQA 205
Query: 317 I 317
           +
Sbjct: 206 L 206

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           +++P+  TVY G +A  +T   + + F   G   I E+RV  +KG+ FVR+STH  AA A
Sbjct: 20  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ--IMEIRVFPEKGYSFVRFSTHESAAHA 77
Query: 317 IQMGNTT 323
           I   N T
Sbjct: 78  IVSVNGT 84

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           SG  NIF+ +L   + +  L+  FS + +    +V+ D+    S+G+GFV F  Q+ A+ 
Sbjct: 9   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 66
Query: 199 AINDLTGKWLGSRQI 213
           AI  + G  L  R++
Sbjct: 67  AIEKMNGMLLNDRKV 81

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V +L   +TD  L   F  Y S     ++ D+ TGR RG  FV +  +++AQ AI+ 
Sbjct: 15  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 203 L 203
           L
Sbjct: 75  L 75

>pdb|1QM9|A Chain A, Nmr, Representative Structure Length = 198

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/176 (23%), Positives = 75/176 (42%), Gaps = 8/176 (4%)
Query: 144 IFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           + V +L+PE VT  +LF  F VY      ++++++K         V   +   AQ A++ 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 60
Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQY 262
           L G  L  + IR   +         +   D     +  N      K+  +       P  
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-VQRDKGFGFVRYSTHAEAALAI 317
            T+++ N+ P V++ DL   F S G GV++  +  Q+D+    ++  +  EA  A+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNG-GVVKGFKFFQKDRKMALIQMGSVEEAVQAL 175

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 46/201 (22%), Positives = 83/201 (41%), Gaps = 35/201 (17%)
Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHY- 101
           +  R +YVGNI   +TE  + + F++             PV   + I +DK+ + F+ + 
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKN-FAFLEFR 59
Query: 102 -FDRRSAAMAILSLNGRHLFGQPIKV----NWAYASGQREDTSGHF-------------N 143
             D  + AMA    +G    GQ +K+    ++    G  E+ S +               
Sbjct: 60  SVDETTQAMA---FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G L   + D  +    + +       ++ D  TG S+G+ F  + +      AI  L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 204 TGKWLGSRQIRCNWATKGAGN 224
            G  LG +++    A+ GA N
Sbjct: 177 NGMQLGDKKLLVQRASVGAKN 197

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/178 (23%), Positives = 76/178 (42%), Gaps = 21/178 (11%)
Query: 55  TCRSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHY-- 101
           + R +YVGNI   +TE  + + F++             PV   + I +DK+ + F+ +  
Sbjct: 5   SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKN-FAFLEFRS 62
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFAC 161
            D  + AMA    +G    GQ +K+   +     +   G   +F+G L   + D  +   
Sbjct: 63  VDETTQAMA---FDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKEL 116
Query: 162 FSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            + +       ++ D  TG S+G+ F  + +      AI  L G  LG +++    A+
Sbjct: 117 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 174

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 39/78 (50%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L P +T          + S     +++ ++TG+S+G+GF  +  +  A  A +DL
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 204 TGKWLGSRQIRCNWATKG 221
            GK LG R +  +W   G
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 39/78 (50%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L P +T          + S     +++ ++TG+S+G+GF  +  +  A  A +DL
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 204 TGKWLGSRQIRCNWATKG 221
            GK LG R +  +W   G
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 39/78 (50%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L P +T          + S     +++ ++TG+S+G+GF  +  +  A  A +DL
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 204 TGKWLGSRQIRCNWATKG 221
            GK LG R +  +W   G
Sbjct: 156 LGKPLGPRTLYVHWTDAG 173

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/178 (23%), Positives = 76/178 (42%), Gaps = 21/178 (11%)
Query: 55  TCRSVYVGNIHTQVTEPLLQEVFSST-----------GPVEGCKLIRKDKSSYGFIHY-- 101
           + R +YVGNI   +TE  + + F++             PV   + I +DK+ + F+ +  
Sbjct: 3   SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDKN-FAFLEFRS 60
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFAC 161
            D  + AMA    +G    GQ +K+   +     +   G   +F+G L   + D  +   
Sbjct: 61  VDETTQAMA---FDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKEL 114
Query: 162 FSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            + +       ++ D  TG S+G+ F  + +      AI  L G  LG +++    A+
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L    T   L + FS       A+++ D+  G S G+GFV++   +DA+ AIN 
Sbjct: 21  NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L S+ I+ ++A
Sbjct: 81  LNGLRLQSKTIKVSYA 96

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 74/153 (48%), Gaps = 10/153 (6%)
Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-----SYG--FIHYFDRRSAAMAI 111
           ++VG +    +E  L+E+F   G V    ++R D+S     S G  F+ ++ R++A  A 
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 112 LSL-NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
            +L N + L G    +    A  ++ +      +F+G +S + T+  +   FS +    +
Sbjct: 77  NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 136
Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
            R++     G SRG  FV+F  +  AQ+AI  +
Sbjct: 137 CRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 168

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 72/150 (48%), Gaps = 10/150 (6%)
Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-----SYG--FIHYFDRRSAAMAIL 112
           +VG +    +E  L+E+F   G V    ++R D+S     S G  F+ ++ R++A  A  
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 113 SL-NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDA 171
           +L N + L G    +    A  ++ +      +F+G +S + T+  +   FS +    + 
Sbjct: 66  ALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEEC 125
Query: 172 RVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           R++     G SRG  FV+F  +  AQ+AI 
Sbjct: 126 RILRG-PDGLSRGCAFVTFTTRAXAQTAIK 154

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 74/153 (48%), Gaps = 10/153 (6%)
Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-----SYG--FIHYFDRRSAAMAI 111
           ++VG +    +E  L+E+F   G V    ++R D+S     S G  F+ ++ R++A  A 
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 112 LSL-NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
            +L N + L G    +    A  ++ +      +F+G +S + T+  +   FS +    +
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
            R++     G SRG  FV+F  +  AQ+AI  +
Sbjct: 125 CRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156

>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human Apobec-1 Complementation Factor, Acf Length = 99

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
           S+ + +YV N+    +E ++++ F++  P  VE  K IR     Y F+H+ +R  A  A+
Sbjct: 13  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR----DYAFVHFSNREDAVEAM 68
Query: 112 LSLNGRHLFGQPIKVNWA 129
            +LNG+ L G PI+V  A
Sbjct: 69  KALNGKVLDGSPIEVTLA 86

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           + ++V N+   VTE +L++ FS  G +E  K ++     Y FIH+ +R  A  A+  +NG
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK----DYAFIHFDERDGAVKAMEEMNG 67
Query: 117 RHLFGQPIKVNWAYASGQR 135
           + L G+ I++ +A    Q+
Sbjct: 68  KDLEGENIEIVFAKPPDQK 86

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE----GCKLIRKDKSSYGFIHYFDRRSAA 108
             +C ++YVGN+    TE  + E+FS +G ++    G   ++K    + F+ Y+ R  A 
Sbjct: 37  KKSC-TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 109 MAILSLNGRHLFGQPIKVNW 128
            A+  +NG  L  + I+ +W
Sbjct: 96  NAMRYINGTRLDDRIIRTDW 115

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 50  GFDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIH 100
           G +P   RSV     +V  +H + TE  + + F+  G ++   L    ++ Y      + 
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWAYA 131
           Y   + A  A+  LNG+ L GQPI V+W + 
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 38/74 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  +  E T+  +   F+ Y    +  +  D++TG  +G+  V +   ++AQ+A+  L
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 204 TGKWLGSRQIRCNW 217
            G+ L  + I  +W
Sbjct: 85  NGQDLMGQPISVDW 98

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 51  FDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHY 101
            +P   RSV     +V +IH +  E  +QE F   G ++   L    ++     Y  + Y
Sbjct: 62  LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 121
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
              + A  A  +LNG  + GQ I+V+W +  G
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 153

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           FN+F+G+L+P  + A L    S   + +D  V+ D +TG +R FG+V F + +D + A+ 
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKAL- 71
Query: 202 DLTGKWLGSRQIRC 215
           +LTG  +   +I+ 
Sbjct: 72  ELTGLKVFGNEIKL 85

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           ++ V  +   +T+   + +F S G +E CKL+R DK +     YGF++Y D   A  AI 
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVR-DKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 113 SLNGRHLFGQPIKVNWAYAS 132
           +LNG  L  + IKV++A  S
Sbjct: 65  TLNGLKLQTKTIKVSYARPS 84

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 40/76 (52%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ +  DA  AIN 
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L ++ I+ ++A
Sbjct: 66  LNGLKLQTKTIKVSYA 81

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 9/93 (9%)
Query: 50  GFDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIH 100
           G +P   RSV     +V  +H + TE  + + F+  G ++   L    ++ Y      + 
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
           Y   + A  A+  LNG+ L GQPI V+W +  G
Sbjct: 72  YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   ++   +   FS Y     +R++ DQ TG SRG GF+ F  + +A+ AI  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 203 LTGK 206
           L G+
Sbjct: 63  LNGQ 66

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
           ++V  +H + TE  + + F+  G ++   L    ++ Y      + Y   + A  A+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 115 NGRHLFGQPIKVNWAYASG 133
           NG+ L GQPI V+W +  G
Sbjct: 70  NGQDLMGQPISVDWCFVRG 88

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 17/70 (24%), Positives = 39/70 (55%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  ++ + T++ L   F VY       +++ +++G+ RG+ F+ + +++D  SA    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 204 TGKWLGSRQI 213
            GK +  R++
Sbjct: 165 DGKKIDGRRV 174

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 38/175 (21%), Positives = 78/175 (44%), Gaps = 18/175 (10%)
Query: 50  GFDPSTCRSVYVGNIHTQVTEPLLQ----EVFSSTG-PVEGCK--LIRKDKSSYGFIHYF 102
           G +P+T  +++VGN++   + P L+    +VF+     V   +  + RK    +G++ + 
Sbjct: 1   GTEPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRK----FGYVDFE 56
Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACF 162
                  A L L G  +FG  IK+        +++      +   +L  +VT   L    
Sbjct: 57  SAEDLEKA-LELTGLKVFGNEIKLEKPKGKDSKKERDAR-TLLAKNLPYKVTQDELK--- 111
Query: 163 SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
            V+   ++ R++   K G+S+G  ++ F+ + DA+    +  G  +  R I   +
Sbjct: 112 EVFEDAAEIRLV--SKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYY 164

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 53  PSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFD 103
           P   RSV     +V  +H + TE  + + F+  G ++   L    ++ Y      + Y  
Sbjct: 1   PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
            + A  A+  LNG+ L GQPI V+W +  G
Sbjct: 61  YKEAQAAMEGLNGQDLMGQPISVDWCFVRG 90

>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 = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
           ++V  +H + TE  + + F+  G ++   L    ++ Y      + Y   + A  A+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 115 NGRHLFGQPIKVNWAYASG 133
           NG+ L GQPI V+W +  G
Sbjct: 70  NGQDLMGQPISVDWCFVRG 88

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 34/58 (58%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
            +F+G LS E T+ +L   +  +   +D  VM D  + RSRGFGFV+F +  +  +A+
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/70 (24%), Positives = 39/70 (55%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  ++ + T++ L   F VY       +++ +++G+ RG+ F+ + +++D  SA    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 204 TGKWLGSRQI 213
            GK +  R++
Sbjct: 165 DGKKIDGRRV 174

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 38/85 (44%)
Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           D  G   + V +L+   +  +L   F  Y    D  +  +  T   RGF FV F +++DA
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 197 QSAINDLTGKWLGSRQIRCNWATKG 221
           Q A   + G  L  R++R   A  G
Sbjct: 69  QDAEAAMDGAELDGRELRVQVARYG 93

>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1 Length = 101

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 11/90 (12%)
Query: 116 GRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMW 175
           G H+   P+         +  +++  FN+F+G+L+P  + A L    S   + +D  V+ 
Sbjct: 1   GSHMLEDPV---------EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV- 50
Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           D +TG +R FG+V F + +D + A+ +LTG
Sbjct: 51  DVRTGTNRKFGYVDFESAEDLEKAL-ELTG 79

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG LS   T   +   F  +    DA +M+D+ T R RGFGFV+F + +D    + ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 204 TGKWLGSRQIRCNWA 218
               + ++ + C  A
Sbjct: 61  HFHEINNKMVECKKA 75

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 9/94 (9%)
Query: 51  FDPSTCRSV-----YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHY 101
            +P   RSV     +V +IH +  E  +QE F   G ++   L    ++     Y  + Y
Sbjct: 16  LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
              + A  A  +LNG  + GQ I+V+W +  G +
Sbjct: 76  ETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 29/50 (58%)
Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
            +FVG L    T  TL + FS Y    D  +M D+ T +SRGFGFV F++
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
           ++V  +H + TE  + + F+  G ++   L    ++ Y      + Y   + A  A+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 115 NGRHLFGQPIKVNWAY 130
           NG+ L GQPI V+W +
Sbjct: 70  NGQDLMGQPISVDWCF 85

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
           P  C+ VYVGN+     +  L+  F   GP+    + R +   + F+ + D R AA A+ 
Sbjct: 71  PLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVR 128
Query: 113 SLNGRHLFGQPIKV 126
            L+GR L G  ++V
Sbjct: 129 DLDGRTLCGCRVRV 142

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
           P  C+ VYVGN+     +  L+  F   GP+    + R +   + F+ + D R AA A+ 
Sbjct: 71  PLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVR 128
Query: 113 SLNGRHLFGQPIKV 126
            L+GR L G  ++V
Sbjct: 129 ELDGRTLCGCRVRV 142

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR-----DKGFGFVRYSTHAEAA 314
           P +  ++VG L  + ++ D+ R F + G   IEE  + R      KG  FV+YS+HAEA 
Sbjct: 13  PSHRKLFVGMLNKQQSEDDVRRLFEAFGN--IEECTILRGPDGNSKGCAFVKYSSHAEAQ 70
Query: 315 LAIQMGNTTQS 325
            AI   + +Q+
Sbjct: 71  AAINALHGSQT 81

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 42/88 (47%)
Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG       +  I V +LS +  +  L   F  + S S   +  D+ TG+S+GF F+SF
Sbjct: 5   SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
             ++DA  AI  ++G       +   WA
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVEWA 92

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 47/92 (51%), Gaps = 5/92 (5%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++ +LSP VT+  L + F+ +       + +   TGR RG  F++F N++ A  A++ +
Sbjct: 28  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
            G  L  + +   +     G N+ ++SS   S
Sbjct: 88  NGYKLYGKILVIEF-----GKNKKQRSSGPSS 114

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 30/58 (51%)
Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           +F+G LS + T   L   FS +    D  +  D  TGRSRGFGFV F+  +     ++
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59

>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleoprotein R (Hnrnp R) Length = 97

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 4/61 (6%)
Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
           + ++V N+ T VTE +L++ FS  G +E  K ++     Y F+H+ DR +A  A+  +NG
Sbjct: 16  KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLK----DYAFVHFEDRGAAVKAMDEMNG 71
Query: 117 R 117
           +
Sbjct: 72  K 72

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	335
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-85
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-49
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-40
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-82
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-39
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-78
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-45
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	9e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-70
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-47
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-70
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-39
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-70
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-42
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-68
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-43
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-35
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-31
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-57
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-33
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-38
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-14
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-54
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-37
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-50
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-36
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-50
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-28
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-47
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-47
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-30
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-46
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-17
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-13
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-43
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-12
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-12
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-42
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-40
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-17
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-39
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-14
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-37
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-15
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-37
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-24
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-35
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-29
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-33
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-15
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-32
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-30
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-31
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-19
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-31
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-30
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-30
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-19
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-15
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-30
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-30
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	8e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-29
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-29
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-29
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-13
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-29
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-15
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-29
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-29
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-21
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-19
2div_A	99	TRNA selenocysteine associated protein; structural	1e-28
2div_A	99	TRNA selenocysteine associated protein; structural	8e-18
2div_A	99	TRNA selenocysteine associated protein; structural	1e-12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-28
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-27
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-27
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-27
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-16
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-27
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-23
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-26
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-26
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-26
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-25
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-10
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-25
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-20
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-25
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-16
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-25
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-16
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-25
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-14
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-25
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-25
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-24
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-24
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-24
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-22
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-24
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-24
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-20
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-24
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-18
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-23
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-23
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-23
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-23
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-20
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-23
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-23
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-20
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-22
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-22
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-22
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-22
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-22
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-22
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-21
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-21
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-21
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-19
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-21
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-15
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-21
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-21
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-21
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-13
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-21
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	9e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-21
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-20
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-20
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-20
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-20
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-13
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-20
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	7e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-20
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-16
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-19
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	9e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-19
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-18
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-18
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-19
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-11
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-18
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-18
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-14
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-18
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-18
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-16
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-15
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-18
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-18
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-18
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-09
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-18
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	6e-18
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-18
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-14
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-18
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-09
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-07
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-17
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-17
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-17
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	7e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-17
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-09
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-17
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-17
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-16
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-17
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-16
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-16
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-16
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-16
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-15
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-15
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	9e-15
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	7e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-13
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-13
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	6e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	9e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-12
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-11
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-11
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-11
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	7e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-11
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-10
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-10
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-10
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	8e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	6e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	8e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	8e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-05
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	7e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

>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 =  256 bits (656), Expect = 9e-85
 Identities = 50/290 (17%), Positives = 93/290 (32%), Gaps = 55/290 (18%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
                R + +  +   VT   + ++ S       C + +       F+   +   A  AI
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKY-CFVDKYK--GTAFVTLLNGEQAEAAI 74

Query: 112 LSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDA 171
            + +   L  + + V                 + V +L P +T          + S    
Sbjct: 75  NAFHQSRLRERELSVQLQPTD---------ALLCVANLPPSLTQQQFEELVRPFGSLERC 125

Query: 172 RVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSS 231
            +++ ++TG+S+G+GF  +  +  A  A +DL GK LG R +  +W   G          
Sbjct: 126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG---------- 175

Query: 232 DAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLD-LHRHFHSLGAGV 290
                                 +          + V  L P    +D L R   ++ +  
Sbjct: 176 ----------------------QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHS-- 211

Query: 291 IEEVRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
               ++        KGF  + Y T   A  A Q  +      L G  ++V
Sbjct: 212 PTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLS---LGGSHLRV 258

>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 =  166 bits (422), Expect = 1e-49
 Identities = 40/177 (22%), Positives = 70/177 (39%), Gaps = 6/177 (3%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           + V N+   +T+   +E+    G +E C L+  +++     YGF  Y  + SAA A   L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 115 NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDA-TLFACFSVYPSCSDARV 173
            G+ L  + + V+W  A            + V  L P   D   L    S   S +  ++
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQL 217

Query: 174 MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
              Q  G+ +GF  + +   + A+ A     G  LG   +R ++   G        +
Sbjct: 218 ACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAA 273

>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 =  142 bits (361), Expect = 1e-40
 Identities = 37/224 (16%), Positives = 59/224 (26%), Gaps = 62/224 (27%)

Query: 118 HLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ 177
            L  + I+    +             I +  L  +VT+  +    S Y            
Sbjct: 2   MLDPEEIRKRLEH---TERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYC------- 51

Query: 178 KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVV 237
              + +G  FV+  N + A++AIN      L  R++                        
Sbjct: 52  FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ------------------- 92

Query: 238 ELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ 297
                                 P    + V NL P +TQ            G +E   + 
Sbjct: 93  ----------------------PTDALLCVANLPPSLTQQQFEELVRP--FGSLERCFLV 128

Query: 298 RD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                   KG+GF  Y     AA A           L  + + V
Sbjct: 129 YSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP---LGPRTLYV 169

>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 = 77.3 bits (191), Expect = 2e-16
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 4/77 (5%)

Query: 57  RSVYVGNIHTQVTEP-LLQEVFSSTGPVEGCKLIRKDKSS---YGFIHYFDRRSAAMAIL 112
           R + V  +     +   L    S+      C+L          +  + Y     A  A  
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQ 244

Query: 113 SLNGRHLFGQPIKVNWA 129
             +G  L G  ++V++ 
Sbjct: 245 QADGLSLGGSHLRVSFC 261

>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 =  245 bits (628), Expect = 4e-82
 Identities = 69/168 (41%), Positives = 103/168 (61%), Gaps = 6/168 (3%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
           R +YVGN+   +TE +L++ F   GP+   K++  DK++    Y F+ Y     A +A+ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMI-DKNNKNVNYAFVEYHQSHDANIALQ 59

Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
           +LNG+ +    +K+NWA+ S Q+  +   FN+FVGDL+  V D TL   F  +PS     
Sbjct: 60  TLNGKQIENNIVKINWAFQS-QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           VMWD +TG SRG+GFVSF +Q DAQ+A++ + G+ L  R +R NWA K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score =  136 bits (345), Expect = 1e-39
 Identities = 39/198 (19%), Positives = 74/198 (37%), Gaps = 45/198 (22%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+L   +T+  L   F V    ++ ++M D K  ++  + FV +    DA  A+  L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
            GK + +  ++ NWA +   ++ D                               N    
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSD----------------------------DTFN---- 89

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            ++VG+L   V    L   F            V  D      +G+GFV +++  +A  A+
Sbjct: 90  -LFVGDLNVNVDDETLRNAFKDF--PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146

Query: 318 QMGNTTQSSYLFGKQMKV 335
                     L G+ +++
Sbjct: 147 DSMQ---GQDLNGRPLRI 161

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 75.3 bits (186), Expect = 1e-16
 Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 4/87 (4%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFD 103
                     +++VG+++  V +  L+  F          ++   ++     YGF+ +  
Sbjct: 79  SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAY 130
           +  A  A+ S+ G+ L G+P+++NWA 
Sbjct: 139 QDDAQNAMDSMQGQDLNGRPLRINWAA 165

>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 = 70.6 bits (174), Expect = 6e-15
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK-----GFGFVRYSTHAEAALAIQ 318
            +YVGNL   +T+  L ++F     G I  +++  DK      + FV Y    +A +A+Q
Sbjct: 2   VLYVGNLDKAITEDILKQYFQV--GGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59

Query: 319 MGNTTQSSYLFGKQMKV 335
             N  Q   +    +K+
Sbjct: 60  TLNGKQ---IENNIVKI 73

>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 =  236 bits (604), Expect = 8e-78
 Identities = 53/216 (24%), Positives = 100/216 (46%), Gaps = 10/216 (4%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YG 97
           P G++ P        S+YVG++H  VTE +L E FS  GP+   ++ R D  +     Y 
Sbjct: 2   PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR-DMITRRSLGYA 60

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDAT 157
           ++++     A  A+ ++N   + G+P+++ W+         SG  NIF+ +L   + +  
Sbjct: 61  YVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRK-SGVGNIFIKNLDKSIDNKA 119

Query: 158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
           L+  FS + +    +V+ D     S+G+GFV F  Q+ A+ AI  + G  L  R++    
Sbjct: 120 LYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177

Query: 218 AT-KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTN 252
              +     E    +      ++ + +   G+  T+
Sbjct: 178 FKSRKEREAELGARAKEFYPYDVPDYAGSSGRIVTD 213

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  152 bits (385), Expect = 5e-45
 Identities = 45/206 (21%), Positives = 79/206 (38%), Gaps = 42/206 (20%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
               +    +++VGDL P+VT+A L+  FS        RV  D  T RS G+ +V+F+  
Sbjct: 8   PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNT 253
            DA+ A++ +    +  + +R  W+ +     +                           
Sbjct: 68  ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSG------------------------- 102

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYST 309
                      +++ NL   +    L+  F +   G I   +V  D    KG+GFV + T
Sbjct: 103 --------VGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFET 152

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
              A  AI+  N      L  +++ V
Sbjct: 153 QEAAERAIEKMN---GMLLNDRKVFV 175

>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 = 71.2 bits (175), Expect = 9e-15
 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 11/90 (12%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFV 305
           +      +    ++YVG+L P+VT+  L+  F    AG I  +RV RD       G+ +V
Sbjct: 5   SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSP--AGPILSIRVCRDMITRRSLGYAYV 62

Query: 306 RYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            +   A+A  A+   N      + GK +++
Sbjct: 63  NFQQPADAERALDTMNFDV---IKGKPVRI 89

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  217 bits (555), Expect = 2e-70
 Identities = 41/182 (22%), Positives = 82/182 (45%), Gaps = 14/182 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRS 106
             +    VYVG+I+ ++ E  +++ F+  GP++   +   D  +     + F+ Y    +
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW-DSVTMKHKGFAFVEYEVPEA 82

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQR--------EDTSGHFNIFVGDLSPEVTDATL 158
           A +A+  +N   L G+ IKV      GQ         E+      I+V  +  +++D  +
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142

Query: 159 FACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            + F  +     A +  D  TG+ +G+GF+ +   Q +Q A++ +    LG + +R   A
Sbjct: 143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

Query: 219 TK 220
             
Sbjct: 203 VT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  158 bits (401), Expect = 3e-47
 Identities = 42/221 (19%), Positives = 84/221 (38%), Gaps = 37/221 (16%)

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180
           GQ +    A  + ++   +    ++VG +  E+ + T+   F+ +       + WD  T 
Sbjct: 10  GQQMGRGSA--AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTM 67

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELT 240
           + +GF FV +   + AQ A+  +    LG R I+                          
Sbjct: 68  KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP---------------------- 105

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD- 299
             S+    +    +  E    +  +YV ++  +++  D+   F +   G I+   + RD 
Sbjct: 106 --SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF--GKIKSATLARDP 161

Query: 300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                KG+GF+ Y     +  A+   N      L G+ ++V
Sbjct: 162 TTGKHKGYGFIEYEKAQSSQDAVSSMN---LFDLGGQYLRV 199

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 78.9 bits (195), Expect = 2e-17
 Identities = 24/87 (27%), Positives = 43/87 (49%), Gaps = 6/87 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           +YV ++H  +++  ++ VF + G ++   L R D ++     YGFI Y   +S+  A+ S
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLAR-DPTTGKHKGYGFIEYEKAQSSQDAVSS 186

Query: 114 LNGRHLFGQPIKVNWAYASGQREDTSG 140
           +N   L GQ ++V  A        T  
Sbjct: 187 MNLFDLGGQYLRVGKAVTPPMPLLTPA 213

>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 =  215 bits (551), Expect = 2e-70
 Identities = 55/168 (32%), Positives = 86/168 (51%), Gaps = 11/168 (6%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           ++ V  +   +T+   + +F S G +E CKL+R DK +     YGF++Y D + A  AI 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR-DKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDAR 172
           +LNG  L  + IKV++A  S      +   N++V  L   +T   L   FS Y     +R
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSASIRDA---NLYVSGLPKTMTQKELEQLFSQYGRIITSR 119

Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL--GSRQIRCNWA 218
           ++ DQ TG SRG GF+ F  + +A+ AI  L G+     +  I   +A
Sbjct: 120 ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  134 bits (340), Expect = 8e-39
 Identities = 45/187 (24%), Positives = 73/187 (39%), Gaps = 43/187 (22%)

Query: 141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
             N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ + +DA+ AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 201 NDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNP 260
           N L G  L ++ I+ ++A                         S       N        
Sbjct: 62  NTLNGLRLQTKTIKVSYARP-----------------------SSASIRDAN-------- 90

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAA 314
               +YV  L   +TQ +L + F     G I   R+  D      +G GF+R+    EA 
Sbjct: 91  ----LYVSGLPKTMTQKELEQLFSQY--GRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144

Query: 315 LAIQMGN 321
            AI+  N
Sbjct: 145 EAIKGLN 151

>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 = 71.5 bits (176), Expect = 3e-15
 Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
           T + V  L   +TQ +    F S   G IE  ++ RDK      G+GFV Y    +A  A
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGS--IGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           I   N  +   L  K +KV
Sbjct: 61  INTLNGLR---LQTKTIKV 76

>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 =  214 bits (547), Expect = 7e-70
 Identities = 45/172 (26%), Positives = 83/172 (48%), Gaps = 11/172 (6%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAA 108
           ++  ++ V  +   +T+  L  +F + GP+  C+++R D  +     Y F+ +     + 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR-DYKTGYSYGYAFVDFTSEMDSQ 59

Query: 109 MAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSC 168
            AI  LNG  +  + +KV++A   G+    +   N++V +L   +TD  L   F  Y S 
Sbjct: 60  RAIKVLNGITVRNKRLKVSYARPGGESIKDT---NLYVTNLPRTITDDQLDTIFGKYGSI 116

Query: 169 SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL--GSRQIRCNWA 218
               ++ D+ TGR RG  FV +  +++AQ AI+ L       GS+ +    A
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  143 bits (362), Expect = 4e-42
 Identities = 50/189 (26%), Positives = 77/189 (40%), Gaps = 43/189 (22%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           + + N+ V  L  ++TD  L+A F      +  R+M D KTG S G+ FV F ++ D+Q 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPEN 258
           AI  L G  + +++++ ++A                          E  K+         
Sbjct: 61  AIKVLNGITVRNKRLKVSYARP----------------------GGESIKD--------- 89

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAE 312
               T +YV NL   +T   L   F     G I +  + RD      +G  FVRY+   E
Sbjct: 90  ----TNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKREE 143

Query: 313 AALAIQMGN 321
           A  AI   N
Sbjct: 144 AQEAISALN 152

>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 = 73.4 bits (181), Expect = 6e-16
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALA 316
           T + V  L  ++T  +L+  F +   G I   R+ RD       G+ FV +++  ++  A
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRA--IGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           I++ N      +  K++KV
Sbjct: 62  IKVLNGIT---VRNKRLKV 77

>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 =  215 bits (549), Expect = 1e-68
 Identities = 37/288 (12%), Positives = 89/288 (30%), Gaps = 55/288 (19%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSLN 115
           +V V N+     +  + + F   GP+    +    K +  +  I +     A  AI   +
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 102

Query: 116 GRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMW 175
              +    I V+         +      +++ +  P  T   +          + +  + 
Sbjct: 103 KV-VGQNEIIVSHL------TEC----TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLP 151

Query: 176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
             +   SR F ++   +++DA+  +  L G  +    +    +     +     ++    
Sbjct: 152 SLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATL--- 208

Query: 236 VVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLD-LHRHFHSLGAGVIEEV 294
                                    +   + + NL+ E+   + L   F     G IE++
Sbjct: 209 -------------------------EGREIMIRNLSTELLDENLLRESFEG--FGSIEKI 241

Query: 295 RVQRD-------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            +              F+ +     A  A+QM  +     L  +++ V
Sbjct: 242 NIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRS----LLGNREISV 285

>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 =  150 bits (382), Expect = 1e-43
 Identities = 31/172 (18%), Positives = 65/172 (37%), Gaps = 11/172 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +++ N     T+  ++++      V     +   + +    + +I    +  A   +  L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 115 NGRHLFGQPIKVNWAYASGQREDTSGHF----NIFVGDLSPEVTD-ATLFACFSVYPSCS 169
           NG  + G  +    +    + + T         I + +LS E+ D   L   F  + S  
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIE 239

Query: 170 DARVMWDQK-TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
              +   QK    +    F+ F N+  A+ A+  +    LG+R+I  + A K
Sbjct: 240 KINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADK 290

>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 =  127 bits (321), Expect = 9e-35
 Identities = 25/222 (11%), Positives = 57/222 (25%), Gaps = 56/222 (25%)

Query: 121 GQPIKVNWAYASGQREDT--SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK 178
           G P              T       + V +L        ++  F          V     
Sbjct: 19  GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-- 76

Query: 179 TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVE 238
             ++  F  + F     A +AI       +G  +I  +  T+                  
Sbjct: 77  LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLTE------------------ 117

Query: 239 LTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR 298
                                    T+++ N  P  TQ ++      +    +  +R+  
Sbjct: 118 ------------------------CTLWMTNFPPSYTQRNIRDLLQDINVVAL-SIRLPS 152

Query: 299 D-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                 + F ++  ++  +A   ++  N  +   + G  +  
Sbjct: 153 LRFNTSRRFAYIDVTSKEDARYCVEKLNGLK---IEGYTLVT 191

>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 = 75.8 bits (187), Expect = 8e-16
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 57  RSVYVGNIHTQVT-EPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMA 110
           R + + N+ T++  E LL+E F   G +E   +    K         F+ + ++ SA  A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 111 ILSLNGRHLFGQPIKVNWAY 130
           +  +N   L  + I V+ A 
Sbjct: 271 L-QMNRSLLGNREISVSLAD 289

>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 = 74.3 bits (183), Expect = 2e-15
 Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 10/111 (9%)

Query: 229 QSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA 288
              D+K  ++  + ++         EA   N + TTV V NL     Q  ++++F     
Sbjct: 8   ARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKH--C 65

Query: 289 GVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           G I  V V         F  + ++ +  A  AI   +      +   ++ V
Sbjct: 66  GPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK----VVGQNEIIV 112

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  196 bits (501), Expect = 7e-63
 Identities = 37/173 (21%), Positives = 72/173 (41%), Gaps = 15/173 (8%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----------IRKDKSSYGFIHYFDRRS 106
           R +YVGNI   +TE  + + F++   + G             I +DK+ + F+ +     
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-FAFLEFRSVDE 63

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYP 166
              A ++ +G    GQ +K+   +     +   G   +F+G L   + D  +    + + 
Sbjct: 64  TTQA-MAFDGIIFQGQSLKIRRPH---DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFG 119

Query: 167 SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
                 ++ D  TG S+G+ F  + +      AI  L G  LG +++    A+
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  116 bits (292), Expect = 1e-31
 Identities = 26/203 (12%), Positives = 60/203 (29%), Gaps = 52/203 (25%)

Query: 144 IFVGDLSPEVTDATLFACFSVY-----PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           ++VG++   +T+  +   F+        + +    +   +  + + F F+ FR+  +   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPEN 258
           A+    G     + ++                                          + 
Sbjct: 67  AMA-FDGIIFQGQSLKIRRP-----------------------------------HDYQP 90

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAE 312
            P    +++G L   +    +     S G   ++   + +D      KG+ F  Y     
Sbjct: 91  LPGAHKLFIGGLPNYLNDDQVKELLTSFGP--LKAFNLVKDSATGLSKGYAFCEYVDINV 148

Query: 313 AALAIQMGNTTQSSYLFGKQMKV 335
              AI   N      L  K++ V
Sbjct: 149 TDQAIAGLN---GMQLGDKKLLV 168

>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 = 81.5 bits (202), Expect = 9e-19
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRS 106
                  +++G +   + +  ++E+ +S GP++   L++ D ++     Y F  Y D   
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK-DSATGLSKGYAFCEYVDINV 148

Query: 107 AAMAILSLNGRHLFGQPIKVNWA 129
              AI  LNG  L  + + V  A
Sbjct: 149 TDQAIAGLNGMQLGDKKLLVQRA 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 = 68.0 bits (167), Expect = 5e-14
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 13/85 (15%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLG---------AGVIEEVRVQRDKGFGFVRYSTH 310
                +YVGN+   +T+  +   F++              +  V++ +DK F F+ + + 
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            E   A+            G+ +K+
Sbjct: 62  DETTQAMAFDGII----FQGQSLKI 82

>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 =  183 bits (467), Expect = 2e-57
 Identities = 40/195 (20%), Positives = 74/195 (37%), Gaps = 29/195 (14%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL----------IRKDKSSYGFIHYFDRRS 106
           R +YVGNI   +TE  + + F++   + G             I +DK+ + F+ +     
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-FAFLEFRSVDE 63

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQREDTS-----------------GHFNIFVGDL 149
              A+ + +G    GQ +K+   +        S                     +F+G L
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122

Query: 150 SPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG 209
              + D  +    + +       ++ D  TG S+G+ F  + +      AI  L G  LG
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 182

Query: 210 SRQIRCNWATKGAGN 224
            +++    A+ GA N
Sbjct: 183 DKKLLVQRASVGAKN 197

>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 =  119 bits (301), Expect = 7e-33
 Identities = 27/203 (13%), Positives = 61/203 (30%), Gaps = 32/203 (15%)

Query: 144 IFVGDLSPEVTDATLFACFSVY-----PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           ++VG++   +T+  +   F+        + +    +   +  + + F F+ FR+  +   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPEN 258
           A+    G     + ++                        L   S           +   
Sbjct: 67  AMA-FDGIIFQGQSLKIRRP---------------HDYQPLPGMSENPSVYVPGVVSTVV 110

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAE 312
                 +++G L   +    +     S   G ++   + +D      KG+ F  Y     
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTS--FGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168

Query: 313 AALAIQMGNTTQSSYLFGKQMKV 335
              AI   N      L  K++ V
Sbjct: 169 TDQAIAGLN---GMQLGDKKLLV 188

>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 = 81.2 bits (201), Expect = 2e-18
 Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 6/100 (6%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS 94
              +   +    +     P +   +++G +   + +  ++E+ +S GP++   L+ KD +
Sbjct: 93  GMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV-KDSA 151

Query: 95  S-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +     Y F  Y D      AI  LNG  L  + + V  A
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>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 = 66.6 bits (163), Expect = 3e-13
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLG---------AGVIEEVRVQRDKGFGFVRYSTHAEAA 314
            +YVGN+   +T+  +   F++              +  V++ +DK F F+ + +  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A+            G+ +K+
Sbjct: 66  QAMAFDGII----FQGQSLKI 82

>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 =  181 bits (462), Expect = 5e-57
 Identities = 27/175 (15%), Positives = 71/175 (40%), Gaps = 10/175 (5%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI-RKDKSS--YGFIHYFDRR 105
            G + +T  ++++GN++   +   L+   S         ++  +  ++  +G++ +    
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65

Query: 106 SAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY 165
               A+  L G  +FG  IK+        ++       +   +LS  +T+  L   F   
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKV-RAARTLLAKNLSFNITEDELKEVFEDA 123

Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
                  +    + G+S+G  ++ F+++ DA+  + +  G  +  R +   +  +
Sbjct: 124 -----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  133 bits (336), Expect = 4e-38
 Identities = 38/206 (18%), Positives = 80/206 (38%), Gaps = 47/206 (22%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +  +++  FN+F+G+L+P  + A L    S   + +D  V+ D +TG +R FG+V F + 
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNT 253
           +D + A+ +LTG  +   +I+                                       
Sbjct: 65  EDLEKAL-ELTGLKVFGNEIKLEKPKG--------------------------------- 90

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYST 309
              +      T+   NL+  +T+ +L   F         E+R+       KG  ++ + +
Sbjct: 91  RDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKS 145

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
            A+A   ++         + G+ + +
Sbjct: 146 EADAEKNLEEKQGA---EIDGRSVSL 168

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 69.2 bits (170), Expect = 2e-14
 Identities = 13/89 (14%), Positives = 34/89 (38%), Gaps = 11/89 (12%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVR 306
           +      +     +++GNL P  +  +L             ++ V        + FG+V 
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISE--LFAKNDLAVVDVRTGTNRKFGYVD 60

Query: 307 YSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           + +  +   A+++        +FG ++K+
Sbjct: 61  FESAEDLEKALELTGLK----VFGNEIKL 85

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  177 bits (451), Expect = 3e-54
 Identities = 44/183 (24%), Positives = 76/183 (41%), Gaps = 13/183 (7%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSA 107
           P     +    ++VGN+ T +TE   + +F   G      + R D+  +GFI    R  A
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-DRG-FGFIRLESRTLA 71

Query: 108 AMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPS 167
            +A   L+G  L  +P+++ +A              + V +LSP V++  L   FS +  
Sbjct: 72  EIAKAELDGTILKSRPLRIRFATHG---------AALTVKNLSPVVSNELLEQAFSQFGP 122

Query: 168 CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK-WLGSRQIRCNWATKGAGNNE 226
              A V+ D   GR+ G GFV F  +  A+ A+       +L +   R          ++
Sbjct: 123 VEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD 181

Query: 227 DKQ 229
           +  
Sbjct: 182 EDG 184

>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 =  132 bits (334), Expect = 7e-37
 Identities = 47/220 (21%), Positives = 77/220 (35%), Gaps = 57/220 (25%)

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180
           G  I +      G++   +    +FVG+L  ++T+      F  Y   S+  +       
Sbjct: 3   GFTIDIKSFLKPGEKT-YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------ 55

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELT 240
           R RGFGF+   ++  A+ A  +L G  L SR +R  +AT GA                  
Sbjct: 56  RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA------------------ 97

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD- 299
                                   + V NL+P V+   L + F   G   +E+  V  D 
Sbjct: 98  -----------------------ALTVKNLSPVVSNELLEQAFSQFGP--VEKAVVVVDD 132

Query: 300 ----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                G GFV ++    A  A++        +L     + 
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCGDGA--FLLTTTPRP 170

>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 =  164 bits (417), Expect = 3e-50
 Identities = 38/176 (21%), Positives = 74/176 (42%), Gaps = 13/176 (7%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-------YGFIHYFDRRS 106
           S    ++VG +    +E  L+E+F   G V    ++R D+S          F+ ++ R++
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR-DRSQNPPQSKGCCFVTFYTRKA 59

Query: 107 AAMAILSLNGRHLFGQPIKVNWA-YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY 165
           A  A  +L+   +            A  ++ +      +F+G +S + T+  +   FS +
Sbjct: 60  ALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSF 119

Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK---WLGSRQIRCNWA 218
               + R++     G SRG  FV+F  +  AQ+AI  +         S  +   +A
Sbjct: 120 GQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  128 bits (323), Expect = 2e-36
 Identities = 41/204 (20%), Positives = 72/204 (35%), Gaps = 40/204 (19%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG--RSRGFGFVSFRNQQDA 196
           S    +FVG +    ++  L   F  Y +  +  V+ D+     +S+G  FV+F  ++ A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 197 QSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAP 256
             A N L    +                                +    +  E       
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKP-------------------ADSEKNNAVEDRK---- 97

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHA 311
                   +++G ++ + T+ D+   F S G   IEE R+ R      +G  FV ++T A
Sbjct: 98  --------LFIGMISKKCTENDIRVMFSSFG--QIEECRILRGPDGLSRGCAFVTFTTRA 147

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
            A  AI+  +  Q+       M V
Sbjct: 148 MAQTAIKAMHQAQTMEGCSSPMVV 171

>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 =  164 bits (416), Expect = 7e-50
 Identities = 41/197 (20%), Positives = 76/197 (38%), Gaps = 8/197 (4%)

Query: 140 GHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           G+  + V +L+PE VT  +LF  F VY      +++++      +    V   +   AQ 
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQL 56

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPEN 258
           A++ L G  L  + IR   +         +   D     +  N      K+  +      
Sbjct: 57  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
            P   T+++ N+ P V++ DL   F S G  V      Q+D+    ++  +  EA  A+ 
Sbjct: 117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALI 176

Query: 319 MGNTTQSSYLFGKQMKV 335
             +           ++V
Sbjct: 177 DLHNHD--LGENHHLRV 191

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score =  107 bits (269), Expect = 3e-28
 Identities = 35/196 (17%), Positives = 69/196 (35%), Gaps = 39/196 (19%)

Query: 59  VYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           + V N++ + VT   L  +F   G V+  K++   K     +   D   A +A+  LNG 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-NALVQMADGNQAQLAMSHLNGH 64

Query: 118 HLFGQPIKVNWA--------------------YASGQREDTSGHF------------NIF 145
            L G+PI++  +                    Y +                       + 
Sbjct: 65  KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 124

Query: 146 VGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG 205
           + ++ P V++  L   FS         V   +   + R    +   + ++A  A+ DL  
Sbjct: 125 LSNIPPSVSEEDLKVLFSSNG----GVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 180

Query: 206 KWLG-SRQIRCNWATK 220
             LG +  +R +++  
Sbjct: 181 HDLGENHHLRVSFSKS 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 = 65.7 bits (160), Expect = 6e-13
 Identities = 25/119 (21%), Positives = 44/119 (36%), Gaps = 3/119 (2%)

Query: 12  QQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEP 71
            Q   L ++    Q      G     + +   S N    F PS    +++ NI   V+E 
Sbjct: 78  HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT--LHLSNIPPSVSEE 135

Query: 72  LLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF-GQPIKVNWA 129
            L+ +FSS G V       +       I       A  A++ L+   L     ++V+++
Sbjct: 136 DLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>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 =  154 bits (391), Expect = 3e-47
 Identities = 53/106 (50%), Positives = 75/106 (70%)

Query: 129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
           + +SGQ++DTS HF++FVGDLSPE+T   + A F+ +   SDARV+ D  TG+S+G+GFV
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAK 234
           SF N+ DA++AI  + G+WLG RQIR NWAT+     +    S+ K
Sbjct: 63  SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTK 108

>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 = 71.6 bits (176), Expect = 8e-16
 Identities = 25/91 (27%), Positives = 49/91 (53%), Gaps = 6/91 (6%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+     D S    V+VG++  ++T   ++  F+  G +   ++++ D ++     YGF
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVK-DMATGKSKGYGF 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           + +F++  A  AI  + G+ L G+ I+ NWA
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 92

>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 = 65.1 bits (159), Expect = 2e-13
 Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 11/92 (11%)

Query: 250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFG 303
           + ++   ++   +  V+VG+L+PE+T  D+   F   G   I + RV +D      KG+G
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGR--ISDARVVKDMATGKSKGYG 60

Query: 304 FVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           FV +    +A  AIQ        +L G+Q++ 
Sbjct: 61  FVSFFNKWDAENAIQQMG---GQWLGGRQIRT 89

>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 =  158 bits (400), Expect = 4e-47
 Identities = 42/215 (19%), Positives = 80/215 (37%), Gaps = 8/215 (3%)

Query: 122 QPIKVNWAYASGQREDTSGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTG 180
            P   +    +      +G+  + V +L+PE VT  +LF  F VY      +++++    
Sbjct: 15  VPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN---- 70

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELT 240
             +    V   +   AQ A++ L G  L  + IR   +         +   D     +  
Sbjct: 71  -KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 129

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK 300
           N      K+  +       P   T+++ N+ P V++ DL   F S G  V      Q+D+
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 189

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
               ++  +  EA  A+   +           ++V
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHD--LGENHHLRV 222

>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 =  114 bits (286), Expect = 2e-30
 Identities = 37/229 (16%), Positives = 73/229 (31%), Gaps = 41/229 (17%)

Query: 26  QSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVE 84
              +H                  PG   +    + V N++ + VT   L  +F   G V+
Sbjct: 6   HHHHHSS--GLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQ 63

Query: 85  GCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFN- 143
             K++   K     +   D   A +A+  LNG  L G+PI++  +     +    G  + 
Sbjct: 64  RVKILFNKKE-NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQ 122

Query: 144 -------------------------------IFVGDLSPEVTDATLFACFSVYPSCSDAR 172
                                          + + ++ P V++  L   FS         
Sbjct: 123 GLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 182

Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG-SRQIRCNWATK 220
                   + R    +   + ++A  A+ DL    LG +  +R +++  
Sbjct: 183 KF----FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 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 = 64.6 bits (157), Expect = 2e-12
 Identities = 25/120 (20%), Positives = 45/120 (37%), Gaps = 3/120 (2%)

Query: 11  QQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTE 70
           + Q   L ++    Q      G     + +   S N    F PS    +++ NI   V+E
Sbjct: 108 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT--LHLSNIPPSVSE 165

Query: 71  PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF-GQPIKVNWA 129
             L+ +FSS G V       +       I       A  A++ L+   L     ++V+++
Sbjct: 166 EDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>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 =  149 bits (379), Expect = 8e-46
 Identities = 46/84 (54%), Positives = 62/84 (73%)

Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
               HF++FVGDLSPE+T A + A F+ +   SDARV+ D  TG+S+G+GFVSF N+ DA
Sbjct: 2   PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61

Query: 197 QSAINDLTGKWLGSRQIRCNWATK 220
           ++AI  + G+WLG RQIR NWAT+
Sbjct: 62  ENAIQQMGGQWLGGRQIRTNWATR 85

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 75.7 bits (187), Expect = 1e-17
 Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 6/83 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRS 106
              +   V+VG++  ++T   +   F+  G +   ++++ D ++     YGF+ +F++  
Sbjct: 2   PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVK-DMATGKSKGYGFVSFFNKWD 60

Query: 107 AAMAILSLNGRHLFGQPIKVNWA 129
           A  AI  + G+ L G+ I+ NWA
Sbjct: 61  AENAIQQMGGQWLGGRQIRTNWA 83

>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 = 63.0 bits (154), Expect = 5e-13
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 11/77 (14%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           V+VG+L+PE+T   +   F   G   I + RV +D      KG+GFV +    +A  AIQ
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGR--ISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66

Query: 319 MGNTTQSSYLFGKQMKV 335
                   +L G+Q++ 
Sbjct: 67  ---QMGGQWLGGRQIRT 80

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  144 bits (366), Expect = 1e-43
 Identities = 36/104 (34%), Positives = 59/104 (56%), Gaps = 3/104 (2%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFS-VYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           G    +   +++FVGDL+P+V D  L+  F  VYPSC   +V+ DQ TG S+G+GFV F 
Sbjct: 1   GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFT 59

Query: 192 NQQDAQSAINDLTGK-WLGSRQIRCNWATKGAGNNEDKQSSDAK 234
           ++ + + A+ +  G   LGS+ +R + A   A   +  +S  + 
Sbjct: 60  DELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 60.8 bits (148), Expect = 5e-12
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTH 310
             + P+Y+ ++VG+L P+V    L+  F  +        +V  D     KG+GFV+++  
Sbjct: 4   GSSGPEYS-LFVGDLTPDVDDGMLYEFFVKVY-PSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            E   A+          L  K +++
Sbjct: 62  LEQKRALTECQGAV--GLGSKPVRL 84

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 60.4 bits (147), Expect = 7e-12
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 7/92 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIRKDKSS----YGFIHYFDRRS 106
                 S++VG++   V + +L E F    P   G K++  D++     YGF+ + D   
Sbjct: 5   SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVL-DQTGVSKGYGFVKFTDELE 63

Query: 107 AAMAILSLNGRHLFGQ-PIKVNWAYASGQRED 137
              A+    G    G  P++++ A     R  
Sbjct: 64  QKRALTECQGAVGLGSKPVRLSVAIPKASRVK 95

>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 =  140 bits (356), Expect = 3e-42
 Identities = 41/79 (51%), Positives = 53/79 (67%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           FN+FVGDL+  V D TL   F  +PS     VMWD +TG SRG+GFVSF +Q DAQ+A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 202 DLTGKWLGSRQIRCNWATK 220
            + G+ L  R +R NWA K
Sbjct: 62  SMQGQDLNGRPLRINWAAK 80

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 70.6 bits (174), Expect = 8e-16
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
           +++VG+++  V +  L+  F          ++  D  +     YGF+ +  +  A  A+ 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW-DMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 113 SLNGRHLFGQPIKVNWA 129
           S+ G+ L G+P+++NWA
Sbjct: 62  SMQGQDLNGRPLRINWA 78

>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 = 62.9 bits (154), Expect = 5e-13
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 11/77 (14%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           ++VG+L   V    L   F    +       V  D      +G+GFV +++  +A  A+ 
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPS--YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 319 MGNTTQSSYLFGKQMKV 335
                    L G+ +++
Sbjct: 62  SMQ---GQDLNGRPLRI 75

>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 =  136 bits (344), Expect = 2e-40
 Identities = 28/94 (29%), Positives = 50/94 (53%), Gaps = 1/94 (1%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVY-PSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           +SG   IF+G+L PE+ +  L+  FS +       ++M D  TG S+G+ F++F +   +
Sbjct: 2   SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 197 QSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
            +AI  + G++L +R I  ++A K         S
Sbjct: 62  DAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 74.9 bits (185), Expect = 3e-17
 Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 5/89 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
            +++GN+  ++ E LL + FS+ G +     I +D  +     Y FI++    ++  AI 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSGH 141
           ++NG++L  +PI V++A+    +      
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 61.1 bits (149), Expect = 3e-12
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 10/78 (12%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            +++GNL PE+ +  L+  F + G  +++  ++ RD      KG+ F+ +++   +  AI
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGV-ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65

Query: 318 QMGNTTQSSYLFGKQMKV 335
           +  N     YL  + + V
Sbjct: 66  EAMN---GQYLCNRPITV 80

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  133 bits (337), Expect = 3e-39
 Identities = 31/109 (28%), Positives = 55/109 (50%)

Query: 110 AILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCS 169
           +  +L+   L    +    A A+G++ +     N+F+  L  E TD  L + F  + +  
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68

Query: 170 DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            A+V  D++T  S+ FGFVSF N   AQ AI  + G  +G+++++    
Sbjct: 69  SAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 70.5 bits (173), Expect = 2e-15
 Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 14/113 (12%)

Query: 30  HPGLLAAPQIEPIPSGNLPPGFDPSTCRS--------VYVGNIHTQVTEPLLQEVFSSTG 81
             G  +A    P+ S  L      +  +         +++ ++  + T+  L   F   G
Sbjct: 6   QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFG 65

Query: 82  PVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            V   K+   DK +     +GF+ + +  SA +AI ++NG  +  + +KV   
Sbjct: 66  NVISAKVFI-DKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 67.0 bits (164), Expect = 5e-14
 Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 11/85 (12%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTH 310
              P+   +++ +L  E T  DL   F   G   +   +V  D      K FGFV +   
Sbjct: 35  IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGN--VISAKVFIDKQTSLSKCFGFVSFDNP 92

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
             A +AI+  N  Q   +  K++KV
Sbjct: 93  DSAQVAIKAMNGFQ---VGTKRLKV 114

>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 =  128 bits (324), Expect = 3e-37
 Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 2/90 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG R       N++V +L   + D  L   FS + + + A+VM +   GRS+GFGFV F
Sbjct: 5   SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCF 62

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            + ++A  A+ ++ G+ + ++ +    A +
Sbjct: 63  SSPEEATKAVTEMNGRIVATKPLYVALAQR 92

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 70.7 bits (174), Expect = 1e-15
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSLNG 116
           +YV N+   + +  L++ FS  G +   K++ +   S  +GF+ +     A  A+  +NG
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 117 RHLFGQPIKVNWAYASGQREDTSGH 141
           R +  +P+ V  A    +R+     
Sbjct: 78  RIVATKPLYVALAQRKEERQSGPSS 102

>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 = 64.5 bits (158), Expect = 2e-13
 Identities = 26/98 (26%), Positives = 37/98 (37%), Gaps = 15/98 (15%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
           GSS    +           Q   +YV NL   +    L + F   G   I   +V  +  
Sbjct: 1   GSSGSSGDRITR------YQVVNLYVKNLDDGIDDERLRKAFSPFG--TITSAKVMMEGG 52

Query: 300 --KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
             KGFGFV +S+  EA  A+   N      +  K + V
Sbjct: 53  RSKGFGFVCFSSPEEATKAVTEMN---GRIVATKPLYV 87

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score =  127 bits (322), Expect = 7e-37
 Identities = 30/138 (21%), Positives = 52/138 (37%), Gaps = 29/138 (21%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
            G  NIF+ +L   + +  L+  FS + +    +V+ D     S+G+GFV F  Q+ A+ 
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPEN 258
           AI  + G  L  R++                                  ++    E    
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKS---------------------------RKEREAELGAR 93

Query: 259 NPQYTTVYVGNLAPEVTQ 276
             ++T VY+ N  P  T+
Sbjct: 94  AKEFTNVYIKNFGPGSTR 111

>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 = 94.2 bits (235), Expect = 3e-24
 Identities = 27/111 (24%), Positives = 52/111 (46%), Gaps = 7/111 (6%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMA 110
           P    ++++ N+   +    L + FS+ G +  CK++  +  S  YGF+H+  + +A  A
Sbjct: 2   PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 61

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQREDTSGH-----FNIFVGDLSPEVTDA 156
           I  +NG  L  + + V    +  +RE   G       N+++ +  P  T A
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQ 318
             +++ NL   +    L+  F +   G I   +V  D    KG+GFV + T   A  AI+
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSA--FGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 63

Query: 319 MGNTTQSSYLFGKQMKV 335
             N      L  +++ V
Sbjct: 64  KMNGM---LLNDRKVFV 77

>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 =  122 bits (309), Expect = 4e-35
 Identities = 37/101 (36%), Positives = 60/101 (59%), Gaps = 4/101 (3%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS--SYGFIHY 101
           SG+     D    R++YVGN+   VTE L+ ++FS  GP + CK+I +  S   Y F+ +
Sbjct: 3   SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEF 62

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE--DTSG 140
           ++ R AA A+ ++NGR + G+ +KVNWA     ++   +SG
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSSG 103

>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 =  106 bits (268), Expect = 4e-29
 Identities = 25/100 (25%), Positives = 49/100 (49%), Gaps = 2/100 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  ED      ++VG+LS +VT+  +   FS    C   +++ +  +     + FV F
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEF 62

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
              +DA +A+  + G+ +  ++++ NWAT  +       S
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.3 bits (178), Expect = 3e-16
 Identities = 23/90 (25%), Positives = 47/90 (52%), Gaps = 9/90 (10%)

Query: 250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFV 305
           + ++   E++ Q  T+YVGNL+ +VT++ + + F     G  +  ++  +      + FV
Sbjct: 3   SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQ--IGPCKSCKMITEHTSNDPYCFV 60

Query: 306 RYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            +  H +AA A+   N  +   + GK++KV
Sbjct: 61  EFYEHRDAAAALAAMNGRK---ILGKEVKV 87

>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 =  116 bits (293), Expect = 8e-33
 Identities = 25/87 (28%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +  +++  FN+F+G+L+P  + A L    S   + +D  V+ D +TG +R FG+V F + 
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 68

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATK 220
           +D + A+ +LTG  +   +I+      
Sbjct: 69  EDLEKAL-ELTGLKVFGNEIKLEKPKG 94

>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 = 68.4 bits (168), Expect = 8e-15
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 12/88 (13%)

Query: 253 TEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRY 307
            E  E+   +  +++GNL P  +  +L      L      ++ V        + FG+V +
Sbjct: 9   VEGSESTTPFN-LFIGNLNPNKSVAELKVAISELF--AKNDLAVVDVRTGTNRKFGYVDF 65

Query: 308 STHAEAALAIQMGNTTQSSYLFGKQMKV 335
            +  +   A+++        +FG ++K+
Sbjct: 66  ESAEDLEKALELTGL----KVFGNEIKL 89

>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 = 65.7 bits (161), Expect = 7e-14
 Identities = 17/96 (17%), Positives = 38/96 (39%), Gaps = 7/96 (7%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KS-SYGFIHYFDR 104
             G + +T  ++++GN++   +   L+   S         ++      +  +G++ +   
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68

Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
                A+  L G  +FG  IK+        R+ T G
Sbjct: 69  EDLEKAL-ELTGLKVFGNEIKLEKPKG---RDGTRG 100

>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 =  117 bits (296), Expect = 2e-32
 Identities = 42/170 (24%), Positives = 76/170 (44%), Gaps = 14/170 (8%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
             +++G ++   TE  L+E F   G V   K+++ D ++     +GF+ +    S     
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMK-DPATGRSRGFGFLSFEKPSSVDEV- 61

Query: 112 LSLNGRHLF-GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
             +  +H+  G+ I    A    +++ T     IFVG + P+V        FS + +  D
Sbjct: 62  --VKTQHILDGKVIDPKRAIPRDEQDKTG---KIFVGGIGPDVRPKEFEEFFSQWGTIID 116

Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           A++M D+ TG+SRGFGFV++ +         +        R+I    A  
Sbjct: 117 AQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEP 165

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  110 bits (278), Expect = 9e-30
 Identities = 39/198 (19%), Positives = 68/198 (34%), Gaps = 49/198 (24%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G L+ + T+  L   F  Y + +D ++M D  TGRSRGFGF+SF         +   
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT- 64

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
               L  + I    A                                      +   +  
Sbjct: 65  -QHILDGKVIDPKRAI-----------------------------------PRDEQDKTG 88

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            ++VG + P+V   +    F     G I + ++  D      +GFGFV Y +        
Sbjct: 89  KIFVGGIGPDVRPKEFEEFFSQW--GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146

Query: 318 QMGNTTQSSYLFGKQMKV 335
           Q            +++++
Sbjct: 147 QNKFID----FKDRKIEI 160

>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 = 55.6 bits (135), Expect = 1e-09
 Identities = 11/68 (16%), Positives = 31/68 (45%), Gaps = 8/68 (11%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAA 314
           +   +++G L  + T+ +L  +F     G + ++++ +D       GFGF+ +   +   
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGK--YGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVD 59

Query: 315 LAIQMGNT 322
             ++  + 
Sbjct: 60  EVVKTQHI 67

>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 = 49.8 bits (120), Expect = 1e-07
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFD 103
           P  +      ++VG I   V     +E FS  G +   +L+  DK +     +GF+  +D
Sbjct: 80  PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML-DKDTGQSRGFGFV-TYD 137

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWA 129
              A   +          + I++  A
Sbjct: 138 SADAVDRVCQNKFIDFKDRKIEIKRA 163

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  114 bits (288), Expect = 1e-31
 Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 2/97 (2%)

Query: 124 IKVNWAYAS--GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGR 181
             V+       G     +    ++VG L+ EV D  L A F  +   +D ++  D +T +
Sbjct: 44  RHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK 103

Query: 182 SRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            RGF FV F   +DA +AI+++    L  R IR N A
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 82.9 bits (205), Expect = 1e-19
 Identities = 27/132 (20%), Positives = 52/132 (39%), Gaps = 9/132 (6%)

Query: 3   HQRLKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVG 62
           H + +    +  + L         +           ++    G+   G   +T R +YVG
Sbjct: 13  HSKCENLSDEMYEILSNLPESVAYT---CVNCTERHVDGGSGGSGGSGGSATTKRVLYVG 69

Query: 63  NIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGR 117
            +  +V + +L   F   G +   ++   D  +     + F+ +     AA AI ++N  
Sbjct: 70  GLAEEVDDKVLHAAFIPFGDITDIQIP-LDYETEKHRGFAFVEFELAEDAAAAIDNMNES 128

Query: 118 HLFGQPIKVNWA 129
            LFG+ I+VN A
Sbjct: 129 ELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 70.6 bits (173), Expect = 3e-15
 Identities = 29/108 (26%), Positives = 46/108 (42%), Gaps = 12/108 (11%)

Query: 234 KSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE 293
            + V  T    + G   +         +   +YVG LA EV    LH  F     G I +
Sbjct: 36  YTCVNCTERHVDGGSGGSGGSGGSATTKRV-LYVGGLAEEVDDKVLHAAFIP--FGDITD 92

Query: 294 VRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           +++  D      +GF FV +    +AA AI   N ++   LFG+ ++V
Sbjct: 93  IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE---LFGRTIRV 137

>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 =  113 bits (284), Expect = 2e-31
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           +      +F+G L+ E  +  L A F  +   S+  ++ D +T +SRGF F++F N  DA
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61

Query: 197 QSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
           ++A  D+ GK L  + I+   A K +  +  ++   A S
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASS 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 = 70.8 bits (174), Expect = 1e-15
 Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 5/97 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +++G ++ +  E +L+ VF   GP+    LI KD++S    + FI + +   A  A   +
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLI-KDRTSKSRGFAFITFENPADAKNAAKDM 68

Query: 115 NGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSP 151
           NG+ L G+ IKV  A     +            + SP
Sbjct: 69  NGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSP 105

>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 = 67.4 bits (165), Expect = 3e-14
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 10/81 (12%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAA 314
                +++G L  E  +  L   F   G   I EV + +D     +GF F+ +   A+A 
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGP--ISEVLLIKDRTSKSRGFAFITFENPADAK 62

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A +  N      L GK +KV
Sbjct: 63  NAAKDMNGKS---LHGKAIKV 80

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score =  109 bits (274), Expect = 4e-30
 Identities = 28/76 (36%), Positives = 42/76 (55%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI++
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 203 LTGKWLGSRQIRCNWA 218
           +    L  R IR N A
Sbjct: 69  MNESELFGRTIRVNLA 84

>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 = 79.5 bits (197), Expect = 5e-19
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
           R +YVG +  +V + +L   F   G +   ++   D  +     + F+ +     AA AI
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP-LDYETEKHRGFAFVEFELAEDAAAAI 66

Query: 112 LSLNGRHLFGQPIKVNWA 129
            ++N   LFG+ I+VN A
Sbjct: 67  DNMNESELFGRTIRVNLA 84

>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 = 66.4 bits (163), Expect = 3e-14
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 11/82 (13%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEA 313
                +YVG LA EV    LH  F     G I ++++  D      +GF FV +    +A
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIP--FGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
           A AI   N ++   LFG+ ++V
Sbjct: 63  AAAIDNMNESE---LFGRTIRV 81

>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 =  109 bits (275), Expect = 6e-30
 Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 3/111 (2%)

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180
           G+ I+    ++S    + +    +++ +LSP VT+  L + F+ +       + +   TG
Sbjct: 7   GEEIRKIPMFSSYNPGEPN--KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTG 64

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSS 231
           R RG  F++F N++ A  A++ + G  L  + +   +  K         SS
Sbjct: 65  RMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG-KNKKQRSSGPSS 114

>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 = 80.0 bits (198), Expect = 6e-19
 Identities = 24/111 (21%), Positives = 48/111 (43%), Gaps = 8/111 (7%)

Query: 36  APQIEPIP-SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS 94
             +I  IP   +  PG +P+    +Y+ N+  +VTE  L  +F+     +G  +  +  +
Sbjct: 7   GEEIRKIPMFSSYNPG-EPNKV--LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT 63

Query: 95  S----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
                  FI + ++  A  A+  +NG  L+G+ + + +     QR      
Sbjct: 64  GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPSS 114

>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 = 69.2 bits (170), Expect = 7e-15
 Identities = 21/103 (20%), Positives = 39/103 (37%), Gaps = 12/103 (11%)

Query: 240 TNGSSEDGKETTNTEAPENNPQ-YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR 298
           ++GSS +        +  N  +    +Y+ NL+P VT+ DL   F        +   +Q 
Sbjct: 2   SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQE--KKGPPIQF 59

Query: 299 D------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                  +G  F+ +     A  A+          L+GK + +
Sbjct: 60  RMMTGRMRGQAFITFPNKEIAWQALH---LVNGYKLYGKILVI 99

>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 =  108 bits (273), Expect = 7e-30
 Identities = 32/91 (35%), Positives = 47/91 (51%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG R +   +  + V  LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F
Sbjct: 5   SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
            N  DA+ A     G  L  R+IR +  + G
Sbjct: 65  ENVDDAKEAKERANGMELDGRRIRVSGPSSG 95

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 74.2 bits (183), Expect = 6e-17
 Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+     +P     + V  +    TE  L+EVFS  GP+    ++  D+ S     + F
Sbjct: 3   SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV-YDQQSRRSRGFAF 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +++ +   A  A    NG  L G+ I+V+  
Sbjct: 62  VYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 11/86 (12%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
             N      + V  L+   T+ DL   F   G   I +V +  D      +GF FV +  
Sbjct: 9   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGP--IADVSIVYDQQSRRSRGFAFVYFEN 66

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
             +A  A +  N  +   L G++++V
Sbjct: 67  VDDAKEAKERANGME---LDGRRIRV 89

>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 =  108 bits (272), Expect = 9e-30
 Identities = 37/90 (41%), Positives = 52/90 (57%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG     S    +FVG LS +  + +L   FS Y   S+  V+ D++T RSRGFGFV+F
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N  DA+ A+  + GK +  RQIR + A K
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGK 91

>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 = 68.8 bits (169), Expect = 6e-15
 Identities = 22/98 (22%), Positives = 46/98 (46%), Gaps = 7/98 (7%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYF 102
             G      + ++VG +     E  L++VFS  G +    ++ KD+ +     +GF+ + 
Sbjct: 5   SSGMASDEGK-LFVGGLSFDTNEQSLEQVFSKYGQISEVVVV-KDRETQRSRGFGFVTFE 62

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           +   A  A++++NG+ + G+ I+V+ A  S        
Sbjct: 63  NIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100

>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 = 59.9 bits (146), Expect = 8e-12
 Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 15/95 (15%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------K 300
           G   ++  A +       ++VG L+ +  +  L + F   G   I EV V +D      +
Sbjct: 1   GSSGSSGMASDEG----KLFVGGLSFDTNEQSLEQVFSKYGQ--ISEVVVVKDRETQRSR 54

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           GFGFV +    +A  A+   N      + G+Q++V
Sbjct: 55  GFGFVTFENIDDAKDAMMAMNGKS---VDGRQIRV 86

>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 =  111 bits (279), Expect = 1e-29
 Identities = 44/210 (20%), Positives = 75/210 (35%), Gaps = 42/210 (20%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           S   ++      +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++ 
Sbjct: 4   SESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETT 251
             ++  +A+N      +  R +    A     +         K                 
Sbjct: 64  TVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVK----------------- 105

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFV 305
                        ++VG +  +  +  L  +F   G   IE + +  D+      GF FV
Sbjct: 106 ------------KIFVGGIKEDTEEHHLRDYFEQYGK--IEVIEIMTDRGSGKKRGFAFV 151

Query: 306 RYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            +  H      +     T    + G   +V
Sbjct: 152 TFDDHDSVDKIVIQKYHT----VNGHNCEV 177

>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 =  108 bits (272), Expect = 1e-28
 Identities = 33/176 (18%), Positives = 68/176 (38%), Gaps = 11/176 (6%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRS 106
           +P   R +++G +  + T+  L+  F   G +  C ++R D ++     +GF+  +    
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR-DPNTKRSRGFGFVT-YATVE 66

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFN---IFVGDLSPEVTDATLFACFS 163
              A ++     + G+ ++   A +    +    H     IFVG +  +  +  L   F 
Sbjct: 67  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126

Query: 164 VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            Y       +M D+ +G+ RGF FV+F +       +       +         A 
Sbjct: 127 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL 181

>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 = 48.4 bits (116), Expect = 6e-07
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYF 102
            PG   +  + ++VG I     E  L++ F   G +E  +++  D+ S     + F+  F
Sbjct: 97  RPGAHLTVKK-IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT-DRGSGKKRGFAFV-TF 153

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWA 129
           D   +   I+      + G   +V  A
Sbjct: 154 DDHDSVDKIVIQKYHTVNGHNCEVRKA 180

>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 =  108 bits (272), Expect = 1e-29
 Identities = 30/90 (33%), Positives = 46/90 (51%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG     +    ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
              +DA +AI+++    L  R IR N A  
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAKP 91

>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 = 77.6 bits (192), Expect = 4e-18
 Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
           R +YVG +  +V + +L   F   G +   ++   D  +     + F+ +     AA AI
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP-LDYETEKHRGFAFVEFELAEDAAAAI 71

Query: 112 LSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
            ++N   LFG+ I+VN A     +E     
Sbjct: 72  DNMNESELFGRTIRVNLAKPMRIKESGPSS 101

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV------QRDKGFGFVRYSTHAEAALA 316
             +YVG LA EV    LH  F     G I ++++      ++ +GF FV +    +AA A
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIP--FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           I   N ++   LFG+ ++V
Sbjct: 71  IDNMNESE---LFGRTIRV 86

>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 =  108 bits (272), Expect = 1e-29
 Identities = 26/89 (29%), Positives = 42/89 (47%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG       +  I V +LS +  +  L   F  + S S   +  D+ TG+S+GF F+SF
Sbjct: 5   SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
             ++DA  AI  ++G       +   WA 
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVEWAK 93

>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 = 83.8 bits (208), Expect = 2e-20
 Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 6/102 (5%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+  P        ++ V N+     E  LQE+F   G +    L + DK++     + F
Sbjct: 3   SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAK-DKTTGQSKGFAF 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           I +  R  AA AI  ++G       + V WA  S     +SG
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.6 bits (153), Expect = 9e-13
 Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 11/86 (12%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
                   T+ V NL+ +  + DL   F   G+  I  + + +D      KGF F+ +  
Sbjct: 9   NRRADDNATIRVTNLSEDTRETDLQELFRPFGS--ISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
             +AA AI   +           + V
Sbjct: 67  REDAARAIAGVSGFG---YDHLILNV 89

>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 =  108 bits (273), Expect = 1e-29
 Identities = 26/90 (28%), Positives = 46/90 (51%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           A+G +++     N+F+  L  E  D  L   F  + +   A+V  D++T  S+ FGFVS+
Sbjct: 15  AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N   AQ+AI  + G  +G ++++      
Sbjct: 75  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>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 = 70.0 bits (172), Expect = 3e-15
 Identities = 27/103 (26%), Positives = 44/103 (42%), Gaps = 12/103 (11%)

Query: 240 TNGSSEDGKETTNTEAPENN-PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR 298
           ++GSS   +++      +   P+   +++ +L  E    DL + F   G   +   +V  
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGN--VVSAKVFI 59

Query: 299 D------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           D      K FGFV Y     A  AIQ  N  Q   +  K++KV
Sbjct: 60  DKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ---IGMKRLKV 99

>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 = 67.0 bits (164), Expect = 3e-14
 Identities = 23/111 (20%), Positives = 44/111 (39%), Gaps = 12/111 (10%)

Query: 31  PGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR 90
            GL              P G +      +++ ++  +  +  L ++F   G V   K+  
Sbjct: 6   SGLTQQSIGAAGSQKEGPEGAN------LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI 59

Query: 91  KDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
            DK +     +GF+ Y +  SA  AI S+NG  +  + +KV    +    +
Sbjct: 60  -DKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109

>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 =  107 bits (269), Expect = 3e-29
 Identities = 22/89 (24%), Positives = 49/89 (55%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +++G +  + T+  +    S      + ++M+D +TGRS+G+ F+ FR+ + + SA+ +
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSS 231
           L G  LGSR ++C +++    +    +  
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 80.4 bits (199), Expect = 3e-19
 Identities = 28/98 (28%), Positives = 46/98 (46%), Gaps = 10/98 (10%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSA 107
           PS  R VY+G+I    TE  + ++ S+ GPV   K++  D  +     Y FI + D  S+
Sbjct: 1   PS--RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF-DPQTGRSKGYAFIEFRDLESS 57

Query: 108 AMAILSLNGRHLFGQPIKVNWA--YASGQREDTSGHFN 143
           A A+ +LNG  L  + +K  ++             H +
Sbjct: 58  ASAVRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
             VY+G++  + T+  +     +   G +  +++  D      KG+ F+ +     +A A
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSN--VGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           ++  N  Q   L  + +K 
Sbjct: 61  VRNLNGYQ---LGSRFLKC 76

>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 =  107 bits (268), Expect = 5e-29
 Identities = 33/97 (34%), Positives = 52/97 (53%), Gaps = 6/97 (6%)

Query: 240 TNGSSEDGKETTNTE-APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR 298
           ++GSS + K+    +   +++P+  TVY G +A  +T   + + F   G   I E+RV  
Sbjct: 2   SSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ--IMEIRVFP 59

Query: 299 DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           +KG+ FVR+STH  AA AI   N T    + G  +K 
Sbjct: 60  EKGYSFVRFSTHESAAHAIVSVNGTT---IEGHVVKC 93

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 86.6 bits (215), Expect = 2e-21
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
                +VY G I + +T+ L+++ FS  G +   ++   +K  Y F+ +    SAA AI+
Sbjct: 22  SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKG-YSFVRFSTHESAAHAIV 79

Query: 113 SLNGRHLFGQPIKVNWA 129
           S+NG  + G  +K  W 
Sbjct: 80  SVNGTTIEGHVVKCYWG 96

>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 = 80.1 bits (198), Expect = 5e-19
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 6/101 (5%)

Query: 130 YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVS 189
           +     + +  +  ++ G ++  +TD  +   FS +    + RV         +G+ FV 
Sbjct: 14  FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVR 67

Query: 190 FRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
           F   + A  AI  + G  +    ++C W  +         S
Sbjct: 68  FSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSS 108

>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 =  105 bits (264), Expect = 1e-28
 Identities = 19/98 (19%), Positives = 47/98 (47%), Gaps = 5/98 (5%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVY-PSCSDARVMWDQKTGRSRGFGFVSFR 191
           G    +    ++++GDL P + +  +   F+    +    +++ ++ TG   G+ FV F 
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 192 NQQDAQSAINDLTGKWLG----SRQIRCNWATKGAGNN 225
           +   A+  ++ + GK L     +++ + N+AT    ++
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSS 98

>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 = 76.6 bits (189), Expect = 8e-18
 Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 11/88 (12%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSS-----YGFIHYFDRRSAAMA 110
            S+++G++   + E  +   F++ G  V   K+IR ++ +     Y F+ + D  +A   
Sbjct: 10  ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIR-NRLTGIPAGYCFVEFADLATAEKC 68

Query: 111 ILSLNGRHLFG----QPIKVNWAYASGQ 134
           +  +NG+ L G    +  K+N+A  SG 
Sbjct: 69  LHKINGKPLPGATPAKRFKLNYATYSGP 96

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 15/70 (21%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHA 311
           ++    ++++G+L P + +  + R F ++G  V+  V++ R+       G+ FV ++  A
Sbjct: 5   SSGMAASLWMGDLEPYMDENFISRAFATMGETVM-SVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 312 EAALAIQMGN 321
            A   +   N
Sbjct: 64  TAEKCLHKIN 73

>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 =  105 bits (264), Expect = 6e-28
 Identities = 26/87 (29%), Positives = 42/87 (48%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
               D  G  ++ V +L+   +  TL   F  Y    D  +  D+ T  SRGF FV F +
Sbjct: 62  HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWAT 219
           ++DA+ A++ + G  L  R++R   A 
Sbjct: 122 KRDAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 71.8 bits (176), Expect = 2e-15
 Identities = 23/101 (22%), Positives = 45/101 (44%), Gaps = 8/101 (7%)

Query: 36  APQIEPIPSGNLPPG--FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK 93
           A +   +  G+       D     S+ V N+  + +   L+ VF   G V    + R D+
Sbjct: 48  ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR-DR 106

Query: 94  SS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            +     + F+ + D+R A  A+ +++G  L G+ ++V  A
Sbjct: 107 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147

>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 = 63.7 bits (155), Expect = 1e-12
 Identities = 29/137 (21%), Positives = 51/137 (37%), Gaps = 26/137 (18%)

Query: 220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQ---------------YTT 264
           KG    E   ++ A+ V +     +    E T  +A +                    T+
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           + V NL    +   L R F   G   + +V + RD      +GF FVR+    +A  A+ 
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGR--VGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 319 MGNTTQSSYLFGKQMKV 335
             +      L G++++V
Sbjct: 131 AMDGAV---LDGRELRV 144

>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 =  103 bits (258), Expect = 1e-27
 Identities = 26/91 (28%), Positives = 49/91 (53%)

Query: 129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
           A A+  ++ ++G   ++VG L   +T+  L   F  +      ++M D +TGRS+G+GF+
Sbjct: 14  AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
           +F + + A+ A+  L G  L  R ++    T
Sbjct: 74  TFSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>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 = 70.8 bits (174), Expect = 1e-15
 Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 8/92 (8%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YG 97
            + NL  G        +YVG++H  +TE +L+ +F   G +E  +L+  D  +     YG
Sbjct: 15  MANNLQKGSAGPM--RLYVGSLHFNITEDMLRGIFEPFGRIESIQLM-MDSETGRSKGYG 71

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           FI + D   A  A+  LNG  L G+P+KV   
Sbjct: 72  FITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>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 = 58.9 bits (143), Expect = 3e-11
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
             +YVG+L   +T+  L   F   G   IE +++  D      KG+GF+ +S    A  A
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGR--IESIQLMMDSETGRSKGYGFITFSDSECAKKA 84

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           ++  N  +   L G+ MKV
Sbjct: 85  LEQLNGFE---LAGRPMKV 100

>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 =  102 bits (255), Expect = 6e-27
 Identities = 30/93 (32%), Positives = 46/93 (49%)

Query: 127 NWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFG 186
             +   G R +   +  + V  LS   T+  L   FS Y   +D  +++DQ++ RSRGF 
Sbjct: 32  RGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91

Query: 187 FVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
           FV F N  DA+ A     G  L  R+IR +++ 
Sbjct: 92  FVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

>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 = 69.4 bits (170), Expect = 7e-15
 Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YG 97
                    DP+ C  + V  +    TE  L+EVFS  GP+    ++  D+ S     + 
Sbjct: 35  RHVGNRANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVY-DQQSRRSRGFA 91

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           F+++ +   A  A    NG  L G+ I+V+++
Sbjct: 92  FVYFENVDDAKEAKERANGMELDGRRIRVDFS 123

>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 = 60.9 bits (148), Expect = 9e-12
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 11/101 (10%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD- 299
            G  + G+ + +     N      + V  L+   T+ DL   F   G   I +V +  D 
Sbjct: 25  TGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGP--IADVSIVYDQ 82

Query: 300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                +GF FV +    +A  A +  N      L G++++V
Sbjct: 83  QSRRSRGFAFVYFENVDDAKEAKERAN---GMELDGRRIRV 120

>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 =  100 bits (252), Expect = 7e-27
 Identities = 25/91 (27%), Positives = 47/91 (51%), Gaps = 5/91 (5%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            S    +Y+GN+   VT   L+++F         +++   KS Y F+ Y D+  A  AI 
Sbjct: 5   SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIE 62

Query: 113 SLNGR-HLFGQPIKVNWAYASGQRED--TSG 140
           +L+G+  L G+ ++V+++ +   R    +SG
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKKLRSSGPSSG 93

>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 = 76.5 bits (189), Expect = 7e-18
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 8/97 (8%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
             +SG   +++G+LSP VT   L   F           +   +     G+ FV + +Q  
Sbjct: 3   SGSSGMNKLYIGNLSPAVTADDLRQLFGDR-----KLPL-AGQVLLKSGYAFVDYPDQNW 56

Query: 196 AQSAINDLTGKW-LGSRQIRCNWATKGAGNNEDKQSS 231
           A  AI  L+GK  L  + +  +++           SS
Sbjct: 57  AIRAIETLSGKVELHGKIMEVDYS-VSKKLRSSGPSS 92

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 71.1 bits (175), Expect = 7e-16
 Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
             +Y+GNL+P VT  DL + F      +    +V    G+ FV Y     A  AI+  + 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGD--RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS- 65

Query: 323 TQSSYLFGKQMKV 335
                L GK M+V
Sbjct: 66  -GKVELHGKIMEV 77

>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 =  100 bits (252), Expect = 8e-27
 Identities = 25/89 (28%), Positives = 46/89 (51%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG   + +    ++VG L  +V++  L+  F       +  +  D+ TG+ +G+GFV F
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            +++DA  AI  +    L  + IR N A+
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKAS 93

>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 = 91.6 bits (228), Expect = 2e-23
 Identities = 32/103 (31%), Positives = 52/103 (50%), Gaps = 6/103 (5%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+  P  + +   +VYVG +  +V+EPLL E+F   GPV    + + D+ +     YGF
Sbjct: 3   SGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK-DRVTGQHQGYGF 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
           + +     A  AI  ++   L+G+PI+VN A A  +       
Sbjct: 62  VEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 68.4 bits (168), Expect = 9e-15
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 11/86 (12%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
                Q  TVYVG L  +V++  L   F    AG +    + +D      +G+GFV + +
Sbjct: 9   ISERNQDATVYVGGLDEKVSEPLLWELFLQ--AGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
             +A  AI++ +  +   L+GK ++V
Sbjct: 67  EEDADYAIKIMDMIK---LYGKPIRV 89

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  101 bits (253), Expect = 1e-26
 Identities = 27/91 (29%), Positives = 43/91 (47%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
                 D  G  ++ V +L+   +  TL   F  Y    D  +  D+ T  SRGF FV F
Sbjct: 37  YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
            +++DA+ A++ + G  L  R++R   A  G
Sbjct: 97  HDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 69.8 bits (171), Expect = 6e-15
 Identities = 23/108 (21%), Positives = 45/108 (41%), Gaps = 6/108 (5%)

Query: 27  SLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC 86
             +   +    Q+         P  D     S+ V N+  + +   L+ VF   G V   
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 87  KLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            + R D+ +     + F+ + D+R A  A+ +++G  L G+ ++V  A
Sbjct: 78  YIPR-DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 61.3 bits (149), Expect = 6e-12
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 11/101 (10%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD- 299
            G        +    P +    T++ V NL    +   L R F   G   + +V + RD 
Sbjct: 26  GGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGR--VGDVYIPRDR 83

Query: 300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                +GF FVR+    +A  A+   +      L G++++V
Sbjct: 84  YTKESRGFAFVRFHDKRDAEDAMDAMDGAV---LDGRELRV 121

>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 =  100 bits (251), Expect = 1e-26
 Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 3/89 (3%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG    +     +FV  LS + T+ TL   F        AR++ D++TG S+GFGFV F
Sbjct: 5   SSGPNARSQPSKTLFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDF 61

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            +++DA++A   +    +   ++  +WA 
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 18/97 (18%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+  P       ++++V  +    TE  L+E F         +++  D+ +     +GF
Sbjct: 3   SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIV-TDRETGSSKGFGF 58

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
           + +     A  A  ++    + G  + ++WA   G+ 
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 14/90 (15%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFV 305
           ++     +    T++V  L+ + T+  L   F           R+  D      KGFGFV
Sbjct: 5   SSGPNARSQPSKTLFVKGLSEDTTEETLKESF-----DGSVRARIVTDRETGSSKGFGFV 59

Query: 306 RYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            +++  +A  A +     +   + G ++ +
Sbjct: 60  DFNSEEDAKAAKEAMEDGE---IDGNKVTL 86

>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 =  101 bits (252), Expect = 8e-26
 Identities = 29/193 (15%), Positives = 61/193 (31%), Gaps = 12/193 (6%)

Query: 139 SGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +    + V  L    +    +F  F +Y +    + M         G   V   +     
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVD 56

Query: 198 SAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPE 257
            AI  L   ++  +++    + + A         +  S        S + + +T  +A +
Sbjct: 57  RAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAK 116

Query: 258 NN--PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV----QRDKGFGFVRYSTHA 311
           N        ++  N   EVT+ +       LG      V+V          G + + + +
Sbjct: 117 NRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176

Query: 312 EAALAIQMGNTTQ 324
           +A   +   N  Q
Sbjct: 177 DALETLGFLNHYQ 189

>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 =  100 bits (249), Expect = 2e-25
 Identities = 28/197 (14%), Positives = 50/197 (25%), Gaps = 36/197 (18%)

Query: 59  VYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
           + V  +    +    +  VF   G VE  K   K K     +   D  +   AI  LN  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVK-FMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 118 HLFGQPIKVNWAY----------------------------------ASGQREDTSGHFN 143
            +FGQ + V  +                                    + +         
Sbjct: 66  FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV 125

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +   +   EVT+   F             V            G + + ++ DA   +  L
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 204 TGKWLGSRQIRCNWATK 220
               + +      +  K
Sbjct: 186 NHYQMKNPNGPYPYTLK 202

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 58.6 bits (141), Expect = 2e-10
 Identities = 17/137 (12%), Positives = 38/137 (27%), Gaps = 10/137 (7%)

Query: 1   MQHQRLKQQQ------QQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPS 54
           + +  +  Q+      +Q      Q   L+  S  +     +                  
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121

Query: 55  TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI----RKDKSSYGFIHYFDRRSAAMA 110
               ++  N   +VTE    E+    G      +     + ++SS G + +  +  A   
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 111 ILSLNGRHLFGQPIKVN 127
           +  LN   +        
Sbjct: 182 LGFLNHYQMKNPNGPYP 198

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 99.0 bits (247), Expect = 1e-25
 Identities = 26/125 (20%), Positives = 50/125 (40%), Gaps = 7/125 (5%)

Query: 94  SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEV 153
           S    +  +D       +  L  +     P        +    +     N+ V  +   V
Sbjct: 2   SQIPLVSQYDPYGQTAQLQQLQQQQQQHIP-------PTQMNPEPDVLRNLMVNYIPTTV 54

Query: 154 TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI 213
            +  L   F  Y      +++ D++T +SRG+GFV F++   AQ AI  L G  + ++++
Sbjct: 55  DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL 114

Query: 214 RCNWA 218
           +   A
Sbjct: 115 KVALA 119

>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 = 83.6 bits (207), Expect = 6e-20
 Identities = 37/131 (28%), Positives = 61/131 (46%), Gaps = 9/131 (6%)

Query: 18  MQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGF---DPSTCRSVYVGNIHTQVTEPLLQ 74
           M Q  L  Q   +       Q++     ++PP     +P   R++ V  I T V E  L+
Sbjct: 1   MSQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLR 60

Query: 75  EVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           ++F   GP+E  K++  D+ +     YGF+ +    SA  AI  LNG ++  + +KV  A
Sbjct: 61  QLFERYGPIESVKIVC-DRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

Query: 130 YASGQREDTSG 140
            +  QR   +G
Sbjct: 120 ASGHQRPGIAG 130

>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 = 67.5 bits (165), Expect = 5e-14
 Identities = 23/113 (20%), Positives = 43/113 (38%), Gaps = 11/113 (9%)

Query: 229 QSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA 288
           Q        +L     +  +    T+          + V  +   V ++ L + F   G 
Sbjct: 9   QYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGP 68

Query: 289 GVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
             IE V++  D      +G+GFV++ + + A  AI   N      +  K++KV
Sbjct: 69  --IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN---ILNKRLKV 116

>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 = 97.2 bits (243), Expect = 1e-25
 Identities = 26/82 (31%), Positives = 43/82 (52%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   ++VG L   +T+  L   F  +    +  +M D  TGRS+G+GF++F + + A+
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 198 SAINDLTGKWLGSRQIRCNWAT 219
            A+  L G  L  R +R    T
Sbjct: 62  RALEQLNGFELAGRPMRVGHVT 83

>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 = 70.7 bits (174), Expect = 9e-16
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
            +YVG++H  +TE +L+ +F   G ++   L+ KD  +     YGFI + D   A  A+ 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLM-KDSDTGRSKGYGFITFSDSECARRALE 65

Query: 113 SLNGRHLFGQPIKVNWA 129
            LNG  L G+P++V   
Sbjct: 66  QLNGFELAGRPMRVGHV 82

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 60.6 bits (148), Expect = 4e-12
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 11/79 (13%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
           + +YVG+L   +T+  L   F   G   I+ + + +D      KG+GF+ +S    A  A
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGK--IDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           ++  N  +   L G+ M+V
Sbjct: 64  LEQLNGFE---LAGRPMRV 79

>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 = 96.7 bits (241), Expect = 5e-25
 Identities = 23/111 (20%), Positives = 47/111 (42%), Gaps = 6/111 (5%)

Query: 131 ASGQREDTSGH------FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRG 184
           +  Q  D  G       + +FV  +  E T+  +   F+ Y    +  +  D++TG  +G
Sbjct: 6   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65

Query: 185 FGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
           +  V +   ++AQ+A+  L G+ L  + I  +W          ++    +S
Sbjct: 66  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRS 116

>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 = 73.9 bits (182), Expect = 1e-16
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
            ++V  +H + TE  + + F+  G ++   L   D+ +     Y  + Y   + A  A+ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL-DRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSG 140
            LNG+ L GQPI V+W +  G  +    
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRR 110

>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 = 59.7 bits (145), Expect = 2e-11
 Identities = 22/100 (22%), Positives = 43/100 (43%), Gaps = 11/100 (11%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
              +  ++  +   P+ + +   ++V  +  E T+ D+H  F   G   I+ + +  D  
Sbjct: 2   EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDRR 59

Query: 300 ----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
               KG+  V Y T+ EA  A++  N      L G+ + V
Sbjct: 60  TGYLKGYTLVEYETYKEAQAAMEGLNGQD---LMGQPISV 96

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 95.4 bits (238), Expect = 7e-25
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 132 SGQREDTSGH-FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           SG     +     ++V +L   +T+  L+  FS Y       +M D+ T +S+G  F+ F
Sbjct: 6   SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            ++  AQ+    +  K L  R I+ + A
Sbjct: 66  LDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 76.9 bits (190), Expect = 5e-18
 Identities = 29/92 (31%), Positives = 44/92 (47%), Gaps = 7/92 (7%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YG 97
            S  +  G  PS   +VYV N+   +T   L  +FS  G V    ++ KDK +       
Sbjct: 4   GSSGMSGGLAPSK-STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIM-KDKDTRKSKGVA 61

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           FI + D+ SA     ++N + LFG+ IK + A
Sbjct: 62  FILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 66.5 bits (163), Expect = 3e-14
 Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 11/95 (11%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------K 300
           G   ++  +    P  +TVYV NL   +T  DL+R F   G   + +V + +D      K
Sbjct: 1   GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGK--VVKVTIMKDKDTRKSK 58

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           G  F+ +     A    +  N  Q   LFG+ +K 
Sbjct: 59  GVAFILFLDKDSAQNCTRAINNKQ---LFGRVIKA 90

>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 =  100 bits (250), Expect = 8e-25
 Identities = 38/291 (13%), Positives = 84/291 (28%), Gaps = 33/291 (11%)

Query: 56  CRSVYVGNIHTQVTEP----LLQEVFSSTGPVEGCKLIRKDKSS-YGFIHYFDRRSAAMA 110
             ++Y+ N++ ++ +      L  +FS  G +    + R  K     F+ + +  SA  A
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD 170
           + S+ G   + +P+++ +A                       +                 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDI-----------------IAKMKGTFVERDRKREKR 111

Query: 171 ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
                +    +    G  +       Q  +  +       R +                 
Sbjct: 112 KPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIP 171

Query: 231 SDAKSVVELTNGSSEDGKETTNTEAPENN----PQYTTVYVGNLAPEVTQLDLHRHFHSL 286
               +  ++  G+    +       P       P    +++ NL  E  +L L   F+  
Sbjct: 172 PPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQF 231

Query: 287 GAGVIEEVRVQRDK-GFGFVRYSTHAEAALAIQMGNTTQSSYLF-GKQMKV 335
                +EVR+   +    FV +    +A  A       Q   +     MK+
Sbjct: 232 PG--FKEVRLVPGRHDIAFVEFDNEVQAGAARD---ALQGFKITQNNAMKI 277

>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 = 95.4 bits (238), Expect = 9e-25
 Identities = 25/91 (27%), Positives = 39/91 (42%)

Query: 135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
             D  G   + V +L+   +  +L   F  Y    D  +  +  T   RGF FV F +++
Sbjct: 7   GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 195 DAQSAINDLTGKWLGSRQIRCNWATKGAGNN 225
           DAQ A   + G  L  R++R   A  G  + 
Sbjct: 67  DAQDAEAAMDGAELDGRELRVQVARYGRRDL 97

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 26/103 (25%), Positives = 46/103 (44%), Gaps = 10/103 (9%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YG 97
            SG+  P  D     ++ V N+  + +   L+ VF   G V    +  ++  +     + 
Sbjct: 2   SSGSSGPDVDGMI--TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIP-REPHTKAPRGFA 58

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           F+ + DRR A  A  +++G  L G+ ++V    A   R D SG
Sbjct: 59  FVRFHDRRDAQDAEAAMDGAELDGRELRVQ--VARYGRRDLSG 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 = 59.9 bits (146), Expect = 8e-12
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 11/87 (12%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYS 308
           +  +     T+ V NL    +   L R F   G   + +V + R+      +GF FVR+ 
Sbjct: 6   SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGR--VGDVYIPREPHTKAPRGFAFVRFH 63

Query: 309 THAEAALAIQMGNTTQSSYLFGKQMKV 335
              +A  A    +  +   L G++++V
Sbjct: 64  DRRDAQDAEAAMDGAE---LDGRELRV 87

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 95.1 bits (237), Expect = 1e-24
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 5/89 (5%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVR 306
             +  +       P+ TT Y+GN+    T+ DL   F + G   I + +   +KG  F++
Sbjct: 12  NPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGF--ILDFKHYPEKGCCFIK 69

Query: 307 YSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           Y TH +AA+ I            G+ ++ 
Sbjct: 70  YDTHEQAAVCIVALANFP---FQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 93.1 bits (232), Expect = 6e-24
 Identities = 24/95 (25%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS 94
             PQ+ P    ++     P    + Y+GNI    TE  L  +F + G +   K    +K 
Sbjct: 7   LPPQVNPQAVDHIIRSAPPRVT-TAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKG 64

Query: 95  SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
              FI Y     AA+ I++L      G+ ++  W 
Sbjct: 65  -CCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG 98

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 78.5 bits (194), Expect = 2e-18
 Identities = 21/104 (20%), Positives = 34/104 (32%), Gaps = 7/104 (6%)

Query: 116 GRHLFGQPIKVNW-AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVM 174
           G    G P +VN  A     R         ++G++    T+A L   F  +    D +  
Sbjct: 1   GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY 60

Query: 175 WDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
                   +G  F+ +   + A   I  L       R +R  W 
Sbjct: 61  ------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG 98

>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 = 94.2 bits (235), Expect = 2e-24
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 1/91 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +            +FVG+L   V +  L+  F      +   +  D + G+ + FGFV F
Sbjct: 6   SGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
           ++ +    AI  L G  L  R I  +  + G
Sbjct: 65  KHPESVSYAIALLNGIRLYGRPINVSGPSSG 95

>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 = 86.9 bits (216), Expect = 9e-22
 Identities = 32/95 (33%), Positives = 50/95 (52%), Gaps = 8/95 (8%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGF 98
            SG  P   +    R+V+VGN+  +V E +L E+F   GP+    +  KD+      +GF
Sbjct: 5   SSGMFPAQEEAD--RTVFVGNLEARVREEILYELFLQAGPLTKVTIC-KDREGKPKSFGF 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG 133
           + +    S + AI  LNG  L+G+PI V+   +SG
Sbjct: 62  VCFKHPESVSYAIALLNGIRLYGRPINVSGP-SSG 95

>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 = 73.4 bits (181), Expect = 1e-16
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 10/94 (10%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KG 301
           G   ++   P       TV+VGNL   V +  L+  F    AG + +V + +D     K 
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQ--AGPLTKVTICKDREGKPKS 58

Query: 302 FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           FGFV +      + AI + N  +   L+G+ + V
Sbjct: 59  FGFVCFKHPESVSYAIALLNGIR---LYGRPINV 89

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 94.2 bits (235), Expect = 2e-24
 Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 131 ASGQREDTSGH------FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRG 184
           +  Q  D  G       + +FV  +  E T+  +   F+ Y    +  +  D++TG  +G
Sbjct: 7   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66

Query: 185 FGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
           +  V +   ++AQ+A+  L G+ L  + I  +W  
Sbjct: 67  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
            ++V  +H + TE  + + F+  G ++   L   D+ +     Y  + Y   + A  A+ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL-DRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 113 SLNGRHLFGQPIKVNWA 129
            LNG+ L GQPI V+W 
Sbjct: 84  GLNGQDLMGQPISVDWC 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 11/101 (10%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD- 299
               +  ++  +   P+ + +   ++V  +  E T+ D+H  F   G   I+ + +  D 
Sbjct: 2   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLDR 59

Query: 300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                KG+  V Y T+ EA  A++  N      L G+ + V
Sbjct: 60  RTGYLKGYTLVEYETYKEAQAAMEGLNGQD---LMGQPISV 97

>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 = 93.5 bits (233), Expect = 5e-24
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 6/92 (6%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  +  +    +FVG+L P++T+  +   F  Y    +  +       + +GFGF+  
Sbjct: 5   SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRL 58

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
             +  A+ A  +L    L  +Q+R  +A   A
Sbjct: 59  ETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 90

>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 = 86.9 bits (216), Expect = 1e-21
 Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 5/86 (5%)

Query: 250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYST 309
           + ++   +   Q + ++VGNL P++T+ ++ + F   G     EV + +DKGFGF+R  T
Sbjct: 3   SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGK--AGEVFIHKDKGFGFIRLET 60

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
              A +A    +      L GKQ++V
Sbjct: 61  RTLAEIAKVELDNMP---LRGKQLRV 83

>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 = 83.5 bits (207), Expect = 2e-20
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 2/93 (2%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFD 103
           SG+       +    ++VGN+   +TE  ++++F   G      + + DK  +GFI    
Sbjct: 3   SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-DKG-FGFIRLET 60

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
           R  A +A + L+   L G+ ++V +A  S    
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRFACHSASLT 93

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 93.5 bits (233), Expect = 5e-24
 Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  E  S    + V ++     D  L   F  +    D  ++++     S+GFGFV+F
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTF 62

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N  DA  A   L G  +  R+I  N AT 
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATA 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 = 78.9 bits (195), Expect = 1e-18
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 2/100 (2%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHY 101
           SG+       ST + ++V NI  +  +P L+++F   G +   ++I  ++ S  +GF+ +
Sbjct: 3   SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
            +   A  A   L+G  + G+ I+VN A A          
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.8 bits (161), Expect = 8e-14
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 9/87 (10%)

Query: 253 TEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYS 308
           +   E+      ++V N+       DL + F   G   I +V +  +    KGFGFV + 
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK--ILDVEIIFNERGSKGFGFVTFE 63

Query: 309 THAEAALAIQMGNTTQSSYLFGKQMKV 335
             A+A  A +  + T    + G++++V
Sbjct: 64  NSADADRAREKLHGTV---VEGRKIEV 87

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 93.8 bits (233), Expect = 1e-23
 Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 2/110 (1%)

Query: 129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFG 186
           A         +    ++VG  S   TD  L             + +   ++  G+S+G+ 
Sbjct: 43  AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA 102

Query: 187 FVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSV 236
            V   ++      +  L GK L   ++    AT+   +  + Q+   + V
Sbjct: 103 EVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECV 152

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 63.0 bits (153), Expect = 3e-12
 Identities = 19/102 (18%), Positives = 37/102 (36%), Gaps = 8/102 (7%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE--GCKLIRKD 92
           +       P+         +   +VYVG+     T+  L +V  S G  +    K   ++
Sbjct: 34  SPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFA-EN 92

Query: 93  KSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +++     Y  +      S    +  L G+ L G+ + V  A
Sbjct: 93  RANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 59.9 bits (145), Expect = 3e-11
 Identities = 18/121 (14%), Positives = 40/121 (33%), Gaps = 9/121 (7%)

Query: 221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLH 280
           G  N   +       V +  +    +              +   VYVG+ +   T   L 
Sbjct: 14  GTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLI 73

Query: 281 RHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK 334
           +   S+G   + E++   +      KG+  V  ++       +++        L G+++ 
Sbjct: 74  QVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKV---LNGEKVD 130

Query: 335 V 335
           V
Sbjct: 131 V 131

>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 = 92.4 bits (230), Expect = 1e-23
 Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 6/95 (6%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG   D +    +F+ +LS +  +  L      +      RV+    T  S+G  F  F
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 191 RNQQDAQSAINDL------TGKWLGSRQIRCNWAT 219
             Q+ AQ  +          G  L  RQ++ + A 
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 99

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 18/97 (18%), Positives = 40/97 (41%), Gaps = 12/97 (12%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+     D +  ++V++ N+     E  L EV    G ++  +++     +       F
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV-LHPDTEHSKGCAF 61

Query: 99  IHYFDRRSAAMAILSLN------GRHLFGQPIKVNWA 129
             +  + +A   + + +      G  L G+ +KV+ A
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 98

>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 = 62.4 bits (152), Expect = 2e-12
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 11/92 (11%)

Query: 253 TEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVR 306
           +  P +  +  TV++ NL+ +  +  L       G   ++ VRV         KG  F +
Sbjct: 6   SGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGD--LKYVRVVLHPDTEHSKGCAFAQ 63

Query: 307 YSTHAEAALAIQMGNTTQSS---YLFGKQMKV 335
           + T   A   +   +         L G+Q+KV
Sbjct: 64  FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV 95

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 90.7 bits (226), Expect = 3e-23
 Identities = 19/79 (24%), Positives = 36/79 (45%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   +++  L P  TD  L      Y      + + D+ T + +G+GFV F +   AQ
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 198 SAINDLTGKWLGSRQIRCN 216
            A+  L    + ++  + +
Sbjct: 62  KAVTALKASGVQAQMAKQS 80

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 63.3 bits (155), Expect = 3e-13
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAE 312
           +   + +Y+  L P  T  DL +     G   I   +   D      KG+GFV + + + 
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGK--IVSTKAILDKTTNKCKGYGFVDFDSPSA 59

Query: 313 AALAIQMGNTTQSSYLFGKQMKV 335
           A  A+     +    +  +  K 
Sbjct: 60  AQKAVTALKASG---VQAQMAKQ 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 63.3 bits (155), Expect = 4e-13
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSA 107
            S    +Y+  +    T+  L ++    G +   K I  DK++     YGF+ +    +A
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI-LDKTTNKCKGYGFVDFDSPSAA 60

Query: 108 AMAILSLNGRHLFGQPIKVN 127
             A+ +L    +  Q  K +
Sbjct: 61  QKAVTALKASGVQAQMAKQS 80

>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 = 5e-23
 Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
             S+ + +YV N+    +E ++++ F++  P    + ++K +  Y F+H+ +R  A  A+
Sbjct: 11  TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRD-YAFVHFSNREDAVEAM 68

Query: 112 LSLNGRHLFGQPIKVNWA 129
            +LNG+ L G PI+V  A
Sbjct: 69  KALNGKVLDGSPIEVTLA 86

>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 = 82.7 bits (205), Expect = 5e-20
 Identities = 27/105 (25%), Positives = 42/105 (40%), Gaps = 11/105 (10%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  +  S    ++V +L    ++  +   F+     +  RV       + R + FV F
Sbjct: 5   SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHF 58

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
            N++DA  A+  L GK L    I    A        DK SS   S
Sbjct: 59  SNREDAVEAMKALNGKVLDGSPIEVTLAKPV-----DKDSSGPSS 98

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 71.5 bits (176), Expect = 5e-16
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 11/94 (11%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG 301
           GSS    +       +       +YV NL    ++  + + F+++  G +   RV++ + 
Sbjct: 1   GSSGSSGD------EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAV--ERVKKIRD 52

Query: 302 FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           + FV +S   +A  A++  N      L G  ++V
Sbjct: 53  YAFVHFSNREDAVEAMKALNGKV---LDGSPIEV 83

>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 = 92.6 bits (230), Expect = 6e-23
 Identities = 18/92 (19%), Positives = 36/92 (39%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FV  +  E  +  +   F  Y    +  +  D++TG S+G+  V +   + A +A   
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAK 234
           L G  +  + I+ +W          K     +
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165

>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 = 83.3 bits (206), Expect = 2e-19
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 9/106 (8%)

Query: 43  PSGNLPPGFDPSTCR---SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---- 95
              +      P        ++V +IH +  E  +QE F   G ++   L   D+ +    
Sbjct: 56  NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL-DRRTGFSK 114

Query: 96  -YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
            Y  + Y   + A  A  +LNG  + GQ I+V+W +  G +     
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 = 68.3 bits (167), Expect = 4e-14
 Identities = 24/124 (19%), Positives = 50/124 (40%), Gaps = 13/124 (10%)

Query: 218 ATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQL 277
           A    G      S+  +++       +ED  E      P+ + +   ++V ++  E  + 
Sbjct: 30  AKHRKGRGFGSDSNTREAIHSYERVRNEDDDE--LEPGPQRSVEGWILFVTSIHEEAQED 87

Query: 278 DLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGK 331
           ++   F   G   I+ + +  D      KG+  V Y TH +A  A +  N  +   + G+
Sbjct: 88  EIQEKFCDYGE--IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE---IMGQ 142

Query: 332 QMKV 335
            ++V
Sbjct: 143 TIQV 146

>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 = 89.6 bits (223), Expect = 7e-23
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHA 311
           ++ +   +   TT+YVG L   +T+ DL  HF+  G   I  + V + +   F++++T  
Sbjct: 2   SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGE--IRTITVVQRQQCAFIQFATRQ 59

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
            A +A +   +     + G+++ V
Sbjct: 60  AAEVAAE--KSFNKLIVNGRRLNV 81

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 81.9 bits (203), Expect = 6e-20
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 4/86 (4%)

Query: 45  GNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDR 104
            +   G D +   ++YVG +   +TE  L+  F   G +    +++  +    FI +  R
Sbjct: 2   SSGSSGEDKTI-TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ--RQQCAFIQFATR 58

Query: 105 RSAAMAIL-SLNGRHLFGQPIKVNWA 129
           ++A +A   S N   + G+ + V W 
Sbjct: 59  QAAEVAAEKSFNKLIVNGRRLNVKWG 84

>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 = 61.9 bits (151), Expect = 1e-12
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 7/89 (7%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG   +      ++VG L   +T+  L   F  +       V+        +   F+ F
Sbjct: 2   SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQF 55

Query: 191 RNQQDAQSAIND-LTGKWLGSRQIRCNWA 218
             +Q A+ A         +  R++   W 
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNVKWG 84

>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 = 93.2 bits (231), Expect = 1e-22
 Identities = 16/107 (14%), Positives = 38/107 (35%), Gaps = 2/107 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFV 188
            +     T     +++G+L+   TD  L             + +   ++  G+S+GF  V
Sbjct: 58  PNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
              ++  ++  ++ L  + L  +        K   +  + QS     
Sbjct: 118 GVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQ 164

>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 = 63.6 bits (154), Expect = 5e-12
 Identities = 27/123 (21%), Positives = 43/123 (34%), Gaps = 10/123 (8%)

Query: 219 TKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLD 278
           +  A N +  +  D    +  T G         N        +   +Y+GNL    T  D
Sbjct: 26  SPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIA-LYIGNLTWWTTDED 84

Query: 279 LHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ 332
           L    HSLG   I E++   +      KGF  V   + A +   + +    +   L G+ 
Sbjct: 85  LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE---LHGQN 141

Query: 333 MKV 335
             V
Sbjct: 142 PVV 144

>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 = 60.1 bits (145), Expect = 1e-10
 Identities = 19/116 (16%), Positives = 36/116 (31%), Gaps = 10/116 (8%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRS--VYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIR 90
                + +  G  P      T +   +Y+GN+    T+  L E   S G   +   K   
Sbjct: 45  PPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFE 104

Query: 91  KDKSS-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
            ++++     +  +      S+   +  L  R L GQ   V         +     
Sbjct: 105 -NRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQS 159

>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 = 89.7 bits (223), Expect = 2e-22
 Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  +       +FV +L  +V    L   FS+      A ++ D K G+SRG G V+F
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTF 63

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
               +A  AI+   G+ L  R +      +
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDER 93

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 26/86 (30%), Positives = 35/86 (40%), Gaps = 10/86 (11%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYST 309
           A +     +TV+V NL  +V    L   F    AGV+    +  D     +G G V +  
Sbjct: 8   ALQAGRLGSTVFVANLDYKVGWKKLKEVFSM--AGVVVRADILEDKDGKSRGIGTVTFEQ 65

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
             EA  AI M N      LF + M V
Sbjct: 66  SIEAVQAISMFNGQL---LFDRPMHV 88

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 3/98 (3%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSS--YGFI 99
            SG+           +V+V N+  +V    L+EVFS  G V    ++  KD  S   G +
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRED 137
            +     A  AI   NG+ LF +P+ V     +  + D
Sbjct: 62  TFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGD 99

>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 = 91.0 bits (226), Expect = 2e-22
 Identities = 22/86 (25%), Positives = 40/86 (46%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           Q +       ++VG+LS   T+  ++  FS         +  D+    + GF FV + ++
Sbjct: 32  QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWAT 219
            DA++A+  + G  L  R IR +W  
Sbjct: 92  ADAENAMRYINGTRLDDRIIRTDWDA 117

>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 = 70.6 bits (173), Expect = 5e-15
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
            ++YVGN+    TE  + E+FS +G ++   +   DK       + F+ Y+ R  A  A+
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL-DKMKKTACGFCFVEYYSRADAENAM 98

Query: 112 LSLNGRHLFGQPIKVNWA 129
             +NG  L  + I+ +W 
Sbjct: 99  RYINGTRLDDRIIRTDWD 116

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 62.5 bits (152), Expect = 4e-12
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 11/91 (12%)

Query: 251 TNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGF 304
            N E  +   +  T+YVGNL+   T+  ++  F    +G I+++ +  D       GF F
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK--SGDIKKIIMGLDKMKKTACGFCF 85

Query: 305 VRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           V Y + A+A  A++  N T+   L  + ++ 
Sbjct: 86  VEYYSRADAENAMRYINGTR---LDDRIIRT 113

>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 = 88.4 bits (220), Expect = 3e-22
 Identities = 13/87 (14%), Positives = 35/87 (40%), Gaps = 2/87 (2%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
             +++G+L+   TD  L             + +   ++  G+S+GF  V   ++  ++  
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 200 INDLTGKWLGSRQIRCNWATKGAGNNE 226
           ++ L  + L  +      + K   ++ 
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEHHHH 88

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 9/77 (11%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQ 318
           +Y+GNL    T  DL    HSLG   I E++   +      KGF  V   + A +   + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 319 MGNTTQSSYLFGKQMKV 335
           +    +   L G+   V
Sbjct: 64  LLPKRE---LHGQNPVV 77

>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 = 60.7 bits (148), Expect = 4e-12
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 8/85 (9%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKDKSS-----YGFIHYFDRRSAAMA 110
           ++Y+GN+    T+  L E   S G   +   K   +++++     +  +      S+   
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFF-ENRANGQSKGFALVGVGSEASSKKL 61

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQR 135
           +  L  R L GQ   V  +      
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 88.5 bits (220), Expect = 3e-22
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG---RSRGFGFVSFRNQQ 194
           +SG   +F+ +L+   T+ TL   FS   +     +   +       S GFGFV ++  +
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61

Query: 195 DAQSAINDLTGKWLGSRQIRCNWATKGA 222
            AQ A+  L G  +   ++    + +  
Sbjct: 62  QAQKALKQLQGHTVDGHKLEVRISERAT 89

>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 = 67.7 bits (166), Expect = 1e-14
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-------YGFIHYFDRRSAAMA 110
            +++ N++   TE  L+ VFS  G ++ C + +K   +       +GF+ Y     A  A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQRE 136
           +  L G  + G  ++V  +  + +  
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPA 92

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 14/82 (17%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD---------KGFGFVRYSTHAEA 313
           + +++ NL    T+  L   F  +GA  I+   + +           GFGFV Y    +A
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGA--IKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
             A++         + G +++V
Sbjct: 64  QKALKQLQGHT---VDGHKLEV 82

>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 = 87.7 bits (218), Expect = 7e-22
 Identities = 23/88 (26%), Positives = 39/88 (44%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV +LS   ++  L   FS Y   S+     D  T + +GF FV+F   + A  A  ++
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSS 231
            G+    R +    +T     ++   SS
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 18/91 (19%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
            ++V N+    +E  L+++FS+ GP+        D  +     + F+ +     A  A  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYP-IDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 113 SLNGRHLFGQPIKVNWAYA---SGQREDTSG 140
            ++G+   G+ + V  +     + Q   +SG
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 11/86 (12%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
              +     ++V NL+   ++ DL + F + G   + E+    D      KGF FV +  
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGP--LSELHYPIDSLTKKPKGFAFVTFMF 59

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
              A  A    +        G+ + V
Sbjct: 60  PEHAVKAYAEVD---GQVFQGRMLHV 82

>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 = 87.0 bits (216), Expect = 1e-21
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 4/78 (5%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
             +  + ++V N+   VTE +L++ FS  G +E  K ++     Y FIH+ +R  A  A+
Sbjct: 7   GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK----DYAFIHFDERDGAVKAM 62

Query: 112 LSLNGRHLFGQPIKVNWA 129
             +NG+ L G+ I++ +A
Sbjct: 63  EEMNGKDLEGENIEIVFA 80

>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 = 80.4 bits (199), Expect = 3e-19
 Identities = 18/100 (18%), Positives = 39/100 (39%), Gaps = 8/100 (8%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S      +    +FV +L+  VT+  L   FS +      + +        + + F+ F
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHF 52

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
             +  A  A+ ++ GK L    I   +A       +++++
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKA 92

>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 = 63.1 bits (154), Expect = 6e-13
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
            +   ++V NLA  VT+  L + F   G   +E V+  +D  + F+ +     A  A++ 
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGK--LERVKKLKD--YAFIHFDERDGAVKAMEE 64

Query: 320 GNTTQSSYLFGKQMKV 335
            N      L G+ +++
Sbjct: 65  MNGKD---LEGENIEI 77

>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 = 86.5 bits (215), Expect = 2e-21
 Identities = 27/95 (28%), Positives = 50/95 (52%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++FVG++  E T+  L   FS        R+++D++TG+ +G+GF  +++Q+ A SA+ +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVV 237
           L G+    R +R + A       E K       V+
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>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 = 77.7 bits (192), Expect = 3e-18
 Identities = 35/94 (37%), Positives = 55/94 (58%), Gaps = 7/94 (7%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFD 103
           P  D S  RSV+VGNI  + TE  L+++FS  GPV   +L+  D+ +     YGF  Y D
Sbjct: 2   PAVDRSL-RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY-DRETGKPKGYGFCEYQD 59

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASGQRED 137
           + +A  A+ +LNGR   G+ ++V+ A +   +E+
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 11/86 (12%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYST 309
           P  +    +V+VGN+  E T+  L   F     G +   R+  D      KG+GF  Y  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSE--VGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
              A  A++  N  +     G+ ++V
Sbjct: 60  QETALSAMRNLNGRE---FSGRALRV 82

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 86.6 bits (215), Expect = 2e-21
 Identities = 17/76 (22%), Positives = 34/76 (44%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  +  E  +  +   F  Y    +  +  D++TG S+G+  V +   + A +A   L
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 204 TGKWLGSRQIRCNWAT 219
            G  +  + I+ +W  
Sbjct: 89  NGAEIMGQTIQVDWCF 104

>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 = 79.6 bits (197), Expect = 8e-19
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAIL 112
            ++V +IH +  E  +QE F   G ++   L   D+ +     Y  + Y   + A  A  
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL-DRRTGFSKGYALVEYETHKQALAAKE 86

Query: 113 SLNGRHLFGQPIKVNWAYASGQR 135
           +LNG  + GQ I+V+W +  G +
Sbjct: 87  ALNGAEIMGQTIQVDWCFVKGPK 109

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 60.4 bits (147), Expect = 7e-12
 Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 243 SSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--- 299
              +  +      P+ + +   ++V ++  E  + ++   F   G   I+ + +  D   
Sbjct: 7   RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGE--IKNIHLNLDRRT 64

Query: 300 ---KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
              KG+  V Y TH +A  A +  N  +   + G+ ++V
Sbjct: 65  GFSKGYALVEYETHKQALAAKEALNGAE---IMGQTIQV 100

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 86.2 bits (214), Expect = 3e-21
 Identities = 28/102 (27%), Positives = 39/102 (38%), Gaps = 2/102 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ-KTGRSRGFGFVS 189
           +SGQ         I V ++  +     +   FS +      R+      TG  RGFGFV 
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 190 FRNQQDAQSAINDLT-GKWLGSRQIRCNWATKGAGNNEDKQS 230
           F  +QDA+ A N L     L  R++   WA           S
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 71.2 bits (175), Expect = 1e-15
 Identities = 24/99 (24%), Positives = 49/99 (49%), Gaps = 9/99 (9%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG +P     S    + V NI  Q  +  ++E+FS+ G ++  +L +K   +     +GF
Sbjct: 6   SGQVPKKQTTSK---ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 99  IHYFDRRSAAMAILSL-NGRHLFGQPIKVNWAYASGQRE 136
           + +  ++ A  A  +L +  HL+G+ + + WA +    +
Sbjct: 63  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 20/97 (20%), Positives = 47/97 (48%), Gaps = 14/97 (14%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------- 299
           G   ++ + P+     + + V N+  +  Q ++   F + G   ++ VR+ +        
Sbjct: 1   GSSGSSGQVPKKQTT-SKILVRNIPFQANQREIRELFSTFGE--LKTVRLPKKMTGTGAH 57

Query: 300 KGFGFVRYSTHAEAALAIQ-MGNTTQSSYLFGKQMKV 335
           +GFGFV + T  +A  A   + +   S++L+G+++ +
Sbjct: 58  RGFGFVDFITKQDAKKAFNALCH---STHLYGRRLVL 91

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 85.5 bits (212), Expect = 4e-21
 Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 143 NIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAI 200
            I + +++P     ++    S Y   + ++ R++ D++T ++RGF FV   +  DA   +
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 201 NDLTGK----WLGSRQIRCNWATKG 221
             L        +  + I  ++A   
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAE 312
           +    T+ + N+AP      +        +  +  +R+ +D      +GF FV+ S+  +
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 313 AALAIQMGNTTQSSYLF-GKQMKV 335
           A+  +Q+  +        GK + V
Sbjct: 66  ASQLLQILQSLHPPLKIDGKTIGV 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 14/92 (15%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTG--PVEGCKLIRKDKSS-----YGFIHYFDR 104
                 ++ + NI        +    S      V   +LI+ DK +     + F+     
Sbjct: 7   HHMD--TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIK-DKQTQQNRGFAFVQLSSA 63

Query: 105 RSAAMAILSLNGRHLF----GQPIKVNWAYAS 132
             A+  +  L   H      G+ I V++A ++
Sbjct: 64  MDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 85.8 bits (213), Expect = 5e-21
 Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +    E+ S    + V ++     D  L   F  +    D  +++++    S+GFGFV+F
Sbjct: 19  SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTF 76

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N  DA  A   L G  +  R+I  N AT 
Sbjct: 77  ENSADADRAREKLHGTVVEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 72.0 bits (177), Expect = 5e-16
 Identities = 23/94 (24%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 38  QIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-- 95
               +P G+     + S  + ++V NI  +  +P L+++F   G +   ++I  ++ S  
Sbjct: 11  SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70

Query: 96  YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +GF+ + +   A  A   L+G  + G+ I+VN A
Sbjct: 71  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.5 bits (155), Expect = 5e-13
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 9/84 (10%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHA 311
            EN  Q   ++V N+       DL + F   G   I +V +  +    KGFGFV +   A
Sbjct: 23  TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGK--ILDVEIIFNERGSKGFGFVTFENSA 80

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
           +A  A +  + T    + G++++V
Sbjct: 81  DADRAREKLHGTV---VEGRKIEV 101

>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 = 84.5 bits (210), Expect = 6e-21
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWD-QKTGRSRGFGFVSFRNQQDAQSAIN 201
            + +G L+  VT   +   FS Y       +  +      S+G+ +V F N  +A+ A+ 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 202 DLTGKWLGSRQIRCNWATK 220
            + G  +  ++I       
Sbjct: 66  HMDGGQIDGQEITATAVLA 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 71.8 bits (177), Expect = 3e-16
 Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 8/89 (8%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS------YGFIHYFDRRS 106
               + V++G +   VT+  + E+FS+ G ++   +   ++        Y ++ + +   
Sbjct: 2   MKPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP-VERMHPHLSKGYAYVEFENPDE 59

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQR 135
           A  A+  ++G  + GQ I      A   R
Sbjct: 60  AEKALKHMDGGQIDGQEITATAVLAPWPR 88

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 63.7 bits (156), Expect = 3e-13
 Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 12/83 (14%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-------KGFGFVRYSTHAE 312
            + T V++G L   VT+  +   F + G   I+ + +  +       KG+ +V +    E
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGK--IKMIDMPVERMHPHLSKGYAYVEFENPDE 59

Query: 313 AALAIQMGNTTQSSYLFGKQMKV 335
           A  A++  +  Q   + G+++  
Sbjct: 60  AEKALKHMDGGQ---IDGQEITA 79

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 85.1 bits (211), Expect = 7e-21
 Identities = 13/79 (16%), Positives = 27/79 (34%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +    L+  V +  L      Y    +  ++   +T +  G   V F + + A+  + +
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 203 LTGKWLGSRQIRCNWATKG 221
           L    +    I      KG
Sbjct: 68  LHLTSVMGNIIHAQLDIKG 86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 72.4 bits (178), Expect = 4e-16
 Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 10/89 (11%)

Query: 45  GNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIH 100
           G   P       + V    ++  V E  L+++    G VE  +++   ++        + 
Sbjct: 1   GGQIPL------KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVL 54

Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +   R A   + +L+   + G  I     
Sbjct: 55  FTSTRGAKETVKNLHLTSVMGNIIHAQLD 83

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 64.7 bits (158), Expect = 2e-13
 Identities = 13/82 (15%), Positives = 24/82 (29%), Gaps = 11/82 (13%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEA 313
                V    L   V +  L       G   +EEV +          G   V +++   A
Sbjct: 4   IPLKEVTFARLNDNVRETFLKDMCRKYGE--VEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
              ++  + T    + G  +  
Sbjct: 62  KETVKNLHLTS---VMGNIIHA 80

>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 = 85.4 bits (212), Expect = 8e-21
 Identities = 32/92 (34%), Positives = 49/92 (53%), Gaps = 2/92 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
             G ++DT+    IFVG L    TDA+L   F  +    +A V+ D++TG+SRG+GFV+ 
Sbjct: 8   MHGSQKDTT-FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTM 66

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
            ++  A+ A  D     +  R+   N A  GA
Sbjct: 67  ADRAAAERACKDPNPI-IDGRKANVNLAYLGA 97

>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 = 60.0 bits (146), Expect = 1e-11
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------ 300
              ++     + +  +T ++VG L    T   L ++F   G   IEE  V  D+      
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGD--IEEAVVITDRQTGKSR 59

Query: 301 GFGFVRYSTHAEAALAIQMGN 321
           G+GFV  +  A A  A +  N
Sbjct: 60  GYGFVTMADRAAAERACKDPN 80

>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 = 57.7 bits (140), Expect = 9e-11
 Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 9/114 (7%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           S  +      +T   ++VG +    T+  L++ F   G +E   +I  D+ +     YGF
Sbjct: 5   SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVIT-DRQTGKSRGYGF 63

Query: 99  IHYFDRRSAAMAILSLNGRHLF-GQPIKVNWAYASGQREDTSGHFNIFVGDLSP 151
           +   DR +A  A    N   +  G+   VN AY   +       F I V   S 
Sbjct: 64  VTMADRAAAERACKDPN--PIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115

>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 = 85.0 bits (211), Expect = 8e-21
 Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
            G     +G   + V +L   V+DA +   F+ + +   A V +D ++GRS G   V F 
Sbjct: 21  GGGAGVETGG-KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFE 78

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            + DA  A+    G  L  R +     T
Sbjct: 79  RKADALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS-YGFIH 100
                 G    T   + V N+   V++  +QE+F+  G ++   +   R  +S     +H
Sbjct: 17  DSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVH 76

Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +  +  A  A+   NG  L G+P+ +   
Sbjct: 77  FERKADALKAMKQYNGVPLDGRPMNIQLV 105

>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 = 65.4 bits (160), Expect = 1e-13
 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 10/86 (11%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYST 309
                     + V NL   V+  D+   F   G   +++  V  D      G   V +  
Sbjct: 22  GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGT--LKKAAVHYDRSGRSLGTADVHFER 79

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
            A+A  A++  N      L G+ M +
Sbjct: 80  KADALKAMKQYNGVP---LDGRPMNI 102

>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 = 85.0 bits (211), Expect = 1e-20
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           A   ++      N+++ +L   + +  L      +      R++ D  +G SRG GF   
Sbjct: 15  AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARM 73

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            + +  ++ I    GK++ +        
Sbjct: 74  ESTEKCEAVIGHFNGKFIKTPPGVSAPT 101

>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 = 66.9 bits (164), Expect = 4e-14
 Identities = 16/86 (18%), Positives = 28/86 (32%), Gaps = 10/86 (11%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYST 309
           A +     T +Y+ NL   + + +L         G +   R+ RD     +G GF R  +
Sbjct: 18  AKQQEQDPTNLYISNLPLSMDEQELENMLKP--FGQVISTRILRDSSGTSRGVGFARMES 75

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
             +    I   N      +       
Sbjct: 76  TEKCEAVIGHFNGKF---IKTPPGVS 98

>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 = 63.8 bits (156), Expect = 5e-13
 Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 5/75 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +Y+ N+   + E  L+ +    G V   +++R D S      GF            I   
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 115 NGRHLFGQPIKVNWA 129
           NG+ +   P      
Sbjct: 87  NGKFIKTPPGVSAPT 101

>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 = 83.9 bits (208), Expect = 2e-20
 Identities = 21/110 (19%), Positives = 45/110 (40%), Gaps = 9/110 (8%)

Query: 129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
           +  S   +D      +F+G +   + +  L   F  +    +  V+ D+ TG  +G  F+
Sbjct: 2   SSGSSGMKDHDA-IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 189 SFRNQQDAQSAINDLTGK---WLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
           ++  ++ A  A + L  +      +R I+   A     ++E +  S   S
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVKPA-----DSESRGGSGPSS 105

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 10/86 (11%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRS 106
           D    + +++G I   + E  L+ +F   G +    +++ D+ +       F+ Y +R S
Sbjct: 10  DHDAIK-LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK-DRFTGMHKGCAFLTYCERES 67

Query: 107 AAMAILSLNGRHLF---GQPIKVNWA 129
           A  A  +L+ +       +PI+V  A
Sbjct: 68  ALKAQSALHEQKTLPGMNRPIQVKPA 93

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 8/87 (9%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYS 308
           +   +     +++G +   + + DL   F     G I E+ V +D      KG  F+ Y 
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEE--FGKIYELTVLKDRFTGMHKGCAFLTYC 63

Query: 309 THAEAALAIQMGNTTQSSYLFGKQMKV 335
               A  A    +  ++     + ++V
Sbjct: 64  ERESALKAQSALHEQKTLPGMNRPIQV 90

>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 = 84.7 bits (210), Expect = 2e-20
 Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 1/90 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
             G  E       + V +L   V+DA +   F+ + +   A V +D ++GRS G   V F
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHF 83

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
             + DA  A+    G  L  R +       
Sbjct: 84  ERRADALKAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 69.3 bits (170), Expect = 7e-15
 Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 8/104 (7%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFI 99
                 G    T   + V N+   V++  +QE+F+  G ++   +   D+S        +
Sbjct: 23  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDY-DRSGRSLGTADV 81

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFN 143
           H+  R  A  A+    G  L G+P+ +        + D   H +
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDIQLV---ASQIDLEHHHH 122

>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 = 62.8 bits (153), Expect = 1e-12
 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 10/86 (11%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYST 309
             E       + V NL   V+  D+   F   G   +++  V  D      G   V +  
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT--LKKAAVDYDRSGRSLGTADVHFER 85

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
            A+A  A++         L G+ M +
Sbjct: 86  RADALKAMKQYKGVP---LDGRPMDI 108

>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 = 83.4 bits (207), Expect = 2e-20
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           NI+VG+L    T   +   FS +    + ++++D++T + +GFGFV  +  +    AI  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 203 LTGKWLGSRQIRCNWA 218
           L       R IR   A
Sbjct: 62  LDNTDFMGRTIRVTEA 77

>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 = 64.9 bits (159), Expect = 1e-13
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 7/90 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
           R++YVGN+    T   ++E+FS  G V   KLI  D+ +     +GF+   +  S + AI
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLI-YDRETKKPKGFGFVEMQE-ESVSEAI 59

Query: 112 LSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
             L+     G+ I+V  A      E    H
Sbjct: 60  AKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 51.8 bits (125), Expect = 4e-09
 Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 12/78 (15%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
            +YVGNL    T   +   F   G   +  V++  D      KGFGFV        + AI
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGK--VFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59

Query: 318 QMGNTTQSSYLFGKQMKV 335
              + T      G+ ++V
Sbjct: 60  AKLDNTD---FMGRTIRV 74

>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 = 83.4 bits (207), Expect = 3e-20
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +FVG +   + +  + + F+ Y S  + +++ D +TG S+G+GFVSF N  D Q  +  
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69

Query: 203 LTGKWLGSRQIRCNWATK 220
                   ++++   A +
Sbjct: 70  --QINFHGKKLKLGPAIR 85

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 12/85 (14%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTH 310
           PE      TV+VG +   + + ++   F   G+  ++EV++  D     KG+GFV +   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGS--VKEVKIITDRTGVSKGYGFVSFYND 60

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            +    ++           GK++K+
Sbjct: 61  VDVQKIVESQIN-----FHGKKLKL 80

>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 = 57.6 bits (140), Expect = 7e-11
 Identities = 20/99 (20%), Positives = 42/99 (42%), Gaps = 9/99 (9%)

Query: 46  NLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHY 101
           +LP G       +V+VG I  ++ E  ++  F+  G V+  K+I  D++     YGF+ +
Sbjct: 1   SLPEG--KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSF 57

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           ++       +   +  +  G+ +K+  A           
Sbjct: 58  YNDVDVQKIV--ESQINFHGKKLKLGPAIRKQNLSTYHV 94

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 84.5 bits (209), Expect = 4e-20
 Identities = 28/147 (19%), Positives = 45/147 (30%), Gaps = 20/147 (13%)

Query: 87  KLIRKDKSSYG--FIHYFDRRSAAMAILSLNG-------------RHLFGQPIKVNWAYA 131
           KLI   K+  G       D  +A                         F      +  + 
Sbjct: 4   KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHH 63

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
              R+       ++VG+L        L   F  Y       V  +       GF FV F 
Sbjct: 64  HMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFE 118

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWA 218
           + +DA  A+ +L G+ L   ++R   +
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELS 145

>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 = 76.1 bits (187), Expect = 5e-17
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
            P  C+ VYVGN+     +  L+  F   GP+    + R +   + F+ + D R AA A+
Sbjct: 70  CPLDCK-VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAV 127

Query: 112 LSLNGRHLFGQPIKVNWA 129
             L+GR L G  ++V  +
Sbjct: 128 RELDGRTLCGCRVRVELS 145

>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 = 61.0 bits (148), Expect = 1e-11
 Identities = 28/143 (19%), Positives = 46/143 (32%), Gaps = 34/143 (23%)

Query: 183 RGFGFVSFRNQQDAQSAINDLT------GKWLGSRQIRCNWATKGAGNNEDKQSSDAKSV 236
           +G       +   A+             G+W      +    T+G+ ++      D+   
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC-- 70

Query: 237 VELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV 296
                                  P    VYVGNL     + +L R F     G +  V V
Sbjct: 71  -----------------------PLDCKVYVGNLGNNGNKTELERAFG--YYGPLRSVWV 105

Query: 297 QRD-KGFGFVRYSTHAEAALAIQ 318
            R+  GF FV +    +AA A++
Sbjct: 106 ARNPPGFAFVEFEDPRDAADAVR 128

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 81.6 bits (202), Expect = 1e-19
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG    +     + + +LS   T+ TL   F           +   + G+S+G+ F+ F
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEF 60

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            + +DA+ A+N    + +  R IR     
Sbjct: 61  ASFEDAKEALNSCNKREIEGRAIRLELQG 89

>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 = 67.3 bits (165), Expect = 2e-14
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILSL 114
           +++ + N+    TE  LQEVF     ++  +   ++  S  Y FI +     A  A+ S 
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIKVPQ--NQNGKSKGYAFIEFASFEDAKEALNSC 73

Query: 115 NGRHLFGQPIKVNWAYASGQRE 136
           N R + G+ I++      G   
Sbjct: 74  NKREIEGRAIRLELQGPRGSPN 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
             + +  T+ + NL+   T+  L   F       + + +  + KG+ F+ +++  +A  A
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           +   N      + G+ +++
Sbjct: 70  LNSCN---KREIEGRAIRL 85

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 81.6 bits (202), Expect = 1e-19
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F+  L    T   L      + +  D R++ + + G+ +G  +V + N+  A  A+  
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMK 77

Query: 203 LTGKWLGSRQIRCNWA 218
           + G  +    I+   +
Sbjct: 78  MDGMTIKENIIKVAIS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 72.3 bits (178), Expect = 3e-16
 Identities = 17/93 (18%), Positives = 41/93 (44%), Gaps = 8/93 (8%)

Query: 44  SGNLPPGFDPSTC---RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----Y 96
           S      F  ST      +++  +    T+  L+E+  + G V+  +L+  +++      
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLV-TNRAGKPKGL 60

Query: 97  GFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            ++ Y +   A+ A++ ++G  +    IKV  +
Sbjct: 61  AYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 13/85 (15%), Positives = 35/85 (41%), Gaps = 10/85 (11%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTH 310
              + +   +++  L    T+ +L     +   G ++++R+  +     KG  +V Y   
Sbjct: 11  YSTSLEKHKLFISGLPFSCTKEELEEICKA--HGTVKDLRLVTNRAGKPKGLAYVEYENE 68

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
           ++A+ A+   +      +    +KV
Sbjct: 69  SQASQAVMKMDGMT---IKENIIKV 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 80.7 bits (200), Expect = 2e-19
 Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           SG   IFV +L  + T   L   F+       A +  +   G+S+G G V F + + A+ 
Sbjct: 6   SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAER 63

Query: 199 AINDLTGKWLGSRQIRCNWATKGAG 223
           A   + G  L  R+I        +G
Sbjct: 64  ACRMMNGMKLSGREIDVRIDRNASG 88

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 73.0 bits (180), Expect = 1e-16
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMA 110
            S    ++V N+    T  +L++ F+  G V    +  ++  S   G + +     A  A
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 64

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQRE 136
              +NG  L G+ I V     +    
Sbjct: 65  CRMMNGMKLSGREIDVRIDRNASGPS 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 67.2 bits (165), Expect = 2e-14
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTH 310
               +     ++V NL  + T   L   F+    G +    ++ +    KG G V++ + 
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNE--CGHVLYADIKMENGKSKGCGVVKFESP 58

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
             A  A +M N  +   L G+++ V
Sbjct: 59  EVAERACRMMNGMK---LSGREIDV 80

>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 = 80.8 bits (200), Expect = 2e-19
 Identities = 14/83 (16%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +   +LS  +T+  L   F          +    + G+S+G  ++ F+++ DA+  + +
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 203 LTGKWLGSRQIRCNWATKGAGNN 225
             G  +  R +   +  +  G  
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 70.4 bits (173), Expect = 1e-15
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 8/87 (9%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMAILS 113
            R++   N+   +TE  L+EVF     +   +L+ +D  S    +I +     A   +  
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 114 LNGRHLFGQPIKVNWAYASGQREDTSG 140
             G  + G+ + + +    G++  T G
Sbjct: 73  KQGAEIDGRSVSLYYT---GEKGGTRG 96

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 56.9 bits (138), Expect = 9e-11
 Identities = 13/92 (14%), Positives = 33/92 (35%), Gaps = 13/92 (14%)

Query: 249 ETTNTEAP-ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFG 303
                    +      T+   NL+  +T+ +L   F         E+R+       KG  
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIA 56

Query: 304 FVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           ++ + + A+A   ++     +   + G+ + +
Sbjct: 57  YIEFKSEADAEKNLEEKQGAE---IDGRSVSL 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 79.6 bits (197), Expect = 5e-19
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 8/89 (8%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G    +   + IFVG++S   T   L + F       +  V+        + + FV    
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK 52

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWATKG 221
           + DA++AI  L GK +  ++I    +TKG
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKG 81

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 76.1 bits (188), Expect = 8e-18
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
                 ++VGN+    T   L+ +F   G V  C +++     Y F+H      A  AI 
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK----DYAFVHMEKEADAKAAIA 61

Query: 113 SLNGRHLFGQPIKVNWA 129
            LNG+ + G+ I V  +
Sbjct: 62  QLNGKEVKGKRINVELS 78

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
             ++VGN++   T  +L   F   G   + E  V   K + FV     A+A  AI   N 
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGR--VIECDVV--KDYAFVHMEKEADAKAAIAQLNG 65

Query: 323 TQSSYLFGKQMKV 335
            +   + GK++ V
Sbjct: 66  KE---VKGKRINV 75

>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 = 79.6 bits (197), Expect = 6e-19
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 4/91 (4%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG          +FVG L+ + ++  +   F  +    +  V+     G S+G  FV F
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKF 63

Query: 191 RNQQDAQSAINDLTGKWL---GSRQIRCNWA 218
            +  +AQ+AI+ L G       S  +   +A
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFA 94

>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 = 69.6 bits (171), Expect = 3e-15
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSS--YGFIHYFDRRSAAMAILSLN 115
           ++VG ++ Q +E  +  +F   G ++ C ++R  D SS    F+ +     A  AI +L+
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77

Query: 116 GRHLF---GQPIKVNWAYASGQREDTSG 140
           G          + V +A    +   +SG
Sbjct: 78  GSQTMPGASSSLVVKFADTDKESGPSSG 105

>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 = 67.3 bits (165), Expect = 2e-14
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGF 304
           + ++ +     +   ++VG L  + ++ D+ R F   G   I+E  V R      KG  F
Sbjct: 3   SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGV--IDECTVLRGPDGSSKGCAF 60

Query: 305 VRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           V++S+H EA  AI   + +Q+       + V
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPGASSSLVV 91

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 79.6 bits (197), Expect = 8e-19
 Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 2/100 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG+   T   +  +VG+L        + A F    S    R++ D+ T + +GF +V F
Sbjct: 5   SSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF 63

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
                 + A+    G  LG R +R + A     +     S
Sbjct: 64  DEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQDKSGPSS 102

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 19/106 (17%)

Query: 40  EPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---- 95
           + +P+   PP        + YVGN+     +  +  +F     +   +L+R DK +    
Sbjct: 8   KELPTE--PP-------YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVR-DKDTDKFK 56

Query: 96  -YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
            + ++  FD   +    L+ +G  L  + ++V+   A G+++D SG
Sbjct: 57  GFCYVE-FDEVDSLKEALTYDGALLGDRSLRVD--IAEGRKQDKSG 99

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 22/78 (28%), Positives = 30/78 (38%), Gaps = 13/78 (16%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAI 317
           T YVGNL     Q D+   F  L    I  VR+ RD      KGF +V +        A+
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS---IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73

Query: 318 QMGNTTQSSYLFGKQMKV 335
                     L  + ++V
Sbjct: 74  TYDGAL----LGDRSLRV 87

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 78.5 bits (194), Expect = 2e-18
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           ++V      V E  L E+F   GP++  K++      + F+ + +  SAA AI  ++G+ 
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKILN----GFAFVEFEEAESAAKAIEEVHGKS 89

Query: 119 LFGQPIKVNWAYASGQR 135
              QP++V ++    +R
Sbjct: 90  FANQPLEVVYSKLPAKR 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 71.9 bits (177), Expect = 5e-16
 Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 8/89 (8%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
             ++E    +  +FV     +V ++ L   F  +    + +++         GF FV F 
Sbjct: 22  HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFE 73

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWATK 220
             + A  AI ++ GK   ++ +   ++  
Sbjct: 74  EAESAAKAIEEVHGKSFANQPLEVVYSKL 102

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEA 313
              E     T ++V     +V + +L+  F   G   ++EV++    GF FV +     A
Sbjct: 23  HRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGP--MKEVKIL--NGFAFVEFEEAESA 78

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
           A AI+  +         + ++V
Sbjct: 79  AKAIEEVHGKS---FANQPLEV 97

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 80.3 bits (198), Expect = 2e-18
 Identities = 25/117 (21%), Positives = 41/117 (35%), Gaps = 1/117 (0%)

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFS 163
           R            + L  +     +    G  E       + V +L   V+DA +   F+
Sbjct: 51  RGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFA 110

Query: 164 VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            + +   A V +D ++GRS G   V F  + DA  A+    G  L  R +       
Sbjct: 111 EFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 166

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 68.7 bits (168), Expect = 3e-14
 Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 5/92 (5%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS-YGFIHYFDR 104
             G +      + V N+   V++  +QE+F+  G ++   +   R  +S     +H+  R
Sbjct: 82  GEGVETGAK--LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERR 139

Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
             A  A+    G  L G+P+ +    +    E
Sbjct: 140 ADALKAMKQYKGVPLDGRPMDIQLVASQIDLE 171

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 63.7 bits (155), Expect = 2e-12
 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 10/86 (11%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYST 309
             E       + V NL   V+  D+   F     G +++  V  D      G   V +  
Sbjct: 81  GGEGVETGAKLLVSNLDFGVSDADIQELFAE--FGTLKKAAVDYDRSGRSLGTADVHFER 138

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
            A+A  A++         L G+ M +
Sbjct: 139 RADALKAMKQYKGVP---LDGRPMDI 161

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 77.1 bits (191), Expect = 3e-18
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG LS   T   +   F  +    DA +M+D+ T R RGFGFV+F ++   +      
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 204 TGKWLGSRQIRCNWA 218
               + ++ + C  A
Sbjct: 61  HFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 49.4 bits (119), Expect = 3e-08
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 12/77 (15%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAIQ 318
           ++VG L+   T  D+  +F   G   +++  +  DK      GFGFV + +        +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGK--VDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

Query: 319 MGNTTQSSYLFGKQMKV 335
           +        +  K ++ 
Sbjct: 60  IHFHE----INNKMVEC 72

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.9 bits (97), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           ++VG +    T   ++  F   G V+   L+  DK++     +GF+  F+       +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMF-DKTTNRHRGFGFVT-FESEDIVEKVCE 59

Query: 114 LNGRHLFGQPIKVNWA 129
           ++   +  + ++   A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 77.6 bits (192), Expect = 3e-18
 Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 6/88 (6%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            S    +++GN+  + TE  ++ +F   G V  C +I+    +YGF+H  D+ +A  AI 
Sbjct: 5   SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK----NYGFVHIEDKTAAEDAIR 60

Query: 113 SLNGRHLFGQPIKVNWAYASGQREDTSG 140
           +L+   L G  I V    +  + + +SG
Sbjct: 61  NLHHYKLHGVNINVEA--SKNKSKASSG 86

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 73.0 bits (180), Expect = 1e-16
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           SG   +F+G+L  E T+  + + F  Y    +  ++        + +GFV   ++  A+ 
Sbjct: 6   SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAED 57

Query: 199 AINDLTGKWLGSRQIRCNWAT 219
           AI +L    L    I    + 
Sbjct: 58  AIRNLHHYKLHGVNINVEASK 78

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           +     +++GNL  E T+ ++   F     G + E  +   K +GFV       A  AI+
Sbjct: 5   SSGMVKLFIGNLPREATEQEIRSLFE--QYGKVLECDII--KNYGFVHIEDKTAAEDAIR 60

Query: 319 MGNTTQSSYLFGKQMKV 335
             +  +   L G  + V
Sbjct: 61  NLHHYK---LHGVNINV 74

>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 = 77.7 bits (192), Expect = 3e-18
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
             ++ + ++VGNI    T   L+  F   GPV  C +++     Y F+H      A  AI
Sbjct: 7   GKASTK-LHVGNISPTCTNQELRAKFEEYGPVIECDIVK----DYAFVHMERAEDAVEAI 61

Query: 112 LSLNGRHLFGQPIKVNWAYASGQREDTSG 140
             L+     G+ + V    ++ +    SG
Sbjct: 62  RGLDNTEFQGKRMHVQL--STSRLRTASG 88

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 68.4 bits (168), Expect = 7e-15
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            + VG++SP  T+  L A F  Y    +  ++        + + FV     +DA  AI  
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG 63

Query: 203 LTGKWLGSRQIRCNWAT 219
           L       +++    +T
Sbjct: 64  LDNTEFQGKRMHVQLST 80

>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 = 56.5 bits (137), Expect = 1e-10
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           T ++VGN++P  T  +L   F   G   + E  + +   + FV      +A  AI+  + 
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGP--VIECDIVK--DYAFVHMERAEDAVEAIRGLDN 66

Query: 323 TQSSYLFGKQMKV 335
           T+     GK+M V
Sbjct: 67  TE---FQGKRMHV 76

>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 = 77.7 bits (192), Expect = 3e-18
 Identities = 20/93 (21%), Positives = 42/93 (45%)

Query: 129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
           + +SG      G   I V ++   V+   +   F  Y     +  +   + G   G   V
Sbjct: 3   SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
           +F ++ +A +A+ DL  + +GSR+++ +  + G
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGF 98
            S     G    T   + V N+   V+   + + F     + G   ++ ++         
Sbjct: 4   GSSGSSSGKPGPTV--IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           + +  R  A  A++ LN R +  + +K++  
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 12/85 (14%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
           GSS     ++    P      T + V N+   V+  ++   F+     +   V ++ +  
Sbjct: 1   GSSGSSGSSSGKPGP------TVIKVQNMPFTVSIDEILDFFYGYQV-IPGSVCLKYNEK 53

Query: 300 ---KGFGFVRYSTHAEAALAIQMGN 321
               G   V + +  EA  A+   N
Sbjct: 54  GMPTGEAMVAFESRDEATAAVIDLN 78

>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 = 77.7 bits (192), Expect = 3e-18
 Identities = 23/97 (23%), Positives = 37/97 (38%), Gaps = 4/97 (4%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFD 103
           SG+      P    ++YV      +T  LL+  FS  G +     +   ++   F+ Y  
Sbjct: 3   SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS-MDPPRN-CAFVTYEK 58

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
             SA  A+  LNG  +    +KVN A      +    
Sbjct: 59  MESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPS 95

>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 = 76.6 bits (189), Expect = 8e-18
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 8/90 (8%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG+R        ++V     ++T   L   FS + +  D  +         R   FV++
Sbjct: 5   SSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTY 56

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
              + A  A+ +L G  + S Q++ N A K
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARK 86

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 76.2 bits (188), Expect = 1e-17
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYST 309
           + ++       +  T+YV     ++T   L   F   G   I ++ +   +   FV Y  
Sbjct: 3   SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGN--IIDLSMDPPRNCAFVTYEK 58

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
              A  A+   N TQ   +   Q+KV
Sbjct: 59  MESADQAVAELNGTQ---VESVQLKV 81

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 77.2 bits (191), Expect = 4e-18
 Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +I+VG++    T   L A F    S +   ++ D+ +G  +GF ++ F +++  ++++  
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 203 LTGKWLGSRQIRCNWA 218
           L       RQI+    
Sbjct: 67  LDESLFRGRQIKVIPK 82

>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 = 69.1 bits (170), Expect = 3e-15
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAI 111
           RS+YVGN+    T   L+  F   G V    ++  DK S     + +I  F  + +    
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILC-DKFSGHPKGFAYIE-FSDKESVRTS 64

Query: 112 LSLNGRHLFGQPIKVNWA 129
           L+L+     G+ IKV   
Sbjct: 65  LALDESLFRGRQIKVIPK 82

>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 = 64.5 bits (158), Expect = 1e-13
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 12/79 (15%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
            ++YVGN+    T  +L  HFH    G +  V +  D      KGF ++ +S       +
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHG--CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           + +  +       G+Q+KV
Sbjct: 65  LALDESL----FRGRQIKV 79

>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 = 76.8 bits (190), Expect = 5e-18
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG LS + +   L   F+ +    D  +  D  TGRSRGFGF+ F++    +  ++  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 204 TGKWLGSRQIRCNWA 218
             + L  R I    A
Sbjct: 74  EHR-LDGRVIDPKKA 87

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 8/73 (10%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYS 308
           A +N      ++VG L+ + ++ DL  +F   G   + +  ++ D       GFGF+ + 
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGE--VVDCTIKMDPNTGRSRGFGFILFK 61

Query: 309 THAEAALAIQMGN 321
             A     +    
Sbjct: 62  DAASVEKVLDQKE 74

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 76.4 bits (189), Expect = 6e-18
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS + T   L   F  +    +  VM D  T RSRGFGFV+F +Q      +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 204 TGKWLGSRQIRCNWA 218
           +   L S+ I    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 48.6 bits (117), Expect = 5e-08
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 8/63 (12%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAIQ 318
           +++G L+ + TQ  L  +F   G   ++E  V RD       GFGFV +   A     + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGE--VKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 319 MGN 321
              
Sbjct: 61  QSR 63

>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 = 76.9 bits (190), Expect = 6e-18
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG +     +  L   F  +   ++  +++D +  R RGFGF++F ++Q    A+N +
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71

Query: 204 TGKWLGSRQIRCNWAT 219
               +  +++    A 
Sbjct: 72  HFHDIMGKKVEVKRAE 87

>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 = 55.7 bits (135), Expect = 3e-10
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 12/87 (13%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYS 308
           +  +  +   ++VG +     + +L  +F   G   + EV +  D       GFGF+ + 
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGV--VTEVVMIYDAEKQRPRGFGFITFE 60

Query: 309 THAEAALAIQMGNTTQSSYLFGKQMKV 335
                  A+ M        + GK+++V
Sbjct: 61  DEQSVDQAVNMHFHD----IMGKKVEV 83

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 20/99 (20%), Positives = 36/99 (36%), Gaps = 7/99 (7%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYF 102
             G   S    ++VG I     E  L+E F   G V    +I  D        +GFI  F
Sbjct: 2   SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIY-DAEKQRPRGFGFI-TF 59

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
           +   +    ++++   + G+ ++V  A     +      
Sbjct: 60  EDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSGPSS 98

>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 = 76.9 bits (190), Expect = 7e-18
 Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 10/90 (11%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
           P+T   ++VG +    +   L   F   G +     ++ D  S+ +I Y    +A  A  
Sbjct: 16  PTTR--LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD--SFAYIQYESLDAAQAACA 71

Query: 113 SLNGRHLFGQ--PIKVNWAYASGQREDTSG 140
            + G  L G    ++V++A    +   +SG
Sbjct: 72  KMRGFPLGGPDRRLRVDFA----KSGPSSG 97

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           T ++VG L P  +   L R F   G+  I  +   +   F +++Y +   A  A  
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGS--IRTIDHVKGDSFAYIQYESLDAAQAACA 71

>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 = 60.3 bits (147), Expect = 6e-12
 Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 15/100 (15%)

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG 180
           G   K+ +  A+           ++VG L P  + A L   F  + S      +      
Sbjct: 4   GSSGKIGYGKANPTT-------RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------ 50

Query: 181 RSRGFGFVSFRNQQDAQSAINDLTGKWLG--SRQIRCNWA 218
           +   F ++ + +   AQ+A   + G  LG   R++R ++A
Sbjct: 51  KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA 90

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 77.0 bits (190), Expect = 9e-18
 Identities = 16/87 (18%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +++ +L  ++T   ++  F  Y      RV     T  +RG  +V + +  DA++A++ 
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQ 229
           L+G  + +R +   +        +   
Sbjct: 67  LSGFNVSNRYLVVLYYNANRAFQKMDT 93

>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 = 72.4 bits (178), Expect = 4e-16
 Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-YGFIHYFDRRSAAMAI 111
           P   R +Y+ N+  ++T   + ++F   GP+   ++    ++    ++ Y D   A  A+
Sbjct: 5   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAV 64

Query: 112 LSLNGRHLFGQPIKVNWA 129
             L+G ++  + + V + 
Sbjct: 65  DHLSGFNVSNRYLVVLYY 82

>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 = 60.5 bits (147), Expect = 9e-12
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 11/84 (13%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD---KGFGFVRYSTHA 311
            PE N     +Y+ NL  ++T  +++  F     G I ++RV      +G  +V Y    
Sbjct: 4   PPEVN---RILYIRNLPYKITAEEMYDIFGK--YGPIRQIRVGNTPETRGTAYVVYEDIF 58

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
           +A  A+   +      +  + + V
Sbjct: 59  DAKNAVDHLSGFN---VSNRYLVV 79

>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 = 77.1 bits (190), Expect = 9e-18
 Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 8/108 (7%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY--------PSCSDARVMWDQKTGRS 182
           +SG  ++ S +  I+V  L+  VT   L   F                  +  D++TG+ 
Sbjct: 5   SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64

Query: 183 RGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
           +G   VS+ +   A++A+    GK     +++ + A K    N    S
Sbjct: 65  KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 70.9 bits (174), Expect = 2e-15
 Identities = 22/100 (22%), Positives = 38/100 (38%), Gaps = 14/100 (14%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPV--------EGCKLIRKDKS 94
            SG+     + S   ++YV  ++  VT   L + F   G V            +   DK 
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY-LDKE 60

Query: 95  S-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           +        + Y D  +A  A+   +G+   G  +KV+ A
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100

>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 = 60.9 bits (148), Expect = 5e-12
 Identities = 21/101 (20%), Positives = 37/101 (36%), Gaps = 19/101 (18%)

Query: 249 ETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE--------VRVQRD- 299
            + ++  P+ +   + +YV  L   VT  DL   F     GV++         + +  D 
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQ--CGVVKMNKRTGQPMIHIYLDK 59

Query: 300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                KG   V Y     A  A++  +        G ++KV
Sbjct: 60  ETGKPKGDATVSYEDPPTAKAAVEWFDGKD---FQGSKLKV 97

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 77.0 bits (190), Expect = 9e-18
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F   L+  +    L   FS      D R++ D+ + RS+G  +V F   Q    AI  L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-L 86

Query: 204 TGKWLGSRQIRCNWA 218
           TG+ L    I    +
Sbjct: 87  TGQRLLGVPIIVQAS 101

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 69.3 bits (170), Expect = 5e-15
 Identities = 21/106 (19%), Positives = 41/106 (38%), Gaps = 7/106 (6%)

Query: 40  EPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---- 95
            P+         +    R+V+   +  ++    L++ FS+ G V   ++I  D++S    
Sbjct: 9   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIIS-DRNSRRSK 67

Query: 96  -YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
              ++  F    +    + L G+ L G PI V  + A   R     
Sbjct: 68  GIAYVE-FCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPS 112

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 21/100 (21%), Positives = 32/100 (32%), Gaps = 12/100 (12%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
            S +                  TV+   LA  +   DL   F +   G + +VR+  D  
Sbjct: 5   SSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSA--VGKVRDVRIISDRN 62

Query: 300 ----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
               KG  +V +       LAI +        L G  + V
Sbjct: 63  SRRSKGIAYVEFCEIQSVPLAIGLTGQR----LLGVPIIV 98

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 76.5 bits (189), Expect = 9e-18
 Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 2/100 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG +       ++ V  L  + T+  L   FS +      +V  D KTG S+GFGFV F
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
              +     ++      +  R   C         +    S
Sbjct: 65  TEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQSQDSGPSS 102

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFV 305
           ++       + + + V  L  + T+ DL  +F + G   +  V+V++D       GFGFV
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGE--VLMVQVKKDLKTGHSKGFGFV 62

Query: 306 RYSTHAEAALAIQMGNT 322
           R++ +      +   + 
Sbjct: 63  RFTEYETQVKVMSQRHM 79

>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 = 46.1 bits (110), Expect = 7e-07
 Identities = 17/104 (16%), Positives = 39/104 (37%), Gaps = 10/104 (9%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGF 98
           SG+            + V  +  + TE  L+E FS+ G V   ++ + D  +     +GF
Sbjct: 3   SGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKK-DLKTGHSKGFGF 61

Query: 99  IHYFDRRSAAMAILSLNGRHLF-GQPIKVNWAYASGQREDTSGH 141
           + + +  +       ++ RH+  G+        +   ++     
Sbjct: 62  VRFTEYETQVKV---MSQRHMIDGRWCDCKLPNSKQSQDSGPSS 102

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 75.8 bits (187), Expect = 2e-17
 Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS + T   L   F  +    +  VM D  T RSRGFGFV+F +Q      +   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 86

Query: 204 TGKWLGSRQIRCNWAT 219
           +   L S+ I    A 
Sbjct: 87  SRHELDSKTIDPKVAF 102

>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 = 49.6 bits (119), Expect = 4e-08
 Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 8/72 (11%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYST 309
                    +++G L+ + TQ  L  +F   G   ++E  V RD       GFGFV +  
Sbjct: 19  SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGE--VKECLVMRDPLTKRSRGFGFVTFMD 76

Query: 310 HAEAALAIQMGN 321
            A     +    
Sbjct: 77  QAGVDKVLAQSR 88

>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 = 75.7 bits (187), Expect = 2e-17
 Identities = 26/76 (34%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG L    T  TL + FS Y    D  +M D+ T +SRGFGFV F++     + +   
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS- 77

Query: 204 TGKWLGSRQIRCNWAT 219
               L  R I     T
Sbjct: 78  RPHTLDGRNIDPKPCT 93

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 8/81 (9%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------ 300
           G   ++        +   ++VG L    TQ  L  +F   G   + +  + +DK      
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGE--VVDCVIMKDKTTNQSR 58

Query: 301 GFGFVRYSTHAEAALAIQMGN 321
           GFGFV++         +    
Sbjct: 59  GFGFVKFKDPNCVGTVLASRP 79

>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 = 75.0 bits (185), Expect = 3e-17
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 143 NIFVGDLSPEVTDATLFACFSVY--------PSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
            IFV  L   VT  ++   F                  +  D++TG+ +G   VSF +  
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 195 DAQSAINDLTGKWLGSRQIRCNWAT 219
            A++AI+   GK      I+ ++AT
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFAT 99

>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 = 73.9 bits (182), Expect = 7e-17
 Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 14/98 (14%)

Query: 45  GNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPV--------EGCKLIRKDKSS- 95
           G+       S   +++V  +   VT   + + F   G +            L   D+ + 
Sbjct: 2   GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY-TDRETG 60

Query: 96  ----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
                  + + D  SA  AI   +G+   G PIKV++A
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 19/96 (19%)

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE--------VRVQRD------ 299
               ++    T++V  L   VT   +  +F     G+I+         + +  D      
Sbjct: 5   HHHHSHSDNNTIFVQGLGENVTIESVADYFKQ--IGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           KG   V +     A  AI   +  +     G  +KV
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKE---FSGNPIKV 95

>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 = 74.1 bits (183), Expect = 3e-17
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG LSP+  +  +   F  +       +  D KT + RGF F++F+ ++  +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 204 TGKWLGSRQIRCNWA 218
               +G  +     A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 46.7 bits (112), Expect = 2e-07
 Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 12/77 (15%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYSTHAEAALAIQ 318
           ++VG L+P+  +  +  +F   G   +E + +  D       GF F+ +         ++
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGE--VESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

Query: 319 MGNTTQSSYLFGKQMKV 335
                    +   + ++
Sbjct: 60  KKYHN----VGLSKCEI 72

>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 = 39.8 bits (94), Expect = 7e-05
 Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           ++VG +     E  ++E F   G VE  +L   D  +     + FI  F        I+ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPM-DNKTNKRRGFCFIT-FKEEEPVKKIME 59

Query: 114 LNGRHLFGQPIKVNWA 129
               ++     ++  A
Sbjct: 60  KKYHNVGLSKCEIKVA 75

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 74.8 bits (184), Expect = 4e-17
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 1/87 (1%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-YGFIHYF 102
           SG+          R + + NI   +   +L  +    G VE C+ +  D  +    + Y 
Sbjct: 3   SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYS 62

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWA 129
            +  A  A+  LNG  L    +KV + 
Sbjct: 63  SKDQARQALDKLNGFQLENFTLKVAYI 89

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 61.3 bits (149), Expect = 3e-12
 Identities = 12/89 (13%), Positives = 31/89 (34%), Gaps = 3/89 (3%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG          + + ++ P +    L +    Y        +    T        V++
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTY 61

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWAT 219
            ++  A+ A++ L G  L +  ++  +  
Sbjct: 62  SSKDQARQALDKLNGFQLENFTLKVAYIP 90

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 52.1 bits (125), Expect = 4e-09
 Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 13/97 (13%)

Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGV-IEEVRVQR 298
           ++GSS    +               + + N+ P +    L       G     E+V    
Sbjct: 2   SSGSSGSVPKRQRI---------RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS 52

Query: 299 DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           +     V YS+  +A  A+   N  Q   L    +KV
Sbjct: 53  ETAVVNVTYSSKDQARQALDKLNGFQ---LENFTLKV 86

>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 = 74.6 bits (184), Expect = 7e-17
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS E T+ +L   +  +   +D  VM D  + RSRGFGFV+F +  +  +A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88

Query: 204 TGKWLGSRQIRCNWAT 219
               +  R +    A 
Sbjct: 89  RPHSIDGRVVEPKRAV 104

>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 = 52.7 bits (127), Expect = 5e-09
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK 300
           +G  +  +            Q+  +++G L+ E T+  L  ++   G   + +  V RD 
Sbjct: 6   SGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGK--LTDCVVMRDP 63

Query: 301 ------GFGFVRYSTHAEAALAIQMGN 321
                 GFGFV +S+ AE   A+    
Sbjct: 64  ASKRSRGFGFVTFSSMAEVDAAMAARP 90

>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 = 73.9 bits (182), Expect = 8e-17
 Identities = 19/90 (21%), Positives = 39/90 (43%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG      G   I V ++   V+   +   F  Y     +  +   + G   G   V+F
Sbjct: 5   SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            ++ +A +A+ DL  + +GSR+++    + 
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 15/91 (16%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGF 98
            S     G    T   + V N+   V+   + + F     + G   ++ ++         
Sbjct: 4   GSSGASSGKPGPTI--IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           + +  R  A  A++ LN R +  + +K+   
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLG 92

>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 = 53.1 bits (128), Expect = 3e-09
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 6/72 (8%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYST 309
           A    P  T + V N+   V+  ++   F+     +   V ++ +      G   V + +
Sbjct: 8   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQV-IPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 310 HAEAALAIQMGN 321
             EA  A+   N
Sbjct: 67  RDEATAAVIDLN 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 73.9 bits (182), Expect = 8e-17
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR 117
            VYVGN+ T   +  L+  FS  GP+    + R +   + F+ + D R A  A+  L+G+
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR-NPPGFAFVEFEDPRDAEDAVRGLDGK 60

Query: 118 HLFGQPIKVNWAYASGQREDTSG 140
            + G  ++V  +    +R     
Sbjct: 61  VICGSRVRVELSTGMPRRSRFDR 83

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 4e-16
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            ++VG+L        L   FS Y       +          GF FV F + +DA+ A+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRG 56

Query: 203 LTGKWLGSRQIRCNWATKG 221
           L GK +   ++R   +T  
Sbjct: 57  LDGKVICGSRVRVELSTGM 75

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 6/72 (8%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAIQMGNTT 323
           VYVGNL     + +L R F   G   +  V + R+  GF FV +    +A  A++  +  
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGP--LRTVWIARNPPGFAFVEFEDPRDAEDAVRGLD-- 58

Query: 324 QSSYLFGKQMKV 335
               + G +++V
Sbjct: 59  -GKVICGSRVRV 69

>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 = 74.0 bits (182), Expect = 9e-17
 Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 8/90 (8%)

Query: 52  DPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMA 110
                R V++GN++T  V +  ++ +FS  G V GC +       Y F+ Y + R A  A
Sbjct: 24  KSINSR-VFIGNLNTALVKKSDVETIFSKYGRVAGCSV----HKGYAFVQYSNERHARAA 78

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           +L  NGR L GQ + +N   A   + D SG
Sbjct: 79  VLGENGRVLAGQTLDINM--AGEPKPDRSG 106

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 71.3 bits (175), Expect = 9e-16
 Identities = 22/111 (19%), Positives = 49/111 (44%), Gaps = 9/111 (8%)

Query: 121 GQPIKVNWAYASGQREDTSGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKT 179
           G  +K+  +  + + +  S +  +F+G+L+   V  + +   FS Y   +   V      
Sbjct: 7   GMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH----- 61

Query: 180 GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
              +G+ FV + N++ A++A+    G+ L  + +  N A +   +     S
Sbjct: 62  ---KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 8/97 (8%)

Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQR 298
           ++G S   + +  T   +     + V++GNL    V + D+   F     G +    V  
Sbjct: 5   SSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFS--KYGRVAGCSVH- 61

Query: 299 DKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            KG+ FV+YS    A  A+   N      L G+ + +
Sbjct: 62  -KGYAFVQYSNERHARAAVLGENGRV---LAGQTLDI 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 73.6 bits (181), Expect = 1e-16
 Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 8/98 (8%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVY--------PSCSDARVMWDQKTGRSRGFGF 187
           +D S +  IFV  L   VT  ++   F                  +  D++TG+ +G   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 188 VSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNN 225
           VSF +   A++AI+   GK      I+ ++AT+ A  N
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 68.6 bits (168), Expect = 1e-14
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 14/102 (13%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE--------GCKLIRKDKSS-----YGF 98
           D S   +++V  +   VT   + + F   G ++           L   D+ +        
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY-TDRETGKLKGEAT 61

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           + + D  SA  AI   +G+   G PIKV++A          G
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGG 103

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 55.5 bits (134), Expect = 4e-10
 Identities = 19/91 (20%), Positives = 31/91 (34%), Gaps = 19/91 (20%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEE--------VRVQRD------KGFGF 304
           N    T++V  L   VT   +  +F     G+I+         + +  D      KG   
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQ--IGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 305 VRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           V +     A  AI   +  +     G  +KV
Sbjct: 62  VSFDDPPSAKAAIDWFDGKE---FSGNPIKV 89

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 20/97 (20%), Positives = 43/97 (44%), Gaps = 6/97 (6%)

Query: 34  LAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKD 92
           + +       S  L P       R +++GN+  + V++  L  +FS  G +    +    
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMKSR-LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---- 55

Query: 93  KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           K+++GFI + + +S   AI   +    FG+ + +  +
Sbjct: 56  KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS 92

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 144 IFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +F+G+L  + V+   LF  FS Y       +           FGF+ F N Q  + AI  
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76

Query: 203 LTGKWLGSRQIRCNWATKGA 222
            + +    +++    ++  A
Sbjct: 77  ESQEMNFGKKLILEVSSSNA 96

>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 = 58.9 bits (143), Expect = 2e-11
 Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 8/95 (8%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDK 300
           GSS      ++   P  +   + +++GNL  + V++ DL R F   G   I ++ ++   
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGH--IMQINIK--N 57

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            FGF+++        AI+  +       FGK++ +
Sbjct: 58  AFGFIQFDNPQSVRDAIEXESQEM---NFGKKLIL 89

>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 = 73.1 bits (180), Expect = 2e-16
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 3/93 (3%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-YGFIHYFDRRSA 107
            G   +    +YVGN+   +    +++VF   G +    L  +     + F+ + D R A
Sbjct: 15  RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 74

Query: 108 AMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
             A+   +G    G  ++V +      R   SG
Sbjct: 75  EDAVYGRDGYDYDGYRLRVEF--PRSGRGTGSG 105

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 72.4 bits (178), Expect = 4e-16
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           I+VG+L P++    +   F  Y +  D  +           F FV F + +DA+ A+   
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGR 81

Query: 204 TGKWLGSRQIRCNWATKGAGNN 225
            G      ++R  +   G G  
Sbjct: 82  DGYDYDGYRLRVEFPRSGRGTG 103

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 5/80 (6%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
            S   G                 +YVGNL P++   D+   F+    G I ++ ++    
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFY--KYGAIRDIDLKNRRG 59

Query: 300 -KGFGFVRYSTHAEAALAIQ 318
              F FV +    +A  A+ 
Sbjct: 60  GPPFAFVEFEDPRDAEDAVY 79

>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 = 72.3 bits (178), Expect = 4e-16
 Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 3/101 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK-TGRSRGFGFVS 189
           +SG R   S  +  F+G+L  +VT+ ++   F    + S  R+  +     R +GFG+  
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAE 63

Query: 190 FRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
           F +     SA++ L  + LG+++IR + A +    +    S
Sbjct: 64  FEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 60.0 bits (146), Expect = 1e-11
 Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 16/103 (15%)

Query: 40  EPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---- 95
             +P    PP        + ++GN+   VTE  ++E F     +   +L R+  +     
Sbjct: 8   SRLPKS--PP-------YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 57

Query: 96  -YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRED 137
            +G+   F+   + ++ LSLN   L  + I+V+ A  +  ++ 
Sbjct: 58  GFGYAE-FEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDS 99

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 15/96 (15%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------- 299
           G   ++      +P YT  ++GNL  +VT+  +   F  L    I  VR+ R+       
Sbjct: 1   GSSGSSGSRLPKSPPYT-AFLGNLPYDVTEESIKEFFRGLN---ISAVRLPREPSNPERL 56

Query: 300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           KGFG+  +        A+ +   +    L  K+++V
Sbjct: 57  KGFGYAEFEDLDSLLSALSLNEES----LGNKRIRV 88

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 71.5 bits (176), Expect = 6e-16
 Identities = 20/92 (21%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 53  PSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
           P   R +++GN+  + V++  L  +FS  G +    +    K+++GFI + + +S   AI
Sbjct: 8   PPKSR-LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI----KNAFGFIQFDNPQSVRDAI 62

Query: 112 LSLNGRHLFGQPIKVNWAYASGQREDTSGHFN 143
              +    FG+ + +    +S        H +
Sbjct: 63  ECESQEMNFGKKLILE--VSSSNARPQFDHGD 92

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 60.3 bits (147), Expect = 5e-12
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 9/79 (11%)

Query: 144 IFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +F+G+L  + V+   LF  FS Y       +           FGF+ F N Q  + AI  
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEC 64

Query: 203 LTGKWLGSRQIRCNWATKG 221
            + +    +++    ++  
Sbjct: 65  ESQEMNFGKKLILEVSSSN 83

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 256 PENNPQYTTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
             N P  + +++GNL  + V++ DL R F     G I ++ ++    FGF+++       
Sbjct: 4   MHNIPPKSRLFIGNLPLKNVSKEDLFRIFS--PYGHIMQINIKN--AFGFIQFDNPQSVR 59

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            AI+          FGK++ +
Sbjct: 60  DAIE---CESQEMNFGKKLIL 77

>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 = 71.1 bits (175), Expect = 7e-16
 Identities = 19/100 (19%), Positives = 44/100 (44%), Gaps = 19/100 (19%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQE----VFSSTGPVEGCKLIR 90
           A P+  P                ++Y+ N++ ++ +  L++    +FS  G +    + R
Sbjct: 1   AVPETRP--------------NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46

Query: 91  KDKS-SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
             K     F+ + +  SA  A+ S+ G   + +P+++ +A
Sbjct: 47  SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 16/97 (16%)

Query: 143 NIFVGDLSPEVTD----ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
            I++ +L+ ++       +L A FS +    D  V    ++ + RG  FV F+    A +
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSATN 66

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
           A+  + G     + +R  +A         K  SD  +
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA---------KTDSDIIA 94

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 8/86 (9%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA--GVIEEVRVQRD---KGFGFVRYST 309
           A        T+Y+ NL  ++ + +L +  H++ +  G I ++ V R    +G  FV +  
Sbjct: 1   AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
            + A  A+    + Q    + K M++
Sbjct: 61  VSSATNAL---RSMQGFPFYDKPMRI 83

>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 = 72.1 bits (177), Expect = 7e-16
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 1/88 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S + +      +++VG++    T   L A FS   S +   ++ D+ +G  +G+ ++ F
Sbjct: 26  LSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
             +    +A+  +       R I+    
Sbjct: 86  AERNSVDAAVA-MDETVFRGRTIKVLPK 112

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 71.3 bits (175), Expect = 1e-15
 Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 12/104 (11%)

Query: 238 ELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ 297
           ++T G+  +G     +   +      +VYVGN+    T  DL  HF S   G I  + + 
Sbjct: 12  KMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS--CGSINRITIL 69

Query: 298 RD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            D      KG+ ++ ++       A+ M  T       G+ +KV
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAVAMDETV----FRGRTIKV 109

>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 = 65.9 bits (161), Expect = 1e-13
 Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 7/100 (7%)

Query: 35  AAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS 94
           A    E  P             RSVYVGN+    T   L+  FSS G +    ++  DK 
Sbjct: 15  AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC-DKF 73

Query: 95  S-----YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           S     Y +I  F  R++  A ++++     G+ IKV   
Sbjct: 74  SGHPKGYAYIE-FAERNSVDAAVAMDETVFRGRTIKVLPK 112

>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 = 70.7 bits (174), Expect = 1e-15
 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKT-GRSRGFGFVSFRNQQDAQSAI 200
           +  F+G+L  +VT+ ++   F    + S  R+  +     R +GFG+  F +     SA+
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 201 NDLTGKWLGSRQIRCNWAT 219
           + L  + LG+R+IR + A 
Sbjct: 79  S-LNEESLGNRRIRVDVAD 96

>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 = 59.9 bits (146), Expect = 9e-12
 Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 16/99 (16%)

Query: 244 SEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD---- 299
                    +  P++ P   T ++GNL  +VT+  +   F  L    I  VR+ R+    
Sbjct: 3   GSHHHHHHRSRLPKSPP--YTAFLGNLPYDVTEESIKEFFRGLN---ISAVRLPREPSNP 57

Query: 300 ---KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
              KGFG+  +        A+ +   +    L  ++++V
Sbjct: 58  ERLKGFGYAEFEDLDSLLSALSLNEES----LGNRRIRV 92

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 16/95 (16%)

Query: 40  EPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS---- 95
             +P    PP        + ++GN+   VTE  ++E F     +   +L R+  +     
Sbjct: 12  SRLPKS--PP-------YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 61

Query: 96  -YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            +G+   F+   + ++ LSLN   L  + I+V+ A
Sbjct: 62  GFGYAE-FEDLDSLLSALSLNEESLGNRRIRVDVA 95

>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 = 71.0 bits (174), Expect = 1e-15
 Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 13/96 (13%)

Query: 55  TCRSV-----YVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIRKDKSS-----YGFIHYFD 103
           +  S      ++G I        + E  +     V    +            + F+ Y  
Sbjct: 2   SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 104 RRSAAMAILSLNGR--HLFGQPIKVNWAYASGQRED 137
            R+AAMA   L      L+G  I V+WA      ++
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDE 97

>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 = 66.4 bits (162), Expect = 5e-14
 Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 8/103 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVY-PSCSDARVMWD-QKTGRSRGFGFVSFRNQQDAQSAIN 201
           +F+G +        +    +       D  V        ++RGF FV + + + A  A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 202 DLTGK--WLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNG 242
            L      L   QI  +WA        D      ++V   ++G
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEP----EIDVDEDVMETVSGPSSG 109

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-------KGFGFVRYSTHAEAAL 315
             +++G +     + ++      +  GV  +V V          +GF FV Y +H  AA+
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGV-LDVIVYASAADKMKNRGFAFVEYESHRAAAM 67

Query: 316 AIQMGNTTQSSYLFGKQMKV 335
           A +     +   L+G Q+ V
Sbjct: 68  ARRKLMPGR-IQLWGHQIAV 86

>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 = 70.2 bits (172), Expect = 5e-15
 Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 143 NIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWD---QKTGRSRGFGFVSFRNQQDAQ 197
            I+V +L+  V +  L   F  Y   S    R+M+D    K GR +G  F+   N++ A 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 198 SAINDLTGKWLGSRQIRCNWA 218
            A+ +  G  L  + +   +A
Sbjct: 107 KALKEANGYVLFGKPMVVQFA 127

>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 = 61.0 bits (148), Expect = 1e-11
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 9/88 (10%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-----IRKDKS----SYGFIHYFDRRSAAM 109
           +YV N+   V E  L+ +F                IR  K        FI   + ++AA 
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 110 AILSLNGRHLFGQPIKVNWAYASGQRED 137
           A+   NG  LFG+P+ V +A ++  ++D
Sbjct: 108 ALKEANGYVLFGKPMVVQFARSARPKQD 135

>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 = 57.9 bits (140), Expect = 1e-10
 Identities = 26/88 (29%), Positives = 32/88 (36%), Gaps = 12/88 (13%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD---------KGFGFVRY 307
           E       +YV NLA  V + DL   F        E  R+  D         KG  F+  
Sbjct: 40  EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99

Query: 308 STHAEAALAIQMGNTTQSSYLFGKQMKV 335
                AA A++  N      LFGK M V
Sbjct: 100 PNEKAAAKALKEANGYV---LFGKPMVV 124

>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 = 68.7 bits (168), Expect = 9e-15
 Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 144 IFVGDLSPEVTDATLFA---CFSVYPSCSDARVMWDQKTGRSR---GFGFVSFRNQQDAQ 197
           +FV  LS  + D  +      F  +       +        S+      +V++   +DA 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 198 SAINDLTGKWLGSRQIRCNWAT 219
            AI  +    +  R ++ +  T
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGT 99

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 59.1 bits (143), Expect = 2e-11
 Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 10/81 (12%)

Query: 59  VYVGNIHTQVTEPLL---QEVFSSTGPVEGCKLIR-------KDKSSYGFIHYFDRRSAA 108
           V+V  +  ++ +P +    E F   G +    +         +  S+  ++ Y     A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 109 MAILSLNGRHLFGQPIKVNWA 129
            AI  +N   + G+ +K +  
Sbjct: 78  RAIQCVNNVVVDGRTLKASLG 98

>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 = 53.7 bits (129), Expect = 2e-09
 Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 13/85 (15%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLG-AGVIEEVRVQRDK---------GFGFVRYSTH 310
           Q   V+V  L+  +   ++ +     G  G I +V +                +V Y   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            +A  AIQ  N      + G+ +K 
Sbjct: 74  EDALRAIQCVNNVV---VDGRTLKA 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 68.3 bits (167), Expect = 9e-15
 Identities = 23/87 (26%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
                PPG        VYVGN+        L+      G V   +L  +      F+HY 
Sbjct: 6   SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQGPRRRAFLHYP 64

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWA 129
           D  +A  A+  L G  L    ++V  A
Sbjct: 65  DSAAAQQAVSCLQGLRLGTDTLRVALA 91

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 65.6 bits (160), Expect = 7e-14
 Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 5/91 (5%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S   E      +++VG+L  +   + L             R+ W       R   F+ +
Sbjct: 9   GSPPGEGAPLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQ----GPRRRAFLHY 63

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
            +   AQ A++ L G  LG+  +R   A + 
Sbjct: 64  PDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 55.2 bits (133), Expect = 3e-10
 Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           E  P    VYVGNL  +    DL R    LG+ V   +  Q  +   F+ Y   A A  A
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALRELGS-VPLRLTWQGPRRRAFLHYPDSAAAQQA 72

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           +      +   L    ++V
Sbjct: 73  VSCLQGLR---LGTDTLRV 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 = 65.9 bits (161), Expect = 9e-14
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           SG+ +  S      + ++   +T   +       P   +A  +     G+  G   V F+
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK 65

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           N+ DA+ +   L  K L  R+   +  T 
Sbjct: 66  NEDDARKSER-LHRKKLNGREAFVHVVTL 93

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.0 bits (125), Expect = 7e-09
 Identities = 13/89 (14%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVR 306
           ++   + N      ++ N+   +T++D+ +    +       V V  D      G   V+
Sbjct: 5   SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPV-DENAVHVLVDNNGQGLGQALVQ 63

Query: 307 YSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           +    +A  + ++        L G++  V
Sbjct: 64  FKNEDDARKSERLHR----KKLNGREAFV 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 = 50.5 bits (121), Expect = 3e-08
 Identities = 17/97 (17%), Positives = 31/97 (31%), Gaps = 5/97 (5%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFI 99
           SG+   G   S     ++ NI   +T+  + +        E    +  D +        +
Sbjct: 3   SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALV 62

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
             F     A     L+ + L G+   V+       RE
Sbjct: 63  Q-FKNEDDARKSERLHRKKLNGREAFVHVVTLEDMRE 98

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 65.3 bits (159), Expect = 2e-13
 Identities = 19/101 (18%), Positives = 42/101 (41%), Gaps = 6/101 (5%)

Query: 35  AAPQIEPIPSGNLPPGFDPST-CRSVYVGNIHTQVTEPLLQE----VFSSTGPVEGCKLI 89
           A  + + + S +L      +   + V + NI+ +V +  LQ     + SS G +    + 
Sbjct: 7   AKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD 66

Query: 90  RKDKS-SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
             D +    +I +  + SA   + +  G    G P+ + ++
Sbjct: 67  LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 63.8 bits (155), Expect = 7e-13
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 143 NIFVGDLSPEVTD----ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
            + + +++PEV      A L+A  S      D  V     +  + G  ++ F  Q+ AQ+
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQA 87

Query: 199 AINDLTGKWLGSRQIRCNWA 218
            +    G       +   ++
Sbjct: 88  FVEAFQGYPFQGNPLVITFS 107

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.8 bits (142), Expect = 4e-11
 Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 8/93 (8%)

Query: 248 KETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSL--GAGVIEEVRVQRD---KGF 302
                   P +      V + N+ PEV +  L    ++L    G I ++ V       G 
Sbjct: 15  DSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGK 74

Query: 303 GFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            ++ ++T   A   +      Q     G  + +
Sbjct: 75  AYIVFATQESAQAFV---EAFQGYPFQGNPLVI 104

>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 = 64.4 bits (157), Expect = 2e-13
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 14/82 (17%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFS-----------STGPVEGCKLIRKDKSSYGFIHYFDRR 105
           R +YVGNI   +TE  + + F+              PV   + I +DK ++ F+ +    
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-INQDK-NFAFLEFRSVD 64

Query: 106 SAAMAILSLNGRHLFGQPIKVN 127
               A ++ +G    GQ +K+ 
Sbjct: 65  ETTQA-MAFDGIIFQGQSLKIR 85

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 62.8 bits (153), Expect = 5e-13
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 13/80 (16%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLG---------AGVIEEVRVQRDKGFGFVRYSTHAEAAL 315
           +YVGN+   +T+  +   F++              +  V++ +DK F F+ + +  E   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 316 AIQMGNTTQSSYLFGKQMKV 335
           A+            G+ +K+
Sbjct: 69  AMAFDGII----FQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 55.9 bits (135), Expect = 2e-10
 Identities = 10/76 (13%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 144 IFVGDLSPEVTDATLFACFS-----VYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           ++VG++   +T+  +   F+        + +    +   +  + + F F+ FR+  +   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 199 AINDLTGKWLGSRQIR 214
           A+    G     + ++
Sbjct: 69  AMA-FDGIIFQGQSLK 83

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 63.2 bits (154), Expect = 6e-13
 Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 145 FVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT 204
            +      V    L + FS      +     D+ TG+++GF FV   +  DA+  I    
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 205 GKWL-GSRQIRCNWAT 219
           GK L    ++      
Sbjct: 76  GKRLDLKHRLFLYTMK 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 5/73 (6%)

Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSS--YGFIHYFDRRSAAMAILSLN 115
            + +    V +  L  +FS  G V   +         +  + F+       A   I S +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 116 GRHLFGQP-IKVN 127
           G+ L  +  + + 
Sbjct: 76  GKRLDLKHRLFLY 88

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 8/62 (12%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQM 319
            + +    V +  L   F    AG +  +    D      KGF FV   +  +A   I+ 
Sbjct: 16  VIPSAKVPVLKKALTSLFSK--AGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73

Query: 320 GN 321
            +
Sbjct: 74  FH 75

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 11/84 (13%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHA 311
           +N+ +  +VY+     + T  D+       G   +  ++++R      KG  FV + +  
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQ--VLNIQMRRTLHKAFKGSIFVVFDSIE 63

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
            A   ++              + +
Sbjct: 64  SAKKFVETPGQK----YKETDLLI 83

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 10/92 (10%), Positives = 32/92 (34%), Gaps = 1/92 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++++     + T   +           + ++         +G  FV F + + A+  +  
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVET 71

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAK 234
              K+  +  +        A  NE+++ +  +
Sbjct: 72  PGQKYKETDLLILFKDDYFAKKNEERKQNKVE 103

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.0 bits (125), Expect = 6e-09
 Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 4/78 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-KDKSS--YGFIHYFDRRSAAMAILS 113
           RSVY+    T  T   ++E     G V   ++ R   K+     F+  FD   +A   + 
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVV-FDSIESAKKFVE 70

Query: 114 LNGRHLFGQPIKVNWAYA 131
             G+      + + +   
Sbjct: 71  TPGQKYKETDLLILFKDD 88

>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 = 66.8 bits (162), Expect = 2e-12
 Identities = 17/83 (20%), Positives = 40/83 (48%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FV  ++ + T++ L   F VY       +++ +++G+ RG+ F+ + +++D  SA    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 204 TGKWLGSRQIRCNWATKGAGNNE 226
            GK +  R++  +          
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGW 187

>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 = 62.2 bits (150), Expect = 6e-11
 Identities = 29/187 (15%), Positives = 64/187 (34%), Gaps = 22/187 (11%)

Query: 2   QHQRLKQQQQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYV 61
           + +R ++++ +++Q  ++  L     ++ P      Q +                ++++V
Sbjct: 66  RMERKRREKIERRQQEVETEL----KMWDPHNDPNAQGDAF--------------KTLFV 107

Query: 62  GNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSLNGR 117
             ++   TE  L+  F   GP++   ++   +S     Y FI Y   R    A    +G+
Sbjct: 108 ARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK 167

Query: 118 HLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ 177
            + G+ + V+       +          +G       D  +        S  D R     
Sbjct: 168 KIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSP 227

Query: 178 KTGRSRG 184
              R R 
Sbjct: 228 LPHRDRD 234

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 49.1 bits (116), Expect = 1e-06
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 13/77 (16%)

Query: 256 PENNPQ-----YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGF 304
           P N+P      + T++V  +  + T+  L R F   G   I+ + +   K      G+ F
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGP--IKRIHMVYSKRSGKPRGYAF 148

Query: 305 VRYSTHAEAALAIQMGN 321
           + Y    +   A +  +
Sbjct: 149 IEYEHERDMHSAYKHAD 165

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 61.4 bits (149), Expect = 3e-12
 Identities = 14/89 (15%), Positives = 28/89 (31%), Gaps = 6/89 (6%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
            S         S    V+V  +   V E  L E     G +    ++         + + 
Sbjct: 4   GSSGSHHKVSVS--PVVHVRGLCESVVEADLVEALEKFGTICYVMMMP--FKRQALVEFE 59

Query: 103 DRRSAAMAI--LSLNGRHLFGQPIKVNWA 129
           +  SA   +   +    ++ GQ    N++
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYS 88

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 57.1 bits (138), Expect = 9e-11
 Identities = 15/86 (17%), Positives = 26/86 (30%), Gaps = 3/86 (3%)

Query: 250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYST 309
           + ++ +         V+V  L   V + DL       G   I  V +   K    V +  
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGT--ICYVMMMPFKRQALVEFEN 60

Query: 310 HAEAALAIQMGNTTQSSYLFGKQMKV 335
              A   +         Y+ G+Q   
Sbjct: 61  IDSAKECVTFAADVP-VYIAGQQAFF 85

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 8/79 (10%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            + V  L   V +A L      + +     +M        +    V F N   A+  +  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVEFENIDSAKECVTF 70

Query: 203 LTGK--WLGSRQIRCNWAT 219
                 ++  +Q   N++T
Sbjct: 71  AADVPVYIAGQQAFFNYST 89

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            S  RSV+V      V    L E F + GPV    ++ KDK  +  +       A  A+L
Sbjct: 5   SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGVFAIVE-MGDVGAREAVL 62

Query: 113 SLNGRHLFGQPIKV 126
           S +   L G  ++V
Sbjct: 63  SQSQHSLGGHRLRV 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 7/73 (9%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG-FGFVRYSTHAEAALAIQMGNT 322
           +V+V      V    L  +F +   G +  V + +DKG F  V           +     
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLA--FGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQH 67

Query: 323 TQSSYLFGKQMKV 335
           +    L G +++V
Sbjct: 68  S----LGGHRLRV 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++FV      V  A L   F  +   +   V+ D+  G    F  V   +    ++ ++ 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVAS--VVMDKDKGV---FAIVEMGDVGAREAVLS- 63

Query: 203 LTGKWLGSRQIRC 215
            +   LG  ++R 
Sbjct: 64  QSQHSLGGHRLRV 76

>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 = 61.4 bits (149), Expect = 4e-12
 Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 2/73 (2%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG 116
             +   N+        +QE FS  G +    L   +      + + +   A  A   L  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL--PEGGITAIVEFLEPLEARKAFRHLAY 68

Query: 117 RHLFGQPIKVNWA 129
                 P+ + WA
Sbjct: 69  SKFHHVPLYLEWA 81

>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 = 59.4 bits (144), Expect = 2e-11
 Identities = 23/117 (19%), Positives = 34/117 (29%), Gaps = 12/117 (10%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S  R  T     I   +L      A +   FS + S    RV+             V F
Sbjct: 4   GSSGRSKTV----ILAKNLPAGTLAAEIQETFSRFGSLG--RVLLP----EGGITAIVEF 53

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG--AGNNEDKQSSDAKSVVELTNGSSE 245
               +A+ A   L         +   WA  G      + K S   +   +  +G S 
Sbjct: 54  LEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

>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 = 53.3 bits (128), Expect = 3e-09
 Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 2/56 (3%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           T +   NL       ++   F   G+  +  V +        V +    EA  A +
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGS--LGRVLLPEGGITAIVEFLEPLEARKAFR 64

>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 = 59.5 bits (145), Expect = 9e-12
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG  + ++T+  L   FS Y    D  +         R F FV+F + Q AQS   + 
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCGE- 61

Query: 204 TGKWLGSRQIRCNWAT 219
               +    +  + A 
Sbjct: 62  -DLIIKGISVHISNAE 76

>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 = 50.7 bits (122), Expect = 1e-08
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAI 317
           +   + V+VG    ++T+ +L   F   G   + +V + +  + F FV ++    A    
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGD--VMDVFIPKPFRAFAFVTFADDQIAQSLC 59

Query: 318 QMGNTTQSSYLFGKQMKV 335
                     + G  + +
Sbjct: 60  GEDLI-----IKGISVHI 72

>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 = 40.3 bits (95), Expect = 6e-05
 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI---LSLN 115
           V+VG     +TE  L+E FS  G V    +  K   ++ F+ + D + A       L + 
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIP-KPFRAFAFVTFADDQIAQSLCGEDLIIK 66

Query: 116 GR 117
           G 
Sbjct: 67  GI 68

>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 = 60.3 bits (146), Expect = 9e-12
 Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 6/92 (6%)

Query: 40  EPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFI 99
                G+      PS  R +++  +   VTE  +  +    G V    +++    +  FI
Sbjct: 17  RGSHMGDSRSAGVPS--RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK--GKNQAFI 72

Query: 100 HYFDRRSAAMAI--LSLNGRHLFGQPIKVNWA 129
                 +A   +   +     L GQPI + ++
Sbjct: 73  EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104

>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 = 58.0 bits (140), Expect = 6e-11
 Identities = 11/95 (11%), Positives = 34/95 (35%), Gaps = 3/95 (3%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK 300
           + S    + +   ++         +++  L  +VT+ ++         G +  + + + K
Sbjct: 10  HSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLMLKGK 67

Query: 301 GFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
              F+  +T   A   +    +     L G+ + +
Sbjct: 68  NQAFIEMNTEEAANTMVNYYTSVT-PVLRGQPIYI 101

>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 = 47.2 bits (112), Expect = 4e-07
 Identities = 9/78 (11%), Positives = 29/78 (37%), Gaps = 8/78 (10%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND- 202
           I +  L  +VT+  + +    +   ++  ++      + +   F+    ++ A + +N  
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 87

Query: 203 -LTGKWLGSRQIRCNWAT 219
                 L  + I   ++ 
Sbjct: 88  TSVTPVLRGQPIYIQFSN 105

>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 = 59.8 bits (145), Expect = 9e-12
 Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 6/104 (5%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           SG   DT+    + +  L    +   +   FS      +   +     GRS G  FV F 
Sbjct: 6   SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFA 65

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
           +Q+ A+ A+     + +G R I    +++      + ++S   S
Sbjct: 66  SQEIAEKAL-KKHKERIGHRYIEIFKSSR-----AEVRTSGPSS 103

>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 = 44.7 bits (106), Expect = 2e-06
 Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 12/83 (14%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
           GSS             +      V +  L    ++ ++ + F  L   V   + +  D  
Sbjct: 1   GSSGSS------GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEI-VPNGMTLPVDFQ 53

Query: 300 ---KGFGFVRYSTHAEAALAIQM 319
               G  FV++++   A  A++ 
Sbjct: 54  GRSTGEAFVQFASQEIAEKALKK 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 = 42.0 bits (99), Expect = 2e-05
 Identities = 15/97 (15%), Positives = 33/97 (34%), Gaps = 8/97 (8%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFI 99
           SG+     D +    V +  +    ++  + + FS    V     +  D         F+
Sbjct: 3   SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
             F  +  A   L  +   +  + I++   + S + E
Sbjct: 63  Q-FASQEIAEKALKKHKERIGHRYIEI---FKSSRAE 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.4 bits (144), Expect = 1e-11
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
            + + P     S    V++  +   V E  L E     GP+    ++ K +     + + 
Sbjct: 10  ENYDDPHKTPAS--PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR--QALVEFE 65

Query: 103 DRRSAAMAI--LSLNGRHLFGQPIKVNWA 129
           D   A  A+   + N  ++ G P  VN++
Sbjct: 66  DVLGACNAVNYAADNQIYIAGHPAFVNYS 94

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 20/84 (23%), Positives = 27/84 (32%), Gaps = 3/84 (3%)

Query: 252 NTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHA 311
           N + P   P    V++  L   V + DL       G   I  V V   K    V +    
Sbjct: 11  NYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGP--ISYVVVMPKKRQALVEFEDVL 68

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
            A  A+      Q  Y+ G    V
Sbjct: 69  GACNAVNYAADNQ-IYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + +  L   V +A L      +   S   VM        +    V F +   A +A+N  
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77

Query: 204 TGK--WLGSRQIRCNWAT 219
                ++       N++T
Sbjct: 78  ADNQIYIAGHPAFVNYST 95

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           + + V NL  +    ++H          ++   V R+K   FV      +A  AIQM + 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD---LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQ 62

Query: 323 TQSSYLFGKQMKV 335
                  GK + V
Sbjct: 63  YS---FRGKDLIV 72

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 57.4 bits (139), Expect = 5e-11
 Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 7/85 (8%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   I V +L  +     +      Y        +      R++   FV+  N + AQ
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDY-------DLKYCYVDRNKRTAFVTLLNGEQAQ 54

Query: 198 SAINDLTGKWLGSRQIRCNWATKGA 222
           +AI          + +        A
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPTDA 79

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 54.7 bits (132), Expect = 5e-10
 Identities = 11/77 (14%), Positives = 23/77 (29%), Gaps = 5/77 (6%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-YGFIHYFDRRSAAMAIL 112
           S    + V N+        + ++          K    D++    F+   +   A  AI 
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDL----KYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 113 SLNGRHLFGQPIKVNWA 129
             +     G+ + V   
Sbjct: 59  MFHQYSFRGKDLIVQLQ 75

>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 = 58.4 bits (142), Expect = 2e-11
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 7/76 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG  + ++T   L   F  Y    D  +         R F FV+F + + AQS   + 
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIP-----KPFRAFAFVTFADDKVAQSLCGE- 67

Query: 204 TGKWLGSRQIRCNWAT 219
               +    +  + A 
Sbjct: 68  -DLIIKGISVHISNAE 82

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 12/65 (18%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEA 313
           +  ++   + V+VG    ++T  +L + F   G   + +V + +  + F FV ++    A
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGE--VVDVFIPKPFRAFAFVTFADDKVA 61

Query: 314 ALAIQ 318
                
Sbjct: 62  QSLCG 66

>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 = 38.0 bits (89), Expect = 4e-04
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 4/69 (5%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
                  V+VG     +T   LQ+ F   G V    +  K   ++ F+ + D + A    
Sbjct: 7   HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIP-KPFRAFAFVTFADDKVAQSLC 65

Query: 112 ---LSLNGR 117
              L + G 
Sbjct: 66  GEDLIIKGI 74

>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 = 59.2 bits (143), Expect = 2e-11
 Identities = 18/84 (21%), Positives = 31/84 (36%), Gaps = 5/84 (5%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            +    V  G +   V+   L  V    G V+    +  +K  Y F  Y     +  A +
Sbjct: 24  ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL-MPPNKP-YSFARYRTTEESKRAYV 81

Query: 113 SLNGRHLF---GQPIKVNWAYASG 133
           +LNG+ +    GQ I +   +   
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFVEK 105

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 57.2 bits (138), Expect = 1e-10
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 2/94 (2%)

Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD 299
           ++G+          E      Q   V  G L   V++  L       G   ++ + +  +
Sbjct: 5   SSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGL--VDALLMPPN 62

Query: 300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM 333
           K + F RY T  E+  A    N  +     G+++
Sbjct: 63  KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI 96

>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 = 44.1 bits (104), Expect = 4e-06
 Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 6/63 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +  G L   V+   L              +        ++ + F  +R  ++++ A   L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 83

Query: 204 TGK 206
            GK
Sbjct: 84  NGK 86

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           S  R      F +++  L  E  +  +   F       D+  +     G++ G GFV FR
Sbjct: 16  SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           N+ D ++A+     +++G+R I+ +  TK
Sbjct: 76  NEADYKAAL-CRHKQYMGNRFIQVHPITK 103

>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 = 51.4 bits (123), Expect = 2e-08
 Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 8/85 (9%)

Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD 299
           ++G S  G++ + + +P        VY+  L  E     +   F  L   V + + +   
Sbjct: 5   SSGKSPSGQKRSRSRSPHEAG--FCVYLKGLPFEAENKHVIDFFKKLD-IVEDSIYIAYG 61

Query: 300 -----KGFGFVRYSTHAEAALAIQM 319
                 G GFV +   A+   A+  
Sbjct: 62  PNGKATGEGFVEFRNEADYKAALCR 86

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 43.7 bits (103), Expect = 7e-06
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           VY+  +  +     + + F     VE    I    +      GF+  F   +   A L  
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV-EFRNEADYKAALCR 86

Query: 115 NGRHLFGQPIKVNWAYASGQRED 137
           + +++  + I+V+     G  E 
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLEK 109

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 58.5 bits (141), Expect = 5e-11
 Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 36  APQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS 95
           A     + +G    G   S    + V N+   VT  +L ++FS  G V       K+   
Sbjct: 10  AASAAAVDAGMAMAG--QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 67

Query: 96  YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA 131
              + Y D  SA  A LSL+G++++     +   ++
Sbjct: 68  QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 61.0 bits (147), Expect = 5e-11
 Identities = 17/97 (17%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 48  PPGFDPSTCRSVYVGNIH---------TQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGF 98
             G      +++YVG I              E  ++ VFS  G ++  + +     + GF
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES--KNCGF 183

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
           + +  + +A  A  +++ + L     K       G  
Sbjct: 184 VKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 53.3 bits (127), Expect = 2e-08
 Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 12/79 (15%)

Query: 255 APENNPQYTTVYVGNL---------APEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFV 305
                 +  T+YVG +          P   +  +   F  LG   I+ +R    K  GFV
Sbjct: 127 IGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGD--IDRIRYVESKNCGFV 184

Query: 306 RYSTHAEAALAIQ-MGNTT 323
           ++   A A  A + M N T
Sbjct: 185 KFKYQANAEFAKEAMSNQT 203

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 39.8 bits (92), Expect = 7e-04
 Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 15/87 (17%)

Query: 143 NIFVGDLSPEVTDAT---------LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
            ++VG +   +             +   FS        R +       S+  GFV F+ Q
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQ 189

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATK 220
            +A+ A   ++ + L     +     +
Sbjct: 190 ANAEFAKEAMSNQTLLLPSDKEWDDRR 216

>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 = 59.3 bits (143), Expect = 6e-11
 Identities = 28/122 (22%), Positives = 46/122 (37%), Gaps = 2/122 (1%)

Query: 10  QQQQQQALMQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVT 69
                    Q AL    S+    L  A     + +G    G   S    + V N+   VT
Sbjct: 2   HHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAG--QSPVLRIIVENLFYPVT 59

Query: 70  EPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
             +L ++FS  G V       K+      + Y D  SA  A LSL+G++++     +   
Sbjct: 60  LDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID 119

Query: 130 YA 131
           ++
Sbjct: 120 FS 121

>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 = 44.7 bits (105), Expect = 6e-06
 Identities = 21/123 (17%), Positives = 41/123 (33%), Gaps = 8/123 (6%)

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA--SGQREDTSGHFNIFVGDLSPEVTDAT 157
           H+    SA  A+ ++N        +  + A           S    I V +L   VT   
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62

Query: 158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL--GSRQIRC 215
           L   FS + +              ++    + + +   AQ A   L G+ +      +R 
Sbjct: 63  LHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 118

Query: 216 NWA 218
           +++
Sbjct: 119 DFS 121

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 57.9 bits (140), Expect = 6e-11
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
            PS  R +++  +   VTE  +  +    G V    +++       FI      +A   +
Sbjct: 14  VPS--RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN--QAFIEMNTEEAANTMV 69

Query: 112 --LSLNGRHLFGQPIKVNWA 129
              +     L GQPI + ++
Sbjct: 70  NYYTSVTPVLRGQPIYIQFS 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 10/72 (13%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
            +++  L  +VT+ ++         G +  + + + K   F+  +T   A   +    + 
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLP--FGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSV 75

Query: 324 QSSYLFGKQMKV 335
               L G+ + +
Sbjct: 76  T-PVLRGQPIYI 86

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 10/78 (12%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           I +  L  +VT+  + +    +   ++  ++      + +   F+    ++ A + +N  
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 72

Query: 204 T--GKWLGSRQIRCNWAT 219
           T     L  + I   ++ 
Sbjct: 73  TSVTPVLRGQPIYIQFSN 90

>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 = 57.1 bits (138), Expect = 1e-10
 Identities = 11/87 (12%), Positives = 25/87 (28%), Gaps = 3/87 (3%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
            SG+        +   V V  +    +   L++     G V    + R      G + + 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFV 58

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWA 129
            +     A+  L+         +  + 
Sbjct: 59  RKEDMTYAVRKLDNTKFRSHEGETAYI 85

>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 = 56.7 bits (137), Expect = 1e-10
 Identities = 14/77 (18%), Positives = 21/77 (27%), Gaps = 7/77 (9%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
             + V  L P  +   L            A V          G G V F  ++D   A+ 
Sbjct: 16  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTYAVR 68

Query: 202 DLTGKWLGSRQIRCNWA 218
            L      S +    + 
Sbjct: 69  KLDNTKFRSHEGETAYI 85

>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 = 54.8 bits (132), Expect = 7e-10
 Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
            P +      V V  L P  +  DL  H     AG +    V RD G G V +    +  
Sbjct: 8   GPPSRRSENRVVVSGLPPSGSWQDLKDHMRE--AGDVCYADVYRD-GTGVVEFVRKEDMT 64

Query: 315 LAIQMGN 321
            A++  +
Sbjct: 65  YAVRKLD 71

>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 = 56.4 bits (136), Expect = 2e-10
 Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFD 103
           S        PS  R +++  +  +VTE  +  +    G V    +++    +  F+    
Sbjct: 5   SSGDKMDGAPS--RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK--GKNQAFLELAT 60

Query: 104 RRSAAMAI--LSLNGRHLFGQPIKVNWA 129
             +A   +   S    HL  QPI + ++
Sbjct: 61  EEAAITMVNYYSAVTPHLRNQPIYIQYS 88

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.4 bits (131), Expect = 7e-10
 Identities = 10/81 (12%), Positives = 29/81 (35%), Gaps = 3/81 (3%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
              +      +++  L  EVT+ ++         G +  + + + K   F+  +T   A 
Sbjct: 8   DKMDGAPSRVLHIRKLPGEVTETEVIALGLP--FGKVTNILMLKGKNQAFLELATEEAAI 65

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
             +   +     +L  + + +
Sbjct: 66  TMVNYYSAVT-PHLRNQPIYI 85

>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 = 45.2 bits (107), Expect = 2e-06
 Identities = 10/79 (12%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + +  L  EVT+  + A    +   ++  ++      + +   F+    ++ A + +N  
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVNYY 71

Query: 204 TGK--WLGSRQIRCNWATK 220
           +     L ++ I   ++  
Sbjct: 72  SAVTPHLRNQPIYIQYSNH 90

>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 = 55.6 bits (134), Expect = 5e-10
 Identities = 14/87 (16%), Positives = 26/87 (29%), Gaps = 4/87 (4%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
           P G   P    S  R V V  +    +   L++     G V    + R      G + + 
Sbjct: 4   PRGRYGPPSRRSENR-VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFV 59

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWA 129
            +     A+  L+         +  + 
Sbjct: 60  RKEDMTYAVRKLDNTKFRSHEGETAYI 86

>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 = 54.1 bits (130), Expect = 1e-09
 Identities = 14/77 (18%), Positives = 21/77 (27%), Gaps = 7/77 (9%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
             + V  L P  +   L            A V          G G V F  ++D   A+ 
Sbjct: 17  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDMTYAVR 69

Query: 202 DLTGKWLGSRQIRCNWA 218
            L      S +    + 
Sbjct: 70  KLDNTKFRSHEGETAYI 86

>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 = 54.1 bits (130), Expect = 2e-09
 Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
            P +      V V  L P  +  DL  H     AG +    V RD G G V +    +  
Sbjct: 9   GPPSRRSENRVVVSGLPPSGSWQDLKDHMRE--AGDVCYADVYRD-GTGVVEFVRKEDMT 65

Query: 315 LAIQMGN 321
            A++  +
Sbjct: 66  YAVRKLD 72

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 12/92 (13%), Positives = 25/92 (27%), Gaps = 5/92 (5%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY-PSCSDARVMWDQKTGRSRGFGFVS 189
            S   +  +  + I + +L    +   L           + + V     T    G G + 
Sbjct: 18  GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN----TRDFDGTGALE 73

Query: 190 FRNQQDAQSAINDLTGKWLGSRQIRCNWATKG 221
           F +++    A+  L         I        
Sbjct: 74  FPSEEILVEALERLNNIEFRGSVITVERDDNP 105

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.5 bits (126), Expect = 5e-09
 Identities = 13/99 (13%), Positives = 26/99 (26%), Gaps = 10/99 (10%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-YGFIHY 101
           P G+          R + + N+    +   L+++            +        G + +
Sbjct: 16  PRGSHMSKLPAKRYR-ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEF 74

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
                   A+  LN     G  I V          D + 
Sbjct: 75  PSEEILVEALERLNNIEFRGSVITV--------ERDDNP 105

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 11/72 (15%), Positives = 22/72 (30%), Gaps = 4/72 (5%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVI-EEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
           + + NL    +  DL               V  +   G G + + +      A++  N  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 324 QSSYLFGKQMKV 335
           +     G  + V
Sbjct: 91  E---FRGSVITV 99

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 15/90 (16%), Positives = 29/90 (32%), Gaps = 3/90 (3%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +            + V  +     +  +   F          ++ D   GR+ G G V F
Sbjct: 6   SGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD-HVGRNNGNGLVKF 63

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            + QD   A+       +  R +  + AT+
Sbjct: 64  LSPQDTFEAL-KRNRMLMIQRYVEVSPATE 92

>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 = 53.2 bits (128), Expect = 2e-09
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 247 GKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KG 301
           G   ++ +    NP    V V  +     + D+   FH L    ++ V + +D      G
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR---VDAVHLLKDHVGRNNG 57

Query: 302 FGFVRYSTHAEAALAIQM 319
            G V++ +  +   A++ 
Sbjct: 58  NGLVKFLSPQDTFEALKR 75

>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 = 38.6 bits (90), Expect = 4e-04
 Identities = 14/88 (15%), Positives = 24/88 (27%), Gaps = 4/88 (4%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIH-Y 101
               LP   D      V V  +     E  +++ F          L      + G     
Sbjct: 6   SGKPLPINPDDLY---VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVK 62

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           F         L  N   +  + ++V+ A
Sbjct: 63  FLSPQDTFEALKRNRMLMIQRYVEVSPA 90

>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 = 53.7 bits (129), Expect = 3e-09
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
              D++    + +  L    T   +   FS      +   +     G+  G  FV F +Q
Sbjct: 35  NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94

Query: 194 QDAQSAINDLTGKWLGSRQIR 214
           + A+ A+     + +G R I 
Sbjct: 95  ELAEKAL-GKHKERIGHRYIE 114

>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 = 49.9 bits (119), Expect = 6e-08
 Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 6/83 (7%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
            S   G++        ++     V +  L    T+ ++ + F  L   V   + +  D  
Sbjct: 22  ASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLE-IVPNGITLPVDPE 80

Query: 300 ---KGFGFVRYSTHAEAALAIQM 319
               G  FV++++   A  A+  
Sbjct: 81  GKITGEAFVQFASQELAEKALGK 103

>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 = 46.0 bits (109), Expect = 1e-06
 Identities = 17/98 (17%), Positives = 32/98 (32%), Gaps = 8/98 (8%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGF 98
             G      D +    V +  +    T+  + + FS    V     +  D     +   F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 99  IHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
           +  F  +  A   L  +   +  + I+V   + S Q E
Sbjct: 89  VQ-FASQELAEKALGKHKERIGHRYIEV---FKSSQEE 122

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 3/83 (3%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           SG    ++    + +  L    T+  ++  FS   +     +      GR  G   V F 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIG-PDGRVTGEADVEFA 63

Query: 192 NQQDAQSAINDLTGKWLGSRQIR 214
             +DA +A+       +  R + 
Sbjct: 64  THEDAVAAM-AKDKANMQHRYVE 85

>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 = 46.2 bits (110), Expect = 5e-07
 Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 14/83 (16%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-- 299
           GSS     +  +           V++  L    T+ D++  F  L       V ++    
Sbjct: 1   GSSGSSGSSFQSTTG------HCVHMRGLPYRATENDIYNFFSPLN---PMRVHIEIGPD 51

Query: 300 ---KGFGFVRYSTHAEAALAIQM 319
               G   V ++TH +A  A+  
Sbjct: 52  GRVTGEADVEFATHEDAVAAMAK 74

>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 = 42.8 bits (101), Expect = 1e-05
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 1/85 (1%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIH-Y 101
            SG+    F  +T   V++  +  + TE  +   FS   P+     I  D    G     
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVE 61

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKV 126
           F     A+A ++ +  ++  + +++
Sbjct: 62  FATHEDAVAAMAKDKANMQHRYVEL 86

>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 = 51.5 bits (124), Expect = 7e-09
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 4/84 (4%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S     T+ H  + +      VT+  +    +        R++ +   G   G+ FV F
Sbjct: 1   GSSGSSGTTCHT-VKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDF 57

Query: 191 RNQQDAQSAINDLTGKWLGSRQIR 214
            N+++ + A+     +++G R I 
Sbjct: 58  SNEEEVKQAL-KCNREYMGGRYIE 80

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 45.8 bits (109), Expect = 7e-07
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 8/61 (13%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTHAEAALAIQ 318
           TV +      VT+ ++      L       +R+ R+      G+ FV +S   E   A++
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLK---PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK 68

Query: 319 M 319
            
Sbjct: 69  C 69

>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 = 44.6 bits (106), Expect = 2e-06
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDR 104
             G   +TC +V +      VTE  + E  +   PV   +++R      + Y F+  F  
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTGYIFVD-FSN 59

Query: 105 RSAAMAILSLNGRHLFGQPIKV 126
                  L  N  ++ G+ I+V
Sbjct: 60  EEEVKQALKCNREYMGGRYIEV 81

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 51.7 bits (124), Expect = 8e-09
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 11/94 (11%)

Query: 135 REDTSGHFNIFVGDLSPEVTDAT-------LFACFSVYPSCSDARVMWDQKTGRSRGFGF 187
           +E       I V ++ P+V           +   FS +         + ++ G+++G+ F
Sbjct: 9   QEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKF--GKITNDFYPEEDGKTKGYIF 65

Query: 188 VSFRNQQDAQSAINDLTGKWL-GSRQIRCNWATK 220
           + + +   A  A+ +  G  L      R N  T 
Sbjct: 66  LEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTD 99

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 18/97 (18%)

Query: 50  GFDPSTCRSVYVGNI------HTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHY 101
           G D      + V N+        +  + ++ ++FS  G +       +D  +  Y F+ Y
Sbjct: 13  GID----SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEY 68

Query: 102 FDRRSAAMAILSLNGRHLFGQ-PIKVNWA-----YAS 132
                A  A+ + +G  L  Q   +VN       Y +
Sbjct: 69  ASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMT 105

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 14/70 (20%)

Query: 263 TTVYVGNLAPEVT-------QLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHA 311
           + + V N+ P+V        +  +H+ F     G I       +    KG+ F+ Y++ A
Sbjct: 16  SVIVVDNV-PQVGPDRLEKLKNVIHKIFSK--FGKITNDFYPEEDGKTKGYIFLEYASPA 72

Query: 312 EAALAIQMGN 321
            A  A++  +
Sbjct: 73  HAVDAVKNAD 82

>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 = 1e-08
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 8/80 (10%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK--TGRSRGFGFVSFRNQQDAQSAIN 201
           +FVG L P++ +  + A F  +           +       +G+ F+ F+ +   Q+ I+
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 202 D---LTGKW---LGSRQIRC 215
                 GK    + S  I+ 
Sbjct: 71  ACLEEDGKLYLCVSSPTIKD 90

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 10/87 (11%)

Query: 259 NPQYTT-VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHA 311
               +  V+VG L P++ + ++   F   G  V++             KG+ F+ +   +
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 312 EAALAIQMGNTTQSSYLF---GKQMKV 335
                I                  +K 
Sbjct: 64  SVQALIDACLEEDGKLYLCVSSPTIKD 90

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.0 bits (88), Expect = 6e-04
 Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 6/66 (9%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS------YGFIHYFDRR 105
             S  R V+VG +   + E  +   F   GP+      + +  S      Y F+ + +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 106 SAAMAI 111
           S    I
Sbjct: 64  SVQALI 69

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 51.5 bits (123), Expect = 2e-08
 Identities = 15/104 (14%), Positives = 37/104 (35%), Gaps = 13/104 (12%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDA---TLFACFSVYPSCSDARVMWDQKTGRSRGFGF 187
           +     +    F + +  L    +        +  +++   +    ++ ++ GR  G  F
Sbjct: 34  SMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAF 92

Query: 188 VSFRNQQDAQSAINDLTGKWLGSRQIRC--------NWATKGAG 223
           V   ++ D + A+     + +G R I          +W  K +G
Sbjct: 93  VELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSG 135

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 41.1 bits (96), Expect = 7e-05
 Identities = 9/104 (8%), Positives = 26/104 (25%), Gaps = 10/104 (9%)

Query: 238 ELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG-AGVIEEVRV 296
            + + +        +        +   V +  L    +  D+               V  
Sbjct: 20  HMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHF 79

Query: 297 QRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                    G  FV   +  +  +A++         +  + ++V
Sbjct: 80  IYTREGRQSGEAFVELGSEDDVKMALKKDR----ESMGHRYIEV 119

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.8 bits (121), Expect = 3e-08
 Identities = 16/94 (17%), Positives = 35/94 (37%), Gaps = 3/94 (3%)

Query: 38  QIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYG 97
           +I    + + P G   +    + + N    +T  +L  V +  G V+   + ++      
Sbjct: 9   RITRPGNTDDPSG--GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQA 65

Query: 98  FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA 131
            + +     A  A  +LNG  ++     +   YA
Sbjct: 66  MVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA 99

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 51.0 bits (122), Expect = 3e-08
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 3/84 (3%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S     ++    + +  L  + T+  ++  FS   +     +      GR  G   V F
Sbjct: 36  DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPD-GRVTGEADVEF 93

Query: 191 RNQQDAQSAINDLTGKWLGSRQIR 214
              ++A +A+       +  R I 
Sbjct: 94  ATHEEAVAAM-SKDRANMQHRYIE 116

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 51.0 bits (122), Expect = 3e-08
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD- 299
            G  + G+ + ++E    +     V++  L  + T+ D++  F  L       V ++   
Sbjct: 25  TGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN---PVRVHIEIGP 81

Query: 300 ----KGFGFVRYSTHAEAALAIQM 319
                G   V ++TH EA  A+  
Sbjct: 82  DGRVTGEADVEFATHEEAVAAMSK 105

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 1/98 (1%)

Query: 30  HPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI 89
           H   +   Q     SG+       +T   V++  +  + TE  +   FS   PV     I
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEI 79

Query: 90  RKDKSSYGFIH-YFDRRSAAMAILSLNGRHLFGQPIKV 126
             D    G     F     A+A +S +  ++  + I++
Sbjct: 80  GPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIEL 117

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 48.5 bits (116), Expect = 6e-08
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 11/81 (13%)

Query: 144 IFVGDLSPEVTDA-------TLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
           I V ++ P+V           +   FS +   ++     +   G+++G+ F+ + +   A
Sbjct: 4   IVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 60

Query: 197 QSAINDLTGKWLGSR-QIRCN 216
             A+ +  G  L  +   R N
Sbjct: 61  VDAVKNADGYKLDKQHTFRVN 81

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 48.2 bits (115), Expect = 7e-08
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 9/78 (11%)

Query: 59  VYVGNI------HTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAMA 110
           + V N+        +  + ++ ++FS  G +       +D  +  Y F+ Y     A  A
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 63

Query: 111 ILSLNGRHLFGQ-PIKVN 127
           + + +G  L  Q   +VN
Sbjct: 64  VKNADGYKLDKQHTFRVN 81

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 14/70 (20%)

Query: 263 TTVYVGNLAPEVT-------QLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHA 311
           + + V N+ P+V        +  +H+ F     G I       +    KG+ F+ Y++ A
Sbjct: 2   SVIVVDNV-PQVGPDRLEKLKNVIHKIFSK--FGKITNDFYPEEDGKTKGYIFLEYASPA 58

Query: 312 EAALAIQMGN 321
            A  A++  +
Sbjct: 59  HAVDAVKNAD 68

>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 = 49.1 bits (117), Expect = 8e-08
 Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 3/85 (3%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV--MWDQKTGRSRGFGFVS 189
           S   E+    F I    L    T   +   FS     +          + G+ RG   + 
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 190 FRNQQDAQSAINDLTGKWLGSRQIR 214
             ++QD Q A+ +    ++G R + 
Sbjct: 62  MESEQDVQKAL-EKHRMYMGQRYVE 85

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 7/69 (10%), Positives = 17/69 (24%), Gaps = 6/69 (8%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG-AGVIEEVRVQRD-----KGFGFVRYSTH 310
           E       +    L    T  D+   F           +    +     +G   +   + 
Sbjct: 6   EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65

Query: 311 AEAALAIQM 319
            +   A++ 
Sbjct: 66  QDVQKALEK 74

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.5 bits (118), Expect = 8e-08
 Identities = 20/107 (18%), Positives = 30/107 (28%), Gaps = 4/107 (3%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDA---TLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
             Q         + +  L    T       F          +  +      GR  G  FV
Sbjct: 14  VAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFV 73

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
            F  ++ AQ+A+       LG R I    +T         + S A  
Sbjct: 74  LFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASG 119

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 47.2 bits (112), Expect = 4e-07
 Identities = 13/86 (15%), Positives = 24/86 (27%), Gaps = 7/86 (8%)

Query: 241 NGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG--AGVIEEVRVQR 298
           +  S  G  +       +      V +  L    T  ++   F       G  E +    
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 299 D-----KGFGFVRYSTHAEAALAIQM 319
                  G  FV ++    A  A++ 
Sbjct: 62  YPDGRPTGDAFVLFACEEYAQNALRK 87

>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 = 47.2 bits (112), Expect = 4e-07
 Identities = 16/107 (14%), Positives = 38/107 (35%), Gaps = 13/107 (12%)

Query: 137 DTSGHFNIFVGDLSPEVTDATL---FACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +    + + +  L    +   +    +  +++   +    ++  + GR  G  FV   ++
Sbjct: 13  EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT-REGRQSGEAFVELESE 71

Query: 194 QDAQSAINDLTGKWLGSRQIRC--------NWATKGAGNNEDKQSSD 232
            D + A+     + +G R I          +W  K +G N     S 
Sbjct: 72  DDVKLAL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSS 117

>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 = 44.9 bits (106), Expect = 3e-06
 Identities = 15/84 (17%), Positives = 24/84 (28%), Gaps = 10/84 (11%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG-AGVIEEVRVQRD- 299
           GSS     +     PE    Y  V +  L    +  D+            +  V      
Sbjct: 1   GSS---GSSGMMLGPEGGEGYV-VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR 56

Query: 300 ----KGFGFVRYSTHAEAALAIQM 319
                G  FV   +  +  LA++ 
Sbjct: 57  EGRQSGEAFVELESEDDVKLALKK 80

>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 = 44.5 bits (105), Expect = 3e-06
 Identities = 12/45 (26%), Positives = 20/45 (44%)

Query: 173 VMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
            + D       G  +V FR ++DA+ A+ DL  +W   + I    
Sbjct: 58  NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 44.8 bits (105), Expect = 1e-05
 Identities = 13/143 (9%), Positives = 44/143 (30%), Gaps = 6/143 (4%)

Query: 72  LLQEVFSSTGPVE-----GCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV 126
           L +++    G V          + +  + +  I     +S A  +     +    +    
Sbjct: 35  LKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSK 94

Query: 127 NWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFG 186
                + + ++   + ++++     + T   +           + ++         +G  
Sbjct: 95  PLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSI 153

Query: 187 FVSFRNQQDAQSAINDLTGKWLG 209
           FV F + + A+  +     K+  
Sbjct: 154 FVVFDSIESAKKFVETPGQKYKE 176

>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 = 41.0 bits (95), Expect = 2e-04
 Identities = 12/73 (16%), Positives = 28/73 (38%), Gaps = 7/73 (9%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYSTH 310
            +N+ +  +VY+     + T  D+       G   +  ++++R      KG  FV + + 
Sbjct: 103 YKNDVKNRSVYIKGFPTDATLDDIKEWLEDKG--QVLNIQMRRTLHKAFKGSIFVVFDSI 160

Query: 311 AEAALAIQMGNTT 323
             A   ++     
Sbjct: 161 ESAKKFVETPGQK 173

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 52  DPSTCRSVYVGNIHTQVTEP----LLQEVFSSTGPVEGCKLIR-KDKSSYGFIHYFDRRS 106
                  V V NI  +++      LLQE F+  G V+  +L    D      +   + + 
Sbjct: 5   SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQD 64

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           A  A+ SL+   +  + I V+   A+G    +SG
Sbjct: 65  AIGAVNSLHRYKIGSKKILVS--LATGASGPSSG 96

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 7/97 (7%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDA----TLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
           G    +    ++ V ++   ++       L   F+ +       +         +    V
Sbjct: 1   GSSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVEL---SPHTDYQLKAVV 57

Query: 189 SFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNN 225
              N QDA  A+N L    +GS++I  + AT  +G +
Sbjct: 58  QMENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPS 94

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 20/76 (26%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDA 196
            +SG   + V  L P V D  L   F          V+  Q   R    G ++FR   DA
Sbjct: 4   GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ---RLGCGGVLTFREPADA 60

Query: 197 QSAIN----DLTGKWL 208
           +  +     +L G  L
Sbjct: 61  ERVLAQADHELHGAQL 76

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 42.1 bits (98), Expect = 2e-04
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 57  RSVYVGN--IHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL 114
           +S+ V N  +   V+   L  V    G V+   L+      Y F  Y     +  A ++L
Sbjct: 19  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDA--LLMPPNKPYSFARYRTTEESKRAYVTL 76

Query: 115 NGRHLFGQPIKVNWAYAS 132
           NG+ +     +    Y +
Sbjct: 77  NGKEVVDDLGQKITLYLN 94

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 7/100 (7%)

Query: 44  SGNLPPGFDPSTCRSVYVGNI-HTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
           SG+        T R V++ +    +     L ++    G +     +  +K +  FI   
Sbjct: 3   SGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVIS--NHLILNKINEAFIEMA 60

Query: 103 DRRSAAMAI--LSLNGRHLFGQPIKVNWAYASGQREDTSG 140
               A  A+   +     +FG+P++V+   +   +   SG
Sbjct: 61  TTEDAQAAVDYYTTTPALVFGKPVRVH--LSQKYKRIKSG 98

>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 14/34 (41%), Positives = 18/34 (52%)

Query: 182 SRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC 215
             G   VSFR+ ++A   I  L G+W G RQI  
Sbjct: 63  PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96

>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 = 38.4 bits (89), Expect = 4e-04
 Identities = 16/99 (16%), Positives = 33/99 (33%), Gaps = 13/99 (13%)

Query: 247 GKETTNTEAPENNPQYT---------TVYVGNL-APEVTQLDLHRHFHSLGAGVIEEVRV 296
           G   ++ + PE  P             +++ NL     +   + +     G   I+   +
Sbjct: 1   GSSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYG--KIKNYIL 58

Query: 297 QRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            R K   F+   T  +A   +         +  G+ +KV
Sbjct: 59  MRMKSQAFIEMETREDAMAMVDHCLKKA-LWFQGRCVKV 96

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 184 GFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC 215
           G  FV F +  D Q A+  LTG+   +R +  
Sbjct: 60  GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 8e-04
 Identities = 50/369 (13%), Positives = 102/369 (27%), Gaps = 115/369 (31%)

Query: 22  LLQQQSLYHPGLLAAPQIEPIPSGNLPPGFDPSTCRSVYVGNI--HTQVTEPLLQEVFSS 79
           L   Q L +       QI+P    N     D S+       NI       +  L+ +  S
Sbjct: 199 LEMLQKLLY-------QIDP----NWTSRSDHSS-------NIKLRIHSIQAELRRLLKS 240

Query: 80  TGPVEGCKLIRKDKSSYGFIHYFD---------R-RSAAMAILSLNGRHLFGQPIKVNWA 129
             P E C L+  +  +    + F+         R +     + +    H+       +  
Sbjct: 241 K-PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISL--DHHSMT 297

Query: 130 YASGQREDTSGHF-NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFV 188
               + +     + +    DL  EV          +  S  D    WD            
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN----------- 346

Query: 189 SFRN-QQDAQSAINDLTGKWLGSRQIRCN---------------------WATKGAGNNE 226
            +++   D  + I + +   L   + R                       W        +
Sbjct: 347 -WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW-------FD 398

Query: 227 DKQSSDAKSVVELTNGS--SEDGKETTNTEAPENNPQYT--TVYVGNLAPEVTQLDLHRH 282
             +S     V +L   S   +  KE+T           +  ++Y+        +  LHR 
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEKQPKEST----------ISIPSIYLELKVKLENEYALHRS 448

Query: 283 FHSLGAGVIEEVRVQR-----DKG--------FGFVRYSTHAEAALAIQMGNTTQSSYL- 328
                  +++   + +     D          +  + +  H +     +     +  +L 
Sbjct: 449 -------IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH--HLKNIEHPERMTLFRMVFLD 499

Query: 329 --FGKQMKV 335
             F +Q K+
Sbjct: 500 FRFLEQ-KI 507

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	335
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.98
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.82
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.8
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.8
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.79
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.79
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.79
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.78
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.78
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.78
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.78
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.78
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.78
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.77
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.77
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.77
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.77
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.76
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.76
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.76
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.76
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.76
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.76
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.76
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.76
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.76
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.76
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.76
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.76
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.75
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.75
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.75
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.75
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.75
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.75
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.75
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.74
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.74
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.74
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.74
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.74
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.74
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.74
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.74
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.74
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.74
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.74
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.74
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.74
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.74
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.74
2div_A	99	TRNA selenocysteine associated protein; structural	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.73
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.73
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.73
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
2div_A	99	TRNA selenocysteine associated protein; structural	99.73
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.73
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.73
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.72
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.72
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.72
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.72
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.72
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.72
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.72
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.71
1x5p_A	97	Negative elongation factor E; structure genomics,	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.71
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.71
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.71
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.71
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.71
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.71
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.71
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.71
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.71
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.71
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.71
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.71
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.71
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.71
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.71
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.7
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.7
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.7
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.7
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.7
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.7
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.7
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.7
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.7
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.7
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.7
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.7
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.69
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.69
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.69
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.69
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.69
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.68
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.68
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.68
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.68
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.68
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.68
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.68
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.68
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.68
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.68
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.67
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.67
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.67
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.67
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.67
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.67
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.66
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.66
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.66
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.66
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.65
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.65
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.65
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.65
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.65
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.64
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.64
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.64
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.63
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.63
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.63
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.63
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.63
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.62
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.41
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.61
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.61
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.61
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.41
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.61
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.6
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.6
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.6
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.6
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.59
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.59
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.59
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.59
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.59
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.59
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.59
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.57
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.56
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.53
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.53
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.51
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.5
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.49
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.48
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.48
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.47
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.46
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.45
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.45
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.42
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.4
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.39
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.32
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.3
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.24
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.17
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.15
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.14
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.93
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.93
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.93
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.86
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.73
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.65
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.51
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.16
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.08
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.02
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.84
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.83
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.55
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.48
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.39
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.3
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.23
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.17
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.88
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	96.75
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.64
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.62
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.59
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.14
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.66
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	89.2

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=4.9e-46  Score=319.38  Aligned_cols=232  Identities=21%  Similarity=0.335  Sum_probs=209.9

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQ  134 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~  134 (335)
                      ++++|||+|||.++|+++|+++|+.|| |.++++  .+++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.    
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~----   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV--DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP----   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE--ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE--ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC----
Confidence            457899999999999999999999999 888887  5667899999999999999999999999999999999864    


Q ss_pred             ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       135 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                           ..++|||+|||.++++++|+++|+.||.|..+.+++++.+|.++|||||+|.+.++|.+|+..|++..++|+.|.
T Consensus        94 -----~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~  168 (284)
T 3smz_A           94 -----TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY  168 (284)
T ss_dssp             -----CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             -----CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence                 336899999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCccc-CHHHHHHHhhhcCCeeeEE
Q 019811          215 CNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEV-TQLDLHRHFHSLGAGVIEE  293 (335)
Q Consensus       215 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~-t~~~l~~~f~~~G~~~i~~  293 (335)
                      |.++..+...                                ......++|||+|||.++ ++++|+++|+.||  .|..
T Consensus       169 v~~a~~~~~~--------------------------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G--~i~~  214 (284)
T 3smz_A          169 VHWTDAGQLT--------------------------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVH--SPTF  214 (284)
T ss_dssp             EEECCGGGCC--------------------------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSS--CCSE
T ss_pred             EEECCCCCCC--------------------------------cccCCccEEEEecCCcccCCHHHHHHHhhCCC--CeEE
Confidence            9998653211                                111344889999999995 9999999999999  4777


Q ss_pred             EEEecc-----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          294 VRVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       294 v~~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +.+.++     +|+|||+|.+.++|.+|+..|+|.   .|+|++|+|
T Consensus       215 v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~---~~~g~~l~v  258 (284)
T 3smz_A          215 CQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGL---SLGGSHLRV  258 (284)
T ss_dssp             EEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTC---EETTEECEE
T ss_pred             EEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCC---ccCCeEEEE
Confidence            777664     789999999999999999999999   999999875

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=100.00  E-value=6.7e-45  Score=313.53  Aligned_cols=238  Identities=15%  Similarity=0.216  Sum_probs=201.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+...++|||+|||.++|+++|+++|+.||.|.+|++..+.  ++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            45678899999999999999999999999999999998864  36899999999999999994 9999999999999986


Q ss_pred             ccCCCccCCCCcceEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          130 YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       130 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                                ..++|||+|||..+++++|.++|+.|| .|..+.+++++. +.++|||||+|.+.++|.+|+..|++..+
T Consensus       116 ----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~  184 (292)
T 2ghp_A          116 ----------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKI  184 (292)
T ss_dssp             ----------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             ----------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEe
Confidence                      346899999999999999999999999 999999998854 77899999999999999999999999999


Q ss_pred             CCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcc-cCHHHHHHHhhhcC
Q 019811          209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPE-VTQLDLHRHFHSLG  287 (335)
Q Consensus       209 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G  287 (335)
                      .|+.|.|.++.+.......                            .......++|||+|||.. +++++|+++|+.||
T Consensus       185 ~g~~l~v~~a~~~~~~~~~----------------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G  236 (292)
T 2ghp_A          185 EGYTLVTKVSNPLEKSKRT----------------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFG  236 (292)
T ss_dssp             TTEECEEEECCCC-------------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGS
T ss_pred             CCcEEEEEECCCCcccccc----------------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccC
Confidence            9999999998764321110                            112334589999999999 99999999999999


Q ss_pred             CeeeEEEEEecc-------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          288 AGVIEEVRVQRD-------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       288 ~~~i~~v~~~~~-------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                        .|..+.+.++       +|+|||+|.+.++|.+|+ .|||.   .|+|++|+|
T Consensus       237 --~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~---~~~g~~i~V  285 (292)
T 2ghp_A          237 --SIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRS---LLGNREISV  285 (292)
T ss_dssp             --CEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTE---EETTEEEEE
T ss_pred             --CeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCC---EECCcEEEE
Confidence              5888888543       689999999999999999 99999   999999975

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2e-34  Score=227.30  Aligned_cols=162  Identities=41%  Similarity=0.796  Sum_probs=151.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ++|||+|||.++|+++|+++|+.||.|.+|++..++   ++|||||+|.+.++|.+|+..++|..+.|+.|+|.++.+..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            589999999999999999999999999999998765   35899999999999999999999999999999999987655


Q ss_pred             CccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       134 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      . ......++|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|+|||+|.+.++|.+|+..|++..++|+.|
T Consensus        81 ~-~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  159 (166)
T 3md3_A           81 Q-SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL  159 (166)
T ss_dssp             C-CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             C-CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Confidence            4 334556799999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEEcc
Q 019811          214 RCNWAT  219 (335)
Q Consensus       214 ~v~~~~  219 (335)
                      +|.|++
T Consensus       160 ~v~~a~  165 (166)
T 3md3_A          160 RINWAA  165 (166)
T ss_dssp             EEEESC
T ss_pred             EEEecC
Confidence            999985

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1e-34  Score=237.90  Aligned_cols=166  Identities=28%  Similarity=0.528  Sum_probs=147.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||.++|+++|+++|++||.|.+|++++++.    +|||||+|.+.++|.+|++.+++..+.|+.+++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            44568899999999999999999999999999999998653    58999999999999999999999999999999998


Q ss_pred             eccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       129 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      +....... .....+|||+|||.++++++|+++|+.||.|..+.++++.  +.++|||||+|.+.++|.+|++.|+|..+
T Consensus        92 ~~~~~~~~-~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~  168 (213)
T 4f02_A           92 SQRDPSLR-KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLL  168 (213)
T ss_dssp             CCCCTHHH-HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             cccccccc-ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            86544322 2234689999999999999999999999999999999884  45799999999999999999999999999


Q ss_pred             CCeeeEEEEccCC
Q 019811          209 GSRQIRCNWATKG  221 (335)
Q Consensus       209 ~g~~l~v~~~~~~  221 (335)
                      +|+.|.|.++.++
T Consensus       169 ~g~~i~V~~a~~~  181 (213)
T 4f02_A          169 NDRKVFVGRFKSR  181 (213)
T ss_dssp             TTEECEEEECCCH
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999998764

>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=100.00  E-value=1.2e-33  Score=223.17  Aligned_cols=161  Identities=27%  Similarity=0.483  Sum_probs=149.3

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ++++|||+|||.++++++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|++.|+|..+.|++|+|.++.
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            468899999999999999999999999999999988753    5899999999999999999999999999999999987


Q ss_pred             cCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       131 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      +...   ....++|+|+|||..+++++|+++|+.||.|..+.+.++..++.++|+|||+|.+.++|.+|+..|++..+.|
T Consensus        82 ~~~~---~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A           82 PGGE---SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG  158 (168)
T ss_dssp             CCSS---TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             CCcc---cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecC
Confidence            6543   3456799999999999999999999999999999999998889999999999999999999999999999977


Q ss_pred             --eeeEEEEc
Q 019811          211 --RQIRCNWA  218 (335)
Q Consensus       211 --~~l~v~~~  218 (335)
                        +.|+|.|+
T Consensus       159 ~~~~l~V~~A  168 (168)
T 1b7f_A          159 GSQPLSVRLA  168 (168)
T ss_dssp             CSSCCEEEEC
T ss_pred             CCeEEEEEeC
Confidence              99999985

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=1.8e-33  Score=231.48  Aligned_cols=169  Identities=23%  Similarity=0.439  Sum_probs=152.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|++.|++..+.|+.|+|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            346789999999999999999999999999999998764    5799999999999999999999999999999999987


Q ss_pred             ccCCCcc--------CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 019811          130 YASGQRE--------DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN  201 (335)
Q Consensus       130 ~~~~~~~--------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~  201 (335)
                      .......        .....++|||+|||.++++++|+++|+.||.|..+.+.+++.++.++|+|||+|.+.++|.+|+.
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  185 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS  185 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHH
Confidence            6554221        22455799999999999999999999999999999999998889999999999999999999999


Q ss_pred             HhCCceeCCeeeEEEEccCCC
Q 019811          202 DLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       202 ~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      .|++..++|+.|.|.|+..+.
T Consensus       186 ~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          186 SMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHTTCBCSSSBCEEEECSSCS
T ss_pred             HccCCEeCCcEEEEEEecCCC
Confidence            999999999999999998754

>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=100.00  E-value=2.7e-33  Score=220.97  Aligned_cols=160  Identities=33%  Similarity=0.541  Sum_probs=147.3

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +++|||+|||.++++++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.+
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            57899999999999999999999999999999988762    48999999999999999999999999999999999876


Q ss_pred             CCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 019811          132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSR  211 (335)
Q Consensus       132 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~  211 (335)
                      ...   ....++|+|+|||..+++++|+++|+.||.|..+.+.++..+|.++|+|||+|.+.++|.+|+..|+|..+.|+
T Consensus        82 ~~~---~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           82 SSA---SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CCG---GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             Ccc---cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            543   23457899999999999999999999999999999999988899999999999999999999999999999996


Q ss_pred             e--eEEEEc
Q 019811          212 Q--IRCNWA  218 (335)
Q Consensus       212 ~--l~v~~~  218 (335)
                      .  |+|.|+
T Consensus       159 ~~~i~v~~A  167 (167)
T 1fxl_A          159 TEPITVKFA  167 (167)
T ss_dssp             SSCCEEEEC
T ss_pred             ccceEEEeC
Confidence            5  888875

>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=100.00  E-value=3.1e-33  Score=226.58  Aligned_cols=171  Identities=19%  Similarity=0.369  Sum_probs=147.8

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+...++|||+|||.++|+++|+++|+.||.|.+|+++.++.    +|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            456788999999999999999999999999999999998753    57999999999999999975 8999999999999


Q ss_pred             eeccCCCcc---CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 019811          128 WAYASGQRE---DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT  204 (335)
Q Consensus       128 ~~~~~~~~~---~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  204 (335)
                      ++.......   .....++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+.. +
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~  166 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K  166 (196)
T ss_dssp             ECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S
T ss_pred             cccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C
Confidence            986654322   223457999999999999999999999999999999999988899999999999999999999986 7


Q ss_pred             CceeCCeeeEEEEccCCCCC
Q 019811          205 GKWLGSRQIRCNWATKGAGN  224 (335)
Q Consensus       205 ~~~~~g~~l~v~~~~~~~~~  224 (335)
                      +..+.|+.|.|.++.++...
T Consensus       167 ~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          167 YHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             CCEETTEECEEEECC-----
T ss_pred             CcEECCEEEEEEecCChhHh
Confidence            99999999999999876543

>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=100.00  E-value=1.6e-32  Score=217.60  Aligned_cols=159  Identities=23%  Similarity=0.449  Sum_probs=144.9

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcc----C-------CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCce
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSST----G-------PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQP  123 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~----G-------~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~  123 (335)
                      ++++|||+|||.++|+++|+++|+.|    |       .|.++++.+  ++|||||+|.+.++|.+|+ .++|..+.|+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~--~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~   79 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ--DKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET--TTTEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC--CCCEEEEEeCCHHHHHHHH-HhCCcEecCce
Confidence            56899999999999999999999999    6       666666644  4689999999999999999 89999999999


Q ss_pred             eEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 019811          124 IKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL  203 (335)
Q Consensus       124 l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  203 (335)
                      |+|.++.....   ....++|||+|||..+++++|+++|+.||.|..+.+.+++.+|.++|+|||+|.+.++|.+|+..|
T Consensus        80 i~v~~~~~~~~---~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           80 LKIRRPHDYQP---LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             CEEECCSSCCC---CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             eeecCCcccCC---CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            99998765432   344679999999999999999999999999999999999888999999999999999999999999


Q ss_pred             CCceeCCeeeEEEEcc
Q 019811          204 TGKWLGSRQIRCNWAT  219 (335)
Q Consensus       204 ~~~~~~g~~l~v~~~~  219 (335)
                      ++..++|+.|.|.|+.
T Consensus       157 ~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTCEETTEECEEEECC
T ss_pred             CCCEECCeEEEEEeCC
Confidence            9999999999999973

>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=100.00  E-value=1.8e-32  Score=217.90  Aligned_cols=162  Identities=23%  Similarity=0.393  Sum_probs=144.0

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC------CCCeEEEEEcCHHHHHHHHHHhCCcccc---CceeE
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD------KSSYGFIHYFDRRSAAMAILSLNGRHLF---GQPIK  125 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~------~~g~afv~f~~~~~A~~a~~~l~~~~~~---g~~l~  125 (335)
                      ++++|||+|||.++|+++|+++|++||.|.++++.+++      ++|||||+|.+.++|.+|++.|+|..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            56899999999999999999999999999999999874      3579999999999999999999998776   57777


Q ss_pred             EeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          126 VNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       126 v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      +.++.....  .....++|||+|||.++++++|+++|+.||.|.++.+.++. +|.++|+|||+|.+.++|.+|+..|+|
T Consensus        82 ~~~~~~~~~--~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           82 MKPADSEKN--NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGCC--SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Ecccccccc--ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            777654432  34456799999999999999999999999999999999885 588999999999999999999999999


Q ss_pred             ceeC---CeeeEEEEcc
Q 019811          206 KWLG---SRQIRCNWAT  219 (335)
Q Consensus       206 ~~~~---g~~l~v~~~~  219 (335)
                      ..+.   ++.|.|.|++
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            8765   4999999974

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1.1e-32  Score=225.82  Aligned_cols=159  Identities=28%  Similarity=0.470  Sum_probs=141.5

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .+.++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|+..+++..+.|+.+++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45579999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEec
Q 019811          219 TKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR  298 (335)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~  298 (335)
                      .......                                 .....+|||+|||..+++++|+++|+.||  .|..+++.+
T Consensus        93 ~~~~~~~---------------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G--~i~~~~i~~  137 (213)
T 4f02_A           93 QRDPSLR---------------------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFG--NILSCKVVC  137 (213)
T ss_dssp             CCCTHHH---------------------------------HHCTTEEEEESCCTTCCHHHHHHHHGGGS--CEEEEEEEE
T ss_pred             ccccccc---------------------------------ccccccceECCcccccHHHHHHHHHhhcC--CeEEEEeec
Confidence            6432100                                 01126799999999999999999999999  588888765


Q ss_pred             c----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          299 D----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       299 ~----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +    +|+|||+|.+.++|.+|+..|||.   .|+|++|+|
T Consensus       138 d~~~~~g~~fV~f~~~~~a~~Ai~~lng~---~~~g~~i~V  175 (213)
T 4f02_A          138 DENGSKGYGFVHFETQEAAERAIEKMNGM---LLNDRKVFV  175 (213)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHHTTC---EETTEECEE
T ss_pred             cCCCCceEEEEEeCCHHHHHHHHHHhCCC---EECCEEEEE
Confidence            4    689999999999999999999999   999999976

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=5e-32  Score=219.79  Aligned_cols=165  Identities=22%  Similarity=0.426  Sum_probs=146.6

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcc----C-------CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCce
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSST----G-------PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQP  123 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~----G-------~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~  123 (335)
                      .+++|||+|||.++|+++|+++|+.|    |       .|.++++  .+++|||||+|.+.++|.+|+ .|+|..+.|+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~--~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~   79 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI--NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE--ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe--cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCce
Confidence            46899999999999999999999999    5       5555555  345789999999999999999 89999999999


Q ss_pred             eEEeeeccCCCc-----------------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEE
Q 019811          124 IKVNWAYASGQR-----------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFG  186 (335)
Q Consensus       124 l~v~~~~~~~~~-----------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~a  186 (335)
                      |+|.++......                 ......++|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|||
T Consensus        80 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~a  159 (198)
T 2yh0_A           80 LKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA  159 (198)
T ss_dssp             EEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEE
T ss_pred             EEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEE
Confidence            999998654221                 112456899999999999999999999999999999999998889999999


Q ss_pred             EEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          187 FVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       187 fv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      ||+|.+.++|.+|+..|++..++|+.|.|.|+.++.
T Consensus       160 fV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             EEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            999999999999999999999999999999997754

>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=100.00  E-value=3.9e-32  Score=220.12  Aligned_cols=160  Identities=16%  Similarity=0.184  Sum_probs=138.4

Q ss_pred             CcceEEEeCCC-CCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           55 TCRSVYVGNIH-TQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        55 ~~~~v~v~nlp-~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ++++|||+||| ..+++++|+++|+.||.|.+|++++++ +|||||+|.+.++|.+|++.|||..+.|+.|+|.++....
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            46789999999 899999999999999999999998764 6899999999999999999999999999999999985322


Q ss_pred             Ccc----------------------------------CCCCcceEEECCCCccccHHHHHHHhccCCCc--eeeEEeecC
Q 019811          134 QRE----------------------------------DTSGHFNIFVGDLSPEVTDATLFACFSVYPSC--SDARVMWDQ  177 (335)
Q Consensus       134 ~~~----------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v--~~~~~~~~~  177 (335)
                      ...                                  ...++++|||+|||+++++++|+++|+.||.|  .++.+..+.
T Consensus        82 ~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~  161 (205)
T 3tyt_A           82 IMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK  161 (205)
T ss_dssp             CCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred             cCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC
Confidence            100                                  01234689999999999999999999999999  888888664


Q ss_pred             CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe----eeEEEE
Q 019811          178 KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSR----QIRCNW  217 (335)
Q Consensus       178 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~----~l~v~~  217 (335)
                        +..+|+|||+|.+.++|.+|+..||+..+.|+    ++.|.+
T Consensus       162 --~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~  203 (205)
T 3tyt_A          162 --SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKL  203 (205)
T ss_dssp             --SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEE
T ss_pred             --CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEe
Confidence              45679999999999999999999999999876    455554

>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=100.00  E-value=1e-32  Score=217.65  Aligned_cols=161  Identities=25%  Similarity=0.405  Sum_probs=145.8

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ++++|||+|||.++|+++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|+..  +..+.|+.|.+.++.
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            56899999999999999999999999999999998764    468999999999999999974  678999999999875


Q ss_pred             cCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       131 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      +...   ....++|||+|||.++++++|+++|+.||.|..+.+.+++.+|.++|+|||+|.+.++|.+|++ +++..++|
T Consensus        80 ~~~~---~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g  155 (167)
T 2cjk_A           80 PRDE---QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKD  155 (167)
T ss_dssp             CHHH---HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSS
T ss_pred             chhh---ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCC
Confidence            4332   2334689999999999999999999999999999999998889999999999999999999998 89999999


Q ss_pred             eeeEEEEccCC
Q 019811          211 RQIRCNWATKG  221 (335)
Q Consensus       211 ~~l~v~~~~~~  221 (335)
                      +.|.|.|+.++
T Consensus       156 ~~i~V~~a~pk  166 (167)
T 2cjk_A          156 RKIEIKRAEPR  166 (167)
T ss_dssp             SCEEEEECCCC
T ss_pred             eEEEEeecCCC
Confidence            99999998764

>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=100.00  E-value=1.8e-31  Score=221.07  Aligned_cols=164  Identities=20%  Similarity=0.334  Sum_probs=145.4

Q ss_pred             CCCCcceEEEeCCCC-CCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           52 DPSTCRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ...++++|||+|||. ++++++|+++|+.||.|.+|++..++ +|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  108 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            345678999999999 99999999999999999999999877 6899999999999999999999999999999999986


Q ss_pred             cCCCc--------------------------------cCCCCcceEEECCCCccccHHHHHHHhccCC-CceeeEEeecC
Q 019811          131 ASGQR--------------------------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQ  177 (335)
Q Consensus       131 ~~~~~--------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~  177 (335)
                      .....                                ....++++|||+|||..+++++|+++|+.|| .|..+.++.+ 
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-  187 (229)
T 2adc_A          109 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  187 (229)
T ss_dssp             CCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-
T ss_pred             CccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-
Confidence            54210                                0012357899999999999999999999999 9999988642 


Q ss_pred             CCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeeeEEEEccCC
Q 019811          178 KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG-SRQIRCNWATKG  221 (335)
Q Consensus       178 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~~~~~  221 (335)
                          .+|+|||+|.+.++|.+|+..|++..+. |+.|+|.|++++
T Consensus       188 ----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          188 ----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             ----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence                3689999999999999999999999999 999999998753

>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=99.98  E-value=2.9e-31  Score=209.50  Aligned_cols=156  Identities=33%  Similarity=0.505  Sum_probs=141.2

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ++++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+++..+.|+.|.|.|+.
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            45799999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~  299 (335)
                      ....                                   ....++|+|+|||..+++++|+++|+.||  .+..+.+.++
T Consensus        82 ~~~~-----------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G--~i~~~~i~~~  124 (168)
T 1b7f_A           82 PGGE-----------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYG--SIVQKNILRD  124 (168)
T ss_dssp             CCSS-----------------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSS--CEEEEEEEEC
T ss_pred             CCcc-----------------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCC--cEEEEEEEEc
Confidence            5431                                   12237899999999999999999999999  5888887755


Q ss_pred             ------cceEEEEeCCHHHHHHHHHhhcCCCcccccC--ccccC
Q 019811          300 ------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFG--KQMKV  335 (335)
Q Consensus       300 ------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g--~~l~v  335 (335)
                            +|+|||+|.+.++|.+|+..|+|.   .++|  ++|+|
T Consensus       125 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~---~~~g~~~~l~V  165 (168)
T 1b7f_A          125 KLTGRPRGVAFVRYNKREEAQEAISALNNV---IPEGGSQPLSV  165 (168)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHHHTTC---CCTTCSSCCEE
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhcCC---EecCCCeEEEE
Confidence                  489999999999999999999999   9987  88765

>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=99.98  E-value=5.1e-31  Score=225.90  Aligned_cols=168  Identities=24%  Similarity=0.373  Sum_probs=155.5

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++++++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            346899999999999999999999999999999987653    5899999999999999999999999999999999998


Q ss_pred             cCCCccCCCCcceEEECCCCccc-cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          131 ASGQREDTSGHFNIFVGDLSPEV-TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       131 ~~~~~~~~~~~~~l~v~nlp~~~-t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      +..........++|||+|||.++ ++++|+++|+.||.|..+.+.++. +|.++|+|||+|.+.++|.+|+..|+|..++
T Consensus       174 ~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  252 (284)
T 3smz_A          174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLG  252 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccC
Confidence            87766666778899999999995 999999999999999999999885 7889999999999999999999999999999


Q ss_pred             CeeeEEEEccCCCC
Q 019811          210 SRQIRCNWATKGAG  223 (335)
Q Consensus       210 g~~l~v~~~~~~~~  223 (335)
                      |+.|.|.|+.++..
T Consensus       253 g~~l~v~~a~~~~~  266 (284)
T 3smz_A          253 GSHLRVSFCAPGPP  266 (284)
T ss_dssp             TEECEEEECCSSSC
T ss_pred             CeEEEEEEecCCCc
Confidence            99999999977553

>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=99.98  E-value=7.1e-31  Score=207.06  Aligned_cols=154  Identities=29%  Similarity=0.456  Sum_probs=139.1

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      +++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|+|||+|.+.++|.+|+..|++..+.|+.|.|.++.+
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            46899999999999999999999999999999999988899999999999999999999999999999999999999865


Q ss_pred             CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-
Q 019811          221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-  299 (335)
                      ....                                   ...++|+|+|||..+++++|+++|+.||  .+..+.+..+ 
T Consensus        82 ~~~~-----------------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G--~i~~~~i~~~~  124 (167)
T 1fxl_A           82 SSAS-----------------------------------IRDANLYVSGLPKTMTQKELEQLFSQYG--RIITSRILVDQ  124 (167)
T ss_dssp             CCGG-----------------------------------GTTCEEEEESCCTTCCHHHHHHHHGGGS--CEEEEEEEECT
T ss_pred             Cccc-----------------------------------CCCCcEEECCCCCcCCHHHHHHHHHhcC--CEeEEEEEecC
Confidence            3210                                   1237899999999999999999999999  5777877654 


Q ss_pred             -----cceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       300 -----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                           +|+|||+|.+.++|.+|+..|||.   .++|+.+.
T Consensus       125 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~---~~~g~~~~  161 (167)
T 1fxl_A          125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQ---KPSGATEP  161 (167)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTC---CCTTCSSC
T ss_pred             CCCCccceEEEEeCCHHHHHHHHHHhcCC---ccCCCccc
Confidence                 689999999999999999999999   99998743

>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=99.98  E-value=1.4e-31  Score=212.73  Aligned_cols=163  Identities=16%  Similarity=0.326  Sum_probs=142.2

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEE---eecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL---IRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~---~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+.+.++|||+|||.++|+++|+++|+.||.+..+.+   ...+++|||||+|.+.++|.+|+ .|+|..+.|+.|+|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            4567889999999999999999999999987655222   22456799999999999999999 5999999999999999


Q ss_pred             eccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          129 AYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       129 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      +...... .....++|||+|||.++++++|+++|+.||.|..+     ..++.++|+|||+|.+.++|.+|+..|++..+
T Consensus        88 ~~~~~~~-~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 1fje_B           88 PKGRDSK-KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI  161 (175)
T ss_dssp             CCCSSCS-TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEE
T ss_pred             CCCcccc-ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            8765432 33456799999999999999999999999988766     35788999999999999999999999999999


Q ss_pred             CCeeeEEEEccCC
Q 019811          209 GSRQIRCNWATKG  221 (335)
Q Consensus       209 ~g~~l~v~~~~~~  221 (335)
                      +|+.|.|.|+.++
T Consensus       162 ~g~~i~v~~a~~k  174 (175)
T 1fje_B          162 DGRSVSLYYTGEK  174 (175)
T ss_dssp             TTEEEEEEECSSC
T ss_pred             CCeEEEEEecCCC
Confidence            9999999999764

>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=99.97  E-value=1.4e-30  Score=223.00  Aligned_cols=162  Identities=19%  Similarity=0.402  Sum_probs=143.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHH----HHHhccCCceeEEEeec-CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQ----EVFSSTGPVEGCKLIRK-DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~----~~f~~~G~v~~v~~~~~-~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ..++++|||+|||.++++++|+    ++|+.||.|.+|++.++ +++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            4567899999999999999966    89999999999998864 357999999999999999999999999999999999


Q ss_pred             eeccCCCc------------------------------------------------------------------------
Q 019811          128 WAYASGQR------------------------------------------------------------------------  135 (335)
Q Consensus       128 ~~~~~~~~------------------------------------------------------------------------  135 (335)
                      |+......                                                                        
T Consensus        86 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  165 (282)
T 3pgw_A           86 YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMP  165 (282)
T ss_pred             EeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCC
Confidence            98654310                                                                        


Q ss_pred             ------------------------------------cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCC
Q 019811          136 ------------------------------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKT  179 (335)
Q Consensus       136 ------------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~  179 (335)
                                                          .....+++|||+|||..+++++|+++|+.||.|.++.++.++  
T Consensus       166 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~--  243 (282)
T 3pgw_A          166 PPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR--  243 (282)
T ss_pred             CCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC--
Confidence                                                112245789999999999999999999999999999998542  


Q ss_pred             CCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeeeEEEEcc
Q 019811          180 GRSRGFGFVSFRNQQDAQSAINDLTGKWLG-SRQIRCNWAT  219 (335)
Q Consensus       180 ~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~~~  219 (335)
                         +|+|||+|.+.++|.+|+..|++..+. |+.|+|.|++
T Consensus       244 ---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          244 ---HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             ---CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence               589999999999999999999999999 9999999985

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=3.9e-31  Score=214.49  Aligned_cols=160  Identities=20%  Similarity=0.347  Sum_probs=143.1

Q ss_pred             cceEEEeCCCC-CCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCC
Q 019811           56 CRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQ  134 (335)
Q Consensus        56 ~~~v~v~nlp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~  134 (335)
                      +++|||+|||. ++++++|+++|+.||.|.+|++..++ +|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.....
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~   81 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   81 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCc
Confidence            57899999999 99999999999999999999998876 68999999999999999999999999999999999864421


Q ss_pred             c--------------------------------cCCCCcceEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCCCC
Q 019811          135 R--------------------------------EDTSGHFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKTGR  181 (335)
Q Consensus       135 ~--------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~  181 (335)
                      .                                ....++++|||+|||..+++++|+++|+.|| .|..+.+..+     
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----  156 (198)
T 1qm9_A           82 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----  156 (198)
T ss_dssp             CCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----
T ss_pred             CCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----
Confidence            0                                0013367899999999999999999999999 9999988643     


Q ss_pred             cceEEEEEeCCHHHHHHHHHHhCCceeC-CeeeEEEEccCC
Q 019811          182 SRGFGFVSFRNQQDAQSAINDLTGKWLG-SRQIRCNWATKG  221 (335)
Q Consensus       182 ~~g~afv~f~~~~~a~~a~~~l~~~~~~-g~~l~v~~~~~~  221 (335)
                      .+|+|||+|.+.++|.+|+..|++..++ |+.|+|.|++++
T Consensus       157 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            3689999999999999999999999999 999999998753

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=9.5e-31  Score=206.13  Aligned_cols=155  Identities=23%  Similarity=0.463  Sum_probs=138.1

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ++|||+|||.++++++|+++|+.||.|.++.+++++ ++.++|+|||+|.+.++|.+|+..+++..+.|+.|.|.++...
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            479999999999999999999999999999999885 4678999999999999999999999999999999999998654


Q ss_pred             CCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc--
Q 019811          222 AGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--  299 (335)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~--  299 (335)
                      ...                                 ...+.++|||+|||.++++++|+++|+.||  .+..+.+..+  
T Consensus        80 ~~~---------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G--~i~~~~i~~~~~  124 (166)
T 3md3_A           80 QQS---------------------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFP--SYLSGHVMWDMQ  124 (166)
T ss_dssp             CCC---------------------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTST--TEEEEEEEECTT
T ss_pred             CCC---------------------------------CCCCCceEEECCCCCCCCHHHHHHHHhccC--CeeEEEEEecCC
Confidence            321                                 112347899999999999999999999999  4778877644  


Q ss_pred             ----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 ----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 ----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                          +|+|||+|.+.++|.+|+..|||.   .++|++|+|
T Consensus       125 ~~~~~g~afV~f~~~~~A~~A~~~l~g~---~~~g~~i~v  161 (166)
T 3md3_A          125 TGSSRGYGFVSFTSQDDAQNAMDSMQGQ---DLNGRPLRI  161 (166)
T ss_dssp             TCCEEEEEEEEESCHHHHHHHHHHHTTC---EETTEECEE
T ss_pred             CCCcceEEEEEeCCHHHHHHHHHHhCCC---ccCCcEEEE
Confidence                689999999999999999999999   999999975

>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=99.97  E-value=2.1e-30  Score=214.67  Aligned_cols=190  Identities=22%  Similarity=0.347  Sum_probs=147.4

Q ss_pred             CCCCcceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          137 DTSGHFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ...++++|||+|||. ++++++|+++|+.||.|..+.+.+++     +|||||+|.+.++|.+|++.|++..+.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999998763     789999999999999999999999999999999


Q ss_pred             EEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEE
Q 019811          216 NWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR  295 (335)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~  295 (335)
                      .++...............................+.........++.++|||+|||..+++++|+++|+.|| ..|..++
T Consensus       105 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G-~~i~~v~  183 (229)
T 2adc_A          105 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG-GVVKGFK  183 (229)
T ss_dssp             ECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTS-CCEEEEE
T ss_pred             EEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcC-CCeeEEE
Confidence            999765433222111111111111111111111111111223345679999999999999999999999998 2488888


Q ss_pred             E-ecccceEEEEeCCHHHHHHHHHhhcCCCccccc-CccccC
Q 019811          296 V-QRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLF-GKQMKV  335 (335)
Q Consensus       296 ~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~-g~~l~v  335 (335)
                      + .+++|+|||+|.+.++|.+|+..|+|.   .++ |++|+|
T Consensus       184 i~~~~~g~afV~f~~~~~A~~Ai~~l~g~---~~~~g~~l~v  222 (229)
T 2adc_A          184 FFQKDRKMALIQMGSVEEAVQALIDLHNH---DLGENHHLRV  222 (229)
T ss_dssp             ECSSSTTCEEEEESSHHHHHHHHHHHTTC---BSSSSCBCEE
T ss_pred             EEECCCcEEEEEECCHHHHHHHHHHHCCC---ccCCCCeEEE
Confidence            8 457999999999999999999999999   999 999875

>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=99.97  E-value=2.5e-30  Score=218.41  Aligned_cols=160  Identities=27%  Similarity=0.394  Sum_probs=145.5

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .......++|||+|||.++|+++|+++|+.||.|.+|++.++  +|||||+|.+.++|.+|+..++|..+.|+.|+|.++
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~--kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD--RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC--CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            334566789999999999999999999999999999998654  589999999999999999999999999999999998


Q ss_pred             ccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-Ccee
Q 019811          130 YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT-GKWL  208 (335)
Q Consensus       130 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~-~~~~  208 (335)
                      .+         +.+|||+|||..+++++|+++|+.||.|..+.++++ .+|.++|+|||+|.+.++|.+|+..|+ +..+
T Consensus        94 ~~---------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~  163 (261)
T 3sde_A           94 TH---------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFL  163 (261)
T ss_dssp             CC---------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEE
T ss_pred             cc---------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEE
Confidence            64         358999999999999999999999999999999999 588999999999999999999999994 5555


Q ss_pred             C---CeeeEEEEccCC
Q 019811          209 G---SRQIRCNWATKG  221 (335)
Q Consensus       209 ~---g~~l~v~~~~~~  221 (335)
                      .   ++.|.|.++...
T Consensus       164 ~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          164 LTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             SSSSCCBCEEEECCCE
T ss_pred             ecCCCceEEEeecccc
Confidence            4   999999998764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=2.4e-30  Score=209.82  Aligned_cols=186  Identities=22%  Similarity=0.334  Sum_probs=145.2

Q ss_pred             cceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          141 HFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       141 ~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      +++|||+|||. ++++++|+++|+.||.|..+.+++++     +|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            47999999999 99999999999999999999998663     6899999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEe-c
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ-R  298 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~-~  298 (335)
                      ..............................+.........+++++|||+|||..+++++|+++|+.|| ..+..+++. .
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~~v~~v~i~~~  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG-GVVKGFKFFQK  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTT-SCCCEEEESST
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcC-CCceEEEEEeC
Confidence            76433222211111111111111111111112222223345679999999999999999999999999 248888884 4


Q ss_pred             ccceEEEEeCCHHHHHHHHHhhcCCCccccc-CccccC
Q 019811          299 DKGFGFVRYSTHAEAALAIQMGNTTQSSYLF-GKQMKV  335 (335)
Q Consensus       299 ~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~-g~~l~v  335 (335)
                      ++|+|||+|.+.++|.+|+..|+|.   .++ |++|+|
T Consensus       157 ~~g~afV~f~~~~~A~~A~~~l~g~---~~~~g~~l~v  191 (198)
T 1qm9_A          157 DRKMALIQMGSVEEAVQALIDLHNH---DLGENHHLRV  191 (198)
T ss_dssp             TSSCEEEECSSHHHHHHHHHHHTSS---CCSSCCSCCE
T ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCC---ccCCCCeEEE
Confidence            6899999999999999999999999   899 999875

>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=99.97  E-value=1.3e-30  Score=224.28  Aligned_cols=167  Identities=19%  Similarity=0.269  Sum_probs=146.7

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccC-CceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G-~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||.++++++|+++|+.|| .|.+|++..++   ++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++
T Consensus       115 ~~~~~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          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3578899999999999999999999999 99999998765   5799999999999999999999999999999999998


Q ss_pred             ccCCCcc----CCCCcceEEECCCCcc-ccHHHHHHHhccCCCceeeEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHh
Q 019811          130 YASGQRE----DTSGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQK-TGRSRGFGFVSFRNQQDAQSAINDL  203 (335)
Q Consensus       130 ~~~~~~~----~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~g~v~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l  203 (335)
                      .+.....    .....++|||+|||.. +++++|+++|+.||.|..+.++++.. +|.++|+|||+|.+.++|.+|+ .|
T Consensus       195 ~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l  273 (292)
T 2ghp_A          195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QM  273 (292)
T ss_dssp             CCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GG
T ss_pred             CCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hh
Confidence            7655432    3355689999999999 99999999999999999999998865 4889999999999999999999 99


Q ss_pred             CCceeCCeeeEEEEccCC
Q 019811          204 TGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       204 ~~~~~~g~~l~v~~~~~~  221 (335)
                      +|..++|+.|.|.|+.++
T Consensus       274 ~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          274 NRSLLGNREISVSLADKK  291 (292)
T ss_dssp             TTEEETTEEEEEEECCCC
T ss_pred             cCCEECCcEEEEEEecCC
Confidence            999999999999999764

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.97  E-value=3.2e-30  Score=208.77  Aligned_cols=163  Identities=26%  Similarity=0.462  Sum_probs=139.1

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            445668999999999999999999999999999999999988899999999999999999999975 8999999999999


Q ss_pred             EccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      ++........                             +......++|||+|||.++++++|+++|+.||  .|..+.+
T Consensus        88 ~~~~~~~~~~-----------------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~v~i  136 (196)
T 1l3k_A           88 RAVSREDSQR-----------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEI  136 (196)
T ss_dssp             ECCC----------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTS--CEEEEEE
T ss_pred             cccCcccccc-----------------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCC--CeEEEEE
Confidence            9865432110                             11123348999999999999999999999999  5888877


Q ss_pred             ecc------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          297 QRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       297 ~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..+      +|+|||+|.+.++|.+|+.. +|.   .|+|+.|+|
T Consensus       137 ~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~---~~~G~~i~v  177 (196)
T 1l3k_A          137 MTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYH---TVNGHNCEV  177 (196)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHC-SCC---EETTEECEE
T ss_pred             eecCCCCCccceEEEEECCHHHHHHHHHh-CCc---EECCEEEEE
Confidence            654      68999999999999999976 788   999999875

>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=99.97  E-value=3.9e-30  Score=208.35  Aligned_cols=185  Identities=13%  Similarity=0.159  Sum_probs=137.0

Q ss_pred             CcceEEECCCC-ccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          140 GHFNIFVGDLS-PEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       140 ~~~~l~v~nlp-~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ++++|||+||| ..+++++|+++|+.||.|.+++++++     .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            45799999999 89999999999999999999999854     3689999999999999999999999999999999998


Q ss_pred             cCCCCCCCCC-CCccccc-chhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          219 TKGAGNNEDK-QSSDAKS-VVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       219 ~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      +......... ....... ........................+++++|||+|||+++++++|+++|+.||.+.+..+++
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            7644211100 0000000 0000000000000000000112235668999999999999999999999999532377887


Q ss_pred             ecc----cceEEEEeCCHHHHHHHHHhhcCCCcccccCcc
Q 019811          297 QRD----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQ  332 (335)
Q Consensus       297 ~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~  332 (335)
                      ..+    +|+|||+|.+.++|.+|+..|||.   .++|+.
T Consensus       158 ~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~---~~~g~~  194 (205)
T 3tyt_A          158 FSGKSERSSSGLLEWDSKSDALETLGFLNHY---QMKNPN  194 (205)
T ss_dssp             CSCCSSSSEEEEEECSSHHHHHHHHHHHTTC---EECCSS
T ss_pred             EcCCCCCceEEEEEeCCHHHHHHHHHHhCCC---CccCCC
Confidence            654    489999999999999999999999   898874

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.97  E-value=4.9e-30  Score=203.83  Aligned_cols=157  Identities=26%  Similarity=0.397  Sum_probs=136.5

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCceeC---CeeeE
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG--RSRGFGFVSFRNQQDAQSAINDLTGKWLG---SRQIR  214 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~~~---g~~l~  214 (335)
                      ..++|||+|||.++++++|+++|+.||.|.++.+++++.++  .++|||||+|.+.++|.+|+..|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            45799999999999999999999999999999999998776  78999999999999999999999998765   67788


Q ss_pred             EEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEE
Q 019811          215 CNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEV  294 (335)
Q Consensus       215 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v  294 (335)
                      +.++......                                  ....++|||+|||.++++++|+++|+.||  .|..+
T Consensus        82 ~~~~~~~~~~----------------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G--~i~~v  125 (175)
T 3nmr_A           82 MKPADSEKNN----------------------------------AVEDRKLFIGMISKKCTENDIRVMFSSFG--QIEEC  125 (175)
T ss_dssp             EEECGGGCCS----------------------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGS--CEEEE
T ss_pred             Eccccccccc----------------------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCC--CEEEE
Confidence            8776543221                                  11237899999999999999999999999  58888


Q ss_pred             EEecc-----cceEEEEeCCHHHHHHHHHhhcCCCccccc---CccccC
Q 019811          295 RVQRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLF---GKQMKV  335 (335)
Q Consensus       295 ~~~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~---g~~l~v  335 (335)
                      .+.++     +|+|||+|.+.++|.+|+..|||.   .+.   |++|+|
T Consensus       126 ~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~---~~~~g~~~~l~V  171 (175)
T 3nmr_A          126 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA---QTMEGCSSPMVV  171 (175)
T ss_dssp             EEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTS---CCCTTCSSCCEE
T ss_pred             EEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCC---cccCCCCCCeEE
Confidence            88765     789999999999999999999998   555   488875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.97  E-value=3.3e-30  Score=212.00  Aligned_cols=166  Identities=23%  Similarity=0.463  Sum_probs=139.4

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            46899999999999999999999999999999999988899999999999999999999999999999999999988754


Q ss_pred             CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-
Q 019811          221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-  299 (335)
                      ......       . ....                .......++|||+|||.++++++|+++|+.||  .|..+.+.++ 
T Consensus       108 ~~~~~~-------~-~~~~----------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G--~v~~v~i~~~~  161 (216)
T 2qfj_A          108 IGQAQP-------I-IDQL----------------AEEARAFNRIYVASVHQDLSDDDIKSVFEAFG--KIKSATLARDP  161 (216)
T ss_dssp             CGGGHH-------H-HHHH----------------HHHHTTSCEEEEECCCTTCCHHHHHHHHTTSS--CEEEEEEEECT
T ss_pred             ccccch-------h-hhhh----------------hcccCCCcEEEEeCCCCcCCHHHHHHHHhccC--CeeEEEEEecC
Confidence            321100       0 0000                00112347899999999999999999999999  5888888765 


Q ss_pred             -----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 -----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                           +|+|||+|.+.++|.+|+..|||.   .|+|+.|+|
T Consensus       162 ~~g~~~g~afV~F~~~~~A~~A~~~l~g~---~~~g~~i~V  199 (216)
T 2qfj_A          162 TTGKHKGYGFIEYEKAQSSQDAVSSMNLF---DLGGQYLRV  199 (216)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTC---BCSSSBCEE
T ss_pred             CCCCcCceEEEEecCHHHHHHHHHHccCC---EeCCcEEEE
Confidence                 689999999999999999999999   999999975

>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=99.97  E-value=2.1e-29  Score=215.59  Aligned_cols=190  Identities=20%  Similarity=0.304  Sum_probs=143.9

Q ss_pred             CCCcceEEECCCCccccHHHHH----HHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          138 TSGHFNIFVGDLSPEVTDATLF----ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      ..++++|||+|||.++++++|+    ++|+.||.|.++.+.+   ++.++|||||+|.+.++|.+|+..|++..+.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4567899999999999999966    8999999999998884   57889999999999999999999999999999999


Q ss_pred             EEEEccCCCCCCCCCCCcccccc-----------------hhc-----------cCCC----------------------
Q 019811          214 RCNWATKGAGNNEDKQSSDAKSV-----------------VEL-----------TNGS----------------------  243 (335)
Q Consensus       214 ~v~~~~~~~~~~~~~~~~~~~~~-----------------~~~-----------~~~~----------------------  243 (335)
                      +|.|+..................                 ...           ....                      
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            99998665421110000000000                 000           0000                      


Q ss_pred             --------CcCCc------------------CCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEe
Q 019811          244 --------SEDGK------------------ETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ  297 (335)
Q Consensus       244 --------~~~~~------------------~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~  297 (335)
                              ...+.                  ............++++|||+|||.++++++|+++|+.||  .|.++++.
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G--~i~~v~~~  240 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFP--GFKEVRLV  240 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcC--CeEEEEEe
Confidence                    00000                  000000112344568999999999999999999999999  58899988


Q ss_pred             ccc-ceEEEEeCCHHHHHHHHHhhcCCCccccc-CccccC
Q 019811          298 RDK-GFGFVRYSTHAEAALAIQMGNTTQSSYLF-GKQMKV  335 (335)
Q Consensus       298 ~~~-g~afV~f~~~~~a~~A~~~l~g~~~~~~~-g~~l~v  335 (335)
                      .++ |+|||+|.+.++|.+|+..|||.   .|+ |+.|+|
T Consensus       241 ~~~~g~afV~f~~~~~A~~A~~~l~g~---~~~~g~~l~v  277 (282)
T 3pgw_A          241 PGRHDIAFVEFDNEVQAGAARDALQGF---KITQNNAMKI  277 (282)
T ss_pred             cCCCcEEEEEeCCHHHHHHHHHHcCCc---EeCCCCEEEE
Confidence            876 99999999999999999999999   998 999876

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.96  E-value=4.1e-30  Score=202.70  Aligned_cols=153  Identities=26%  Similarity=0.506  Sum_probs=135.2

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ++++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+.  ++..+.|+.|.+.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            35799999999999999999999999999999999998889999999999999999999998  4678999999998875


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD  299 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~  299 (335)
                      ....                                   ....++|||+|||.++++++|+++|+.||  .|..+.+..+
T Consensus        80 ~~~~-----------------------------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~~~i~~~  122 (167)
T 2cjk_A           80 PRDE-----------------------------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWG--TIIDAQLMLD  122 (167)
T ss_dssp             CHHH-----------------------------------HHHCEEEEEEEECTTCCHHHHHHHHHTTS--CCSEEECCCS
T ss_pred             chhh-----------------------------------ccCCCeEEECCCCCCCCHHHHHHHHHhCc--cEEEEEEEEc
Confidence            4210                                   01136899999999999999999999999  5778877654


Q ss_pred             ------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 ------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 ------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                            +|+|||+|.+.++|.+|++ ++|.   .++|++|+|
T Consensus       123 ~~~g~~~g~afV~f~~~~~a~~A~~-~~~~---~~~g~~i~V  160 (167)
T 2cjk_A          123 KDTGQSRGFGFVTYDSADAVDRVCQ-NKFI---DFKDRKIEI  160 (167)
T ss_dssp             SSSSTTSEEEEEEESSHHHHHHHHH-CSEE---CSSSSCEEE
T ss_pred             CCCCccceEEEEEECCHHHHHHHHh-CCCE---EeCCeEEEE
Confidence                  5899999999999999997 8999   999999975

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.96  E-value=6.6e-30  Score=203.10  Aligned_cols=159  Identities=23%  Similarity=0.384  Sum_probs=134.5

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|..||.+..+ ++++..++.++|||||+|.+.++|.+|++ |++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            44567899999999999999999999999987663 34444667899999999999999999995 99999999999999


Q ss_pred             EccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEE-E
Q 019811          217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEV-R  295 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v-~  295 (335)
                      ++......                                 .....++|||+|||.++++++|+++|+.||  .+..+ .
T Consensus        87 ~~~~~~~~---------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g--~v~~~~~  131 (175)
T 1fje_B           87 KPKGRDSK---------------------------------KVRAARTLLAKNLSFNITEDELKEVFEDAL--EIRLVSQ  131 (175)
T ss_dssp             CCCCSSCS---------------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCS--EEEEECS
T ss_pred             cCCCcccc---------------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcC--eEEEecC
Confidence            98764321                                 112347999999999999999999999999  45555 1


Q ss_pred             EecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          296 VQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       296 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..+.+|+|||+|.+.++|.+|+..|+|.   .|+|+.|+|
T Consensus       132 ~~~~~g~afV~f~~~~~A~~A~~~l~g~---~~~g~~i~v  168 (175)
T 1fje_B          132 DGKSKGIAYIEFKSEADAEKNLEEKQGA---EIDGRSVSL  168 (175)
T ss_dssp             SSSCCSEEEEECSSHHHHHHHHHHHTEE---EETTEEEEE
T ss_pred             CCCCceEEEEEECCHHHHHHHHHHhCCC---EECCeEEEE
Confidence            1234799999999999999999999999   999999875

>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=99.96  E-value=1.3e-28  Score=195.02  Aligned_cols=149  Identities=17%  Similarity=0.344  Sum_probs=129.7

Q ss_pred             CcceEEECCCCccccHHHHHHHhccC----C-------CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVY----P-------SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      +.++|||+|||.++++++|+++|+.|    |       .|.++.+.      .++|||||+|.+.++|.+|+ .+++..+
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            35799999999999999999999999    5       55555544      55899999999999999999 8999999


Q ss_pred             CCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCC
Q 019811          209 GSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA  288 (335)
Q Consensus       209 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~  288 (335)
                      .|+.|.|.++......                                   ...++|||+|||..+++++|+++|++|| 
T Consensus        76 ~g~~i~v~~~~~~~~~-----------------------------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G-  119 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPL-----------------------------------PGAHKLFIGGLPNYLNDDQVKELLTSFG-  119 (172)
T ss_dssp             TTEECEEECCSSCCCC-----------------------------------TTTTCEEEECCCTTCCHHHHHHHHHTTS-
T ss_pred             cCceeeecCCcccCCC-----------------------------------CCCCEEEEEcCCCcCCHHHHHHHHHhcC-
Confidence            9999999986543211                                   1147899999999999999999999999 


Q ss_pred             eeeEEEEEecc------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          289 GVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       289 ~~i~~v~~~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                       .+..+.+.++      +|+|||+|.+.++|.+|+..|||.   .++|++|+|
T Consensus       120 -~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~---~~~g~~l~V  168 (172)
T 2g4b_A          120 -PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM---QLGDKKLLV  168 (172)
T ss_dssp             -CEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTC---EETTEECEE
T ss_pred             -CceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC---EECCeEEEE
Confidence             5788888655      689999999999999999999999   999999975

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.96  E-value=4.6e-28  Score=196.38  Aligned_cols=168  Identities=15%  Similarity=0.273  Sum_probs=133.4

Q ss_pred             cceEEECCCCccccHHHHHHHhccCC-----------CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYP-----------SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLG  209 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g-----------~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  209 (335)
                      .++|||+|||.++++++|+++|+.||           .|..+.+      +.++|||||+|.+.++|.+|+ .|++..+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            47999999999999999999999995           3444433      466899999999999999999 89999999


Q ss_pred             CeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCe
Q 019811          210 SRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAG  289 (335)
Q Consensus       210 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~  289 (335)
                      |+.|.|.++..............               ...............++|||+|||.++++++|+++|+.||  
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G--  139 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPS---------------VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFG--  139 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSS---------------CCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBS--
T ss_pred             CceEEEeCCCCCCCCCCCcCCCc---------------CCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcC--
Confidence            99999999876543221110000               0000001112234568999999999999999999999999  


Q ss_pred             eeEEEEEecc------cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          290 VIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       290 ~i~~v~~~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .+..+.+..+      +|+|||+|.+.++|.+|+..|+|.   .|+|+.|+|
T Consensus       140 ~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~---~~~g~~l~v  188 (198)
T 2yh0_A          140 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM---QLGDKKLLV  188 (198)
T ss_dssp             CEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTC---EETTEECEE
T ss_pred             CccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCC---EECCEEEEE
Confidence            5788888755      689999999999999999999999   999999875

>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=99.95  E-value=1.9e-27  Score=200.74  Aligned_cols=148  Identities=29%  Similarity=0.477  Sum_probs=130.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++|+++|+++|+.||.|..+.+.      .++|||||+|.+.++|.+|+..+++..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~------~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe------CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEee
Confidence            34556799999999999999999999999999999886      347899999999999999999999999999999999


Q ss_pred             EccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEE
Q 019811          217 WATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRV  296 (335)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~  296 (335)
                      ++..                                         ..+|||+|||..+++++|+++|+.||  .|..+.+
T Consensus        92 ~a~~-----------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G--~i~~v~i  128 (261)
T 3sde_A           92 FATH-----------------------------------------GAALTVKNLSPVVSNELLEQAFSQFG--PVEKAVV  128 (261)
T ss_dssp             ECCC-----------------------------------------SSEEEEESCCTTCCHHHHHHHHGGGS--CEEEEEE
T ss_pred             eccc-----------------------------------------CCcccccCCCCCCCHHHHHHHHHhcC--CeEEEEe
Confidence            9853                                         26899999999999999999999999  5888877


Q ss_pred             ecc-----cceEEEEeCCHHHHHHHHHhhcCCCccccc---CccccC
Q 019811          297 QRD-----KGFGFVRYSTHAEAALAIQMGNTTQSSYLF---GKQMKV  335 (335)
Q Consensus       297 ~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~---g~~l~v  335 (335)
                      ..+     +|+|||+|.+.++|.+|+..|++..  .+.   |++|.|
T Consensus       129 ~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~--~~~~~~~r~i~v  173 (261)
T 3sde_A          129 VVDDRGRATGKGFVEFAAKPPARKALERCGDGA--FLLTTTPRPVIV  173 (261)
T ss_dssp             EEETTSCEEEEEEEEESSHHHHHHHHHHHHHSC--EESSSSCCBCEE
T ss_pred             eeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCe--EEecCCCceEEE
Confidence            654     7899999999999999999995431  443   777754

>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=99.89  E-value=1.8e-22  Score=157.13  Aligned_cols=139  Identities=24%  Similarity=0.297  Sum_probs=111.2

Q ss_pred             eEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCcee-------EEeeeccC---CCccCCCCcceEEECCCCcc
Q 019811           85 GCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPI-------KVNWAYAS---GQREDTSGHFNIFVGDLSPE  152 (335)
Q Consensus        85 ~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l-------~v~~~~~~---~~~~~~~~~~~l~v~nlp~~  152 (335)
                      .++++.++  .+|||||+|.+.++|++|+..+++....+..+       ........   .........++|||+|||.+
T Consensus         2 ~~kl~ln~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~   81 (158)
T 2kn4_A            2 QYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYR   81 (158)
T ss_dssp             EEEEEEECSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTT
T ss_pred             cEEEEecCccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCC
Confidence            35555554  46999999999999999998876533322222       22221111   11223345689999999999


Q ss_pred             ccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCC
Q 019811          153 VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAG  223 (335)
Q Consensus       153 ~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~  223 (335)
                      +++++|+++|+.||.|..+.+++++.+|.++|||||+|.+.++|.+|+..|++..+.|+.|+|.++..+..
T Consensus        82 ~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           82 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             CCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999999999999999988899999999999999999999999999999999999999987543

>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=99.89  E-value=8.2e-23  Score=149.81  Aligned_cols=103  Identities=23%  Similarity=0.470  Sum_probs=73.2

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC--CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~--~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      .+.+|||+|||.++|+++|+++|+.||.|.+|+++.++.  +|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            356799999999999999999999999999999998764  689999999999999999999999999999999998765


Q ss_pred             CCcc-----CCCCcceEEECCCCccccHHH
Q 019811          133 GQRE-----DTSGHFNIFVGDLSPEVTDAT  157 (335)
Q Consensus       133 ~~~~-----~~~~~~~l~v~nlp~~~t~~~  157 (335)
                      ..+.     .....++|||+|||+++|++.
T Consensus        84 ~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccccccccCCCCceEeCCCCCCccccc
Confidence            4432     223345799999999998763

>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=99.86  E-value=9.7e-22  Score=144.09  Aligned_cols=110  Identities=26%  Similarity=0.515  Sum_probs=74.7

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||+++++++|+++|+.||.|.++.++++.  +.++|||||+|.+.++|.+|++.|++..+.|+.|+|.++.
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            35689999999999999999999999999999999885  3579999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHH
Q 019811          220 KGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLD  278 (335)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~  278 (335)
                      .+.......                           ........+|||+|||+++|++.
T Consensus        82 ~~~~~~~~~---------------------------~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAEL---------------------------GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC-------------------------------------------------------
T ss_pred             Ccccccccc---------------------------ccccCCCCceEeCCCCCCccccc
Confidence            643221111                           01112235799999999998863

>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=99.86  E-value=1.6e-21  Score=150.28  Aligned_cols=125  Identities=20%  Similarity=0.282  Sum_probs=110.4

Q ss_pred             CCCCeEEEEEcCHHHHHHHHHHh-CCccccCceeEEeeeccC-------------CCccCCCCcceEEECCCCccccHHH
Q 019811           92 DKSSYGFIHYFDRRSAAMAILSL-NGRHLFGQPIKVNWAYAS-------------GQREDTSGHFNIFVGDLSPEVTDAT  157 (335)
Q Consensus        92 ~~~g~afv~f~~~~~A~~a~~~l-~~~~~~g~~l~v~~~~~~-------------~~~~~~~~~~~l~v~nlp~~~t~~~  157 (335)
                      +-+|+++|+|.+.++|++|+..+ ||..+.| .+.+.++...             .........++|||+|||+++++++
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~   89 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTE   89 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHH
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHH
Confidence            34689999999999999999999 9999999 9999887542             1123345568999999999999999


Q ss_pred             HHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       158 l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      |+++|+.||.|.++.++++     ++|||||+|.+.++|.+|+..|++..+.|+.|+|.|+..+.
T Consensus        90 l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           90 LERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            9999999999999999865     57899999999999999999999999999999999987653

>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=99.84  E-value=1.1e-20  Score=145.54  Aligned_cols=131  Identities=23%  Similarity=0.297  Sum_probs=105.9

Q ss_pred             CCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCC
Q 019811          180 GRSRGFGFVSFRNQQDAQSAINDL-TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPEN  258 (335)
Q Consensus       180 ~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (335)
                      ...+|+++|+|.+.++|.+|+..+ ++..++| .+.+.++..........                   ...........
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~-------------------~~~~~~~~~~~   69 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGS-------------------HHHHHHMHRDS   69 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSS-------------------SSCCCCSCSSS
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccc-------------------ccccccccccC
Confidence            467899999999999999999999 9999999 99998775432110000                   00001111223


Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..+.++|||+|||+++++++|+++|+.||  .|.++++.++ +|+|||+|.+.++|.+|+..|||.   .++|++|+|
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G--~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~---~~~g~~l~v  142 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYG--PLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGR---TLCGCRVRV  142 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHS--CEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSS---CSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhC--CEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCC---EECCeEEEE
Confidence            34558999999999999999999999999  5899999887 999999999999999999999999   999999976

>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=3.3e-20  Score=131.76  Aligned_cols=80  Identities=33%  Similarity=0.517  Sum_probs=77.1

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      +++|||+|||.++|+++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|+|..++|+.|+|.|+.+
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999865

>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=99.82  E-value=3.4e-20  Score=136.15  Aligned_cols=104  Identities=17%  Similarity=0.247  Sum_probs=93.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +..+++|||+|||.++++++|+++|+.||.|.+|.+..+. ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            4456889999999999999999999999999999998765 479999999999999999999999999999999999875


Q ss_pred             CCCccCCCCcceEEECCCCccccHHHHHHHhccCCC
Q 019811          132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPS  167 (335)
Q Consensus       132 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~  167 (335)
                      ....           .+++...++++|.++|++||.
T Consensus        85 ~~~~-----------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           85 NRAF-----------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHT-----------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             Chhh-----------hhhhHhHhHHHHHHHHHHhCC
Confidence            4422           578888999999999999984

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.81  E-value=1.2e-19  Score=128.86  Aligned_cols=77  Identities=36%  Similarity=0.551  Sum_probs=71.6

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++|+++|+++|++||.|.+|++.+++.    +|||||+|.+.++|.+|++.|||..+.|++|+|.|+.
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            356799999999999999999999999999999998653    5899999999999999999999999999999999986


Q ss_pred             c
Q 019811          131 A  131 (335)
Q Consensus       131 ~  131 (335)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
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=99.81  E-value=2.3e-19  Score=139.53  Aligned_cols=137  Identities=20%  Similarity=0.262  Sum_probs=97.9

Q ss_pred             eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCCCCCCCCCcccccchhccCCCCcCCcC
Q 019811          170 DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKE  249 (335)
Q Consensus       170 ~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (335)
                      .+.+..+..  .++|||||+|.+.++|++|+..+++....+..+.+..........                      ..
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~----------------------~~   57 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT----------------------EG   57 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEE----------------------CC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccc----------------------cc
Confidence            345666633  689999999999999999998877543322222222111000000                      00


Q ss_pred             CCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc------cceEEEEeCCHHHHHHHHHhhcCC
Q 019811          250 TTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       250 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~------~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      .............++|||+|||+++++++|+++|+.||  .|..+.+..+      +|+|||+|.+.++|.+|+..|||.
T Consensus        58 ~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G--~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~  135 (158)
T 2kn4_A           58 SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG--RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA  135 (158)
T ss_dssp             CCCSSCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHS--CEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTE
T ss_pred             ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC--CeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            00011112223458999999999999999999999999  5888888754      689999999999999999999999


Q ss_pred             CcccccCccccC
Q 019811          324 QSSYLFGKQMKV  335 (335)
Q Consensus       324 ~~~~~~g~~l~v  335 (335)
                         .|+|++|+|
T Consensus       136 ---~~~g~~l~v  144 (158)
T 2kn4_A          136 ---VLDGRELRV  144 (158)
T ss_dssp             ---ESSSSEEEE
T ss_pred             ---EECCeEEEE
Confidence               999999975

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.7e-19  Score=127.59  Aligned_cols=81  Identities=17%  Similarity=0.207  Sum_probs=73.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC--CccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN--GRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~--~~~~~g~~l~v~~~~  130 (335)
                      +.+.++|||+|||.++|+++|+++|++||.|.+|+++++  +|||||+|.+.++|.+|++.|+  +..+.|++|+|.++.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~--kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~   90 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN   90 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcC
Confidence            456788999999999999999999999999999999876  5899999999999999999886  478999999999997


Q ss_pred             cCCCc
Q 019811          131 ASGQR  135 (335)
Q Consensus       131 ~~~~~  135 (335)
                      .+...
T Consensus        91 ~~~~~   95 (105)
T 1sjq_A           91 HKELK   95 (105)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            76544

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=9.2e-20  Score=130.51  Aligned_cols=93  Identities=27%  Similarity=0.436  Sum_probs=82.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCcc
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE  136 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~  136 (335)
                      ++|||+|||.++|+++|+++|++||.|.+|++..+ ++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.+.....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   79 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRS   79 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcc
Confidence            47999999999999999999999999999999888 77999999999999999999999999999999999997655322


Q ss_pred             -------CCCCcceEEECCCC
Q 019811          137 -------DTSGHFNIFVGDLS  150 (335)
Q Consensus       137 -------~~~~~~~l~v~nlp  150 (335)
                             .......+||+||+
T Consensus        80 ~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           80 RFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCCSCCCSCCCCSCCCSCCCC
T ss_pred             cCCCCCccccCCCceecCCCC
Confidence                   12235689999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.80  E-value=9.8e-20  Score=137.07  Aligned_cols=124  Identities=25%  Similarity=0.384  Sum_probs=82.7

Q ss_pred             eEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEee
Q 019811           96 YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMW  175 (335)
Q Consensus        96 ~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~  175 (335)
                      ++|.+|.+...|..|+..++|....|+. .+.+..   ........++|||+|||.++++++|+++|+.||.|..+.+++
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~---~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   81 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGR---PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR   81 (135)
T ss_dssp             ------------------------------CCSCC---SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCC
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCC-CCCcCC---CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            6788888999999999988887766654 222222   223344567999999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCC
Q 019811          176 DQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAG  223 (335)
Q Consensus       176 ~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~  223 (335)
                      ++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.|+.....
T Consensus        82 ~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            988899999999999999999999999999999999999999987554

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.80  E-value=1e-19  Score=127.18  Aligned_cols=84  Identities=18%  Similarity=0.281  Sum_probs=77.0

Q ss_pred             cceEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CceeCCeeeEEEEc
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT-GKWLGSRQIRCNWA  218 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~-~~~~~g~~l~v~~~  218 (335)
                      +++|||+|||+++|+++|+++|+.|| .|.++.+++++.++.++|||||+|.+.++|.+|++.++ +..++|+.|+|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 79999999999999999999999999999999998774 56799999999999


Q ss_pred             cCCCCC
Q 019811          219 TKGAGN  224 (335)
Q Consensus       219 ~~~~~~  224 (335)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.80  E-value=1.4e-18  Score=124.83  Aligned_cols=86  Identities=37%  Similarity=0.789  Sum_probs=77.5

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ......++|||+|||.++++++|+++|+.||.|.+|++..++  ++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            345667899999999999999999999999999999998865  468999999999999999999999999999999999


Q ss_pred             eccCCCcc
Q 019811          129 AYASGQRE  136 (335)
Q Consensus       129 ~~~~~~~~  136 (335)
                      +.+.....
T Consensus        90 a~~~~~~~   97 (103)
T 2cqi_A           90 ATTPSSQK   97 (103)
T ss_dssp             CCCTTCCC
T ss_pred             CCCCcccc
Confidence            98765443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.79  E-value=9e-19  Score=126.72  Aligned_cols=83  Identities=16%  Similarity=0.218  Sum_probs=78.7

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .+.++|||+|||+++++++|+++|++||.|.++.+++|+.++.++|||||+|.+.++|.+|++.||+..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 019811          219 TKG  221 (335)
Q Consensus       219 ~~~  221 (335)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.79  E-value=6.6e-19  Score=123.31  Aligned_cols=79  Identities=19%  Similarity=0.259  Sum_probs=71.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcc--ccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH--LFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~--~~g~~l~v~~~~  130 (335)
                      ..++++|||+|||.++|+++|+++|++||.|.+|++++  .+|+|||+|.+.++|.+|++.|++..  +.|++|+|.++.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~--~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP--KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc--CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            45678899999999999999999999999999999875  45899999999999999999998875  789999999997


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      .+.
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            543

>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=99.79  E-value=2.3e-18  Score=123.68  Aligned_cols=86  Identities=26%  Similarity=0.350  Sum_probs=77.7

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .....+.++|||+|||.++++++|+++|+.||.|.+|++..++  .+|||||+|.+.++|.+|+..|++..|.|+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445677899999999999999999999999999999998865  37899999999999999999999999999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cq3_A           89 NATARVMT   96 (103)
T ss_dssp             ECCSSCCC
T ss_pred             EcccCCCC
Confidence            99876543

>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=99.79  E-value=5.3e-19  Score=125.19  Aligned_cols=80  Identities=18%  Similarity=0.220  Sum_probs=72.0

Q ss_pred             CCCCcceEEEeCCCC-CCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCc--cccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR--HLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~--~~~g~~l~v~~  128 (335)
                      ...++++|||+|||. ++|+++|+++|++||.|.+|++++++  |||||+|.+.++|..|++.|++.  .+.|++|+|.+
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k--g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   88 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS--SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC--CEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            455788999999999 99999999999999999999998764  79999999999999999988864  59999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +....
T Consensus        89 a~~~~   93 (102)
T 1x4d_A           89 SQKYK   93 (102)
T ss_dssp             ECCCT
T ss_pred             CCCCC
Confidence            97544

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=2.1e-19  Score=125.58  Aligned_cols=79  Identities=14%  Similarity=0.288  Sum_probs=70.8

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccC-CceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHh-CCccccCceeEEeee
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSL-NGRHLFGQPIKVNWA  129 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G-~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l-~~~~~~g~~l~v~~~  129 (335)
                      +++|||+|||.++|+++|+++|+.|| .|.+|++++++    ++|||||+|.+.++|.+|++.+ ++..+.|++|+|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 79999998764    4699999999999999999877 456799999999999


Q ss_pred             ccCCC
Q 019811          130 YASGQ  134 (335)
Q Consensus       130 ~~~~~  134 (335)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.79  E-value=3.7e-18  Score=123.88  Aligned_cols=84  Identities=19%  Similarity=0.379  Sum_probs=76.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      .+.+.++|||+|||.++++++|+++|+.||.|.+|++..+.. +|||||+|.+.++|.+|++.||+..+.|+.|+|.++.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            455678999999999999999999999999999999977653 7899999999999999999999999999999999997


Q ss_pred             cCCCc
Q 019811          131 ASGQR  135 (335)
Q Consensus       131 ~~~~~  135 (335)
                      +....
T Consensus        98 ~~~~~  102 (109)
T 1x4a_A           98 SGRGT  102 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            76543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=9.3e-19  Score=117.89  Aligned_cols=72  Identities=19%  Similarity=0.256  Sum_probs=68.2

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +..|||+||++.+|+++|+++|.+||+|.++++..  ++|||||+|.+.++|.+|++.||+..+.|++|+|.++
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~--~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL--NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC--CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            45699999999999999999999999999999866  6799999999999999999999999999999999877

>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=99.78  E-value=2.3e-18  Score=122.07  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=72.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh--CCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL--NGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l--~~~~~~g~~l~v~~~~  130 (335)
                      ..++++|||+|||.++++++|+++|++||.|.+|.+.++  +|||||+|.+.++|.+|++.|  ++..+.|++|+|.|+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   89 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG--KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   89 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC--CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcC
Confidence            456788999999999999999999999999999988776  689999999999999999976  5678999999999997


Q ss_pred             cCCCc
Q 019811          131 ASGQR  135 (335)
Q Consensus       131 ~~~~~  135 (335)
                      .+...
T Consensus        90 ~~~~~   94 (101)
T 2cq1_A           90 HKELK   94 (101)
T ss_dssp             CSSCC
T ss_pred             cccCc
Confidence            66543

>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=99.78  E-value=3.7e-18  Score=125.15  Aligned_cols=85  Identities=20%  Similarity=0.328  Sum_probs=76.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|++.||+..|.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345668899999999999999999999999999999988763    4799999999999999999999999999999999


Q ss_pred             eeccCCCcc
Q 019811          128 WAYASGQRE  136 (335)
Q Consensus       128 ~~~~~~~~~  136 (335)
                      ++.++....
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpz_A          101 LKRSKNDSK  109 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             EcCCCCcCC
Confidence            998765543

>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=2.2e-18  Score=123.54  Aligned_cols=85  Identities=24%  Similarity=0.443  Sum_probs=76.8

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|++.||+..+.|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            35567899999999999999999999999999999998864    46899999999999999999999999999999999


Q ss_pred             eeccCCCcc
Q 019811          128 WAYASGQRE  136 (335)
Q Consensus       128 ~~~~~~~~~  136 (335)
                      ++.+.....
T Consensus        88 ~a~~~~~~~   96 (102)
T 1x5s_A           88 QAGKSSDNR   96 (102)
T ss_dssp             EEECCCCCC
T ss_pred             ECCCCCCCC
Confidence            998766443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=124.43  Aligned_cols=86  Identities=22%  Similarity=0.439  Sum_probs=77.7

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec--CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~--~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.+.++|||+|||.++++++|+++|+.||.|.+|++..+  ..+|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567889999999999999999999999999999999987  4468999999999999999999999999999999999


Q ss_pred             eccCCCcc
Q 019811          129 AYASGQRE  136 (335)
Q Consensus       129 ~~~~~~~~  136 (335)
                      +.++..+.
T Consensus        90 a~~~~~~~   97 (103)
T 2d9p_A           90 AQRKEERQ   97 (103)
T ss_dssp             CSSCCCCC
T ss_pred             ecccccCC
Confidence            98766543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=2.3e-18  Score=122.12  Aligned_cols=83  Identities=25%  Similarity=0.358  Sum_probs=75.3

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...+...++|||+|||.++++++|+++|+.||.|. +.++.++++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus        13 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            33455678999999999999999999999999996 77778888899999999999999999999999999999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=9.8e-19  Score=126.72  Aligned_cols=83  Identities=25%  Similarity=0.371  Sum_probs=75.5

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .......++|||+|||.++++++|+++|++||.|.+|++..++  .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3345677899999999999999999999999999999998764  47999999999999999999999999999999999


Q ss_pred             eeccC
Q 019811          128 WAYAS  132 (335)
Q Consensus       128 ~~~~~  132 (335)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98754

>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=2.5e-18  Score=123.90  Aligned_cols=85  Identities=33%  Similarity=0.608  Sum_probs=76.8

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ..+...++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345667899999999999999999999999999999998865    3689999999999999999999999999999999


Q ss_pred             eeeccCCCc
Q 019811          127 NWAYASGQR  135 (335)
Q Consensus       127 ~~~~~~~~~  135 (335)
                      .++.+....
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999776543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.78  E-value=5.3e-19  Score=123.98  Aligned_cols=81  Identities=22%  Similarity=0.422  Sum_probs=75.0

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCC--ceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCCeee
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPS--CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK----WLGSRQI  213 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~--v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~----~~~g~~l  213 (335)
                      .-++|||+|||+++|+++|+++|++||.  +.++++++|+.+|.++|||||+|.+.++|.+|++.|++.    .++|+.|
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            3468999999999999999999999995  679999999999999999999999999999999999986    5899999


Q ss_pred             EEEEccC
Q 019811          214 RCNWATK  220 (335)
Q Consensus       214 ~v~~~~~  220 (335)
                      .|+|++.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999864

>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=99.78  E-value=2.7e-18  Score=122.32  Aligned_cols=83  Identities=18%  Similarity=0.293  Sum_probs=76.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+..|||..+.|+.|+|.+
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            4567899999999999999999999999999999998765    468999999999999999999999999999999999


Q ss_pred             eccCCCc
Q 019811          129 AYASGQR  135 (335)
Q Consensus       129 ~~~~~~~  135 (335)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9876654

>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=99.78  E-value=1.5e-18  Score=129.45  Aligned_cols=84  Identities=24%  Similarity=0.345  Sum_probs=76.2

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      ...+.+.++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+..|+|..|.|+.|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3345677899999999999999999999999999999998763    468999999999999999999999999999999


Q ss_pred             EeeeccCC
Q 019811          126 VNWAYASG  133 (335)
Q Consensus       126 v~~~~~~~  133 (335)
                      |.++.++.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99997654

>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=99.78  E-value=2.9e-18  Score=122.34  Aligned_cols=80  Identities=16%  Similarity=0.120  Sum_probs=71.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCC--ccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG--RHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~--~~~~g~~l~v~~~~  130 (335)
                      ..++++|||+|||.++++++|+++|++||.|.+|.+.++  +|||||+|.+.++|.+|++.|++  ..+.|++|+|.|+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~   89 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF--KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC--CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcc
Confidence            345688999999999999999999999999999998765  58999999999999999998865  45999999999997


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      .+..
T Consensus        90 ~~~~   93 (104)
T 1wex_A           90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             Cccc
Confidence            6554

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=4.8e-18  Score=121.04  Aligned_cols=83  Identities=24%  Similarity=0.410  Sum_probs=75.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|++ |++..+.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999998764    46899999999999999998 99999999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99876544

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=3.9e-18  Score=120.55  Aligned_cols=83  Identities=30%  Similarity=0.558  Sum_probs=75.8

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .++++|||+|||.++++++|+++|++||.|.+|++..++    ++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            456889999999999999999999999999999998864    3689999999999999999999999999999999999


Q ss_pred             ccCCCcc
Q 019811          130 YASGQRE  136 (335)
Q Consensus       130 ~~~~~~~  136 (335)
                      .++....
T Consensus        83 ~~~~~~~   89 (95)
T 2dnz_A           83 TERLDGG   89 (95)
T ss_dssp             SCCCCCC
T ss_pred             ccccCCC
Confidence            8766543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.3e-18  Score=123.44  Aligned_cols=85  Identities=27%  Similarity=0.431  Sum_probs=76.6

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|++.||+..+.|+.|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567889999999999999999999999999999998763    46899999999999999999999999999999999


Q ss_pred             eeccCCCcc
Q 019811          128 WAYASGQRE  136 (335)
Q Consensus       128 ~~~~~~~~~  136 (335)
                      ++.+.....
T Consensus        88 ~a~~~~~~~   96 (102)
T 2cqb_A           88 LAKPMRIKE   96 (102)
T ss_dssp             ECCCCCCCC
T ss_pred             eCCCCCCCC
Confidence            998765543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.77  E-value=1.1e-18  Score=125.88  Aligned_cols=81  Identities=14%  Similarity=0.118  Sum_probs=73.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccC-CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G-~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +...++|||+|||+++++++|+++|+.|| .|..+++..+.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++..
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            34567899999999999999999999999 89999987667789999999999999999999999999999999999865


Q ss_pred             CC
Q 019811          132 SG  133 (335)
Q Consensus       132 ~~  133 (335)
                      ..
T Consensus       105 ~p  106 (111)
T 2jvr_A          105 PP  106 (111)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.77  E-value=4.5e-18  Score=124.71  Aligned_cols=86  Identities=26%  Similarity=0.534  Sum_probs=77.7

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      .....+.++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|++.|+|..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33456788999999999999999999999999999999998753    58999999999999999999999999999999


Q ss_pred             EeeeccCCCc
Q 019811          126 VNWAYASGQR  135 (335)
Q Consensus       126 v~~~~~~~~~  135 (335)
                      |.++.++...
T Consensus        89 V~~a~~~~~~   98 (115)
T 2dgo_A           89 TNWATRKPPA   98 (115)
T ss_dssp             EEESSCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999876544

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=1.8e-18  Score=125.07  Aligned_cols=79  Identities=15%  Similarity=0.263  Sum_probs=72.7

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+.++|||+|||.++++++|+++|++||.|.+|+++.++.    +|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4567899999999999999999999999999999998754    589999999999999999999999999999999998


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            543

>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=3.2e-18  Score=120.73  Aligned_cols=79  Identities=28%  Similarity=0.443  Sum_probs=72.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|++.||+..+.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567889999999999999999999999999999998864    36899999999999999999999999999999999


Q ss_pred             eec
Q 019811          128 WAY  130 (335)
Q Consensus       128 ~~~  130 (335)
                      +++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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=99.77  E-value=1.8e-18  Score=125.53  Aligned_cols=83  Identities=17%  Similarity=0.201  Sum_probs=74.0

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC--CccccCceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN--GRHLFGQPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~--~~~~~g~~l~v~~~  129 (335)
                      ...++++|||+|||+++|+++|+++|++||.|.+|+++++  +|||||+|.+.++|.+|++.++  +..+.|++|+|.++
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~--kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a  104 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS  104 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG--GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEc
Confidence            3456789999999999999999999999999999999886  5899999999999999999887  46899999999999


Q ss_pred             ccCCCcc
Q 019811          130 YASGQRE  136 (335)
Q Consensus       130 ~~~~~~~  136 (335)
                      ..+....
T Consensus       105 ~~k~~~~  111 (119)
T 2ad9_A          105 NHKELKT  111 (119)
T ss_dssp             SSSSCCC
T ss_pred             cCCCCCc
Confidence            7765443

>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=99.77  E-value=3.7e-18  Score=117.46  Aligned_cols=80  Identities=51%  Similarity=0.890  Sum_probs=77.1

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|+..|++..++|+.|+|.++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999889999999999999999999999999999999999999999765

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.8e-18  Score=122.49  Aligned_cols=87  Identities=25%  Similarity=0.383  Sum_probs=78.1

Q ss_pred             CCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCcee
Q 019811           49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPI  124 (335)
Q Consensus        49 ~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l  124 (335)
                      +.....+.++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+..|||..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (103)
T 2cq0_A            8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   87 (103)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            344566789999999999999999999999999999999988753    5799999999999999999999999999999


Q ss_pred             EEeeeccCCCc
Q 019811          125 KVNWAYASGQR  135 (335)
Q Consensus       125 ~v~~~~~~~~~  135 (335)
                      +|.++.++...
T Consensus        88 ~v~~a~~~~~~   98 (103)
T 2cq0_A           88 NVEWAKPSTNS   98 (103)
T ss_dssp             EEEESSCCCCS
T ss_pred             EEEECCCCCCC
Confidence            99999876543

>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=99.77  E-value=5.5e-18  Score=121.64  Aligned_cols=81  Identities=16%  Similarity=0.197  Sum_probs=71.8

Q ss_pred             CCCCcceEEEeCCCCC-CCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC--CccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN--GRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~--~~~~~g~~l~v~~  128 (335)
                      ...++++|||+|||.+ +++++|+++|++||.|.+|++.+  .+|||||+|.+.++|..|++.|+  +..+.|++|+|.+
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~--~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   98 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR--MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET--TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec--CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            3556889999999998 99999999999999999999975  46899999999999999999875  4669999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +..+..
T Consensus        99 a~~~~~  104 (112)
T 1x4f_A           99 SEKYKK  104 (112)
T ss_dssp             ECSCSS
T ss_pred             Cccccc
Confidence            976543

>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=6.1e-18  Score=122.38  Aligned_cols=84  Identities=25%  Similarity=0.492  Sum_probs=75.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHh-CCccccCceeE
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSL-NGRHLFGQPIK  125 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l-~~~~~~g~~l~  125 (335)
                      .....++|||+|||..+++++|+++|+.||.|.+|++..+.     .+|||||+|.+.++|.+|+..| |+..+.|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            34567889999999999999999999999999999998772     3689999999999999999999 99999999999


Q ss_pred             EeeeccCCCc
Q 019811          126 VNWAYASGQR  135 (335)
Q Consensus       126 v~~~~~~~~~  135 (335)
                      |.++.+....
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.77  E-value=3.5e-18  Score=125.93  Aligned_cols=79  Identities=20%  Similarity=0.344  Sum_probs=72.9

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ....+.++|||+|||.++++++|+++|++||.|.+|++..++    .+|||||+|.+.++|.+|++.|||..+.|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345667899999999999999999999999999999998764    3689999999999999999999999999999999


Q ss_pred             eee
Q 019811          127 NWA  129 (335)
Q Consensus       127 ~~~  129 (335)
                      .++
T Consensus       115 ~~a  117 (118)
T 2khc_A          115 QLK  117 (118)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            986

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.7e-18  Score=122.59  Aligned_cols=84  Identities=24%  Similarity=0.370  Sum_probs=76.0

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|.+..++    ++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999998764    36899999999999999999999999999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++......
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99866543

>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=99.77  E-value=1.8e-18  Score=120.20  Aligned_cols=79  Identities=25%  Similarity=0.596  Sum_probs=71.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+.++|||+|||.++++++|+++|+.||.|.++++..++    ++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
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            456789999999999999999999999999999998875    3589999999999999999999999999999999998


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            754

>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=99.77  E-value=2.9e-18  Score=119.40  Aligned_cols=79  Identities=20%  Similarity=0.343  Sum_probs=73.1

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..++|||+|||.++++++|+++|+.||.|.++.+..+.     .+|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            45789999999999999999999999999999998865     5789999999999999999999999999999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=5.9e-18  Score=118.27  Aligned_cols=79  Identities=29%  Similarity=0.498  Sum_probs=73.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      +.+.++|||+|||.++++++|+++|+.||.|.++++.    +|||||+|.+.++|.+|++.||+..+.|+.|+|.++.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   80 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNK   80 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCC
Confidence            4567899999999999999999999999999999987    579999999999999999999999999999999999876


Q ss_pred             CCc
Q 019811          133 GQR  135 (335)
Q Consensus       133 ~~~  135 (335)
                      ...
T Consensus        81 ~~~   83 (90)
T 2dnq_A           81 SKA   83 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>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=99.77  E-value=6.7e-18  Score=121.68  Aligned_cols=83  Identities=20%  Similarity=0.410  Sum_probs=75.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccC---ceeEE
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFG---QPIKV  126 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g---~~l~v  126 (335)
                      ....++|||+|||.++++++|+++|+.||.|.+|++..++.   +|||||+|.+.++|.+|++.|||..+.|   +.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            34578899999999999999999999999999999998753   5899999999999999999999999998   99999


Q ss_pred             eeeccCCCc
Q 019811          127 NWAYASGQR  135 (335)
Q Consensus       127 ~~~~~~~~~  135 (335)
                      .++.+...+
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=6.6e-18  Score=121.23  Aligned_cols=88  Identities=27%  Similarity=0.440  Sum_probs=82.1

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34566789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .|+..+..
T Consensus        90 ~~a~~~~~   97 (103)
T 2cq0_A           90 EWAKPSTN   97 (103)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>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=99.77  E-value=3.3e-18  Score=118.85  Aligned_cols=83  Identities=55%  Similarity=0.976  Sum_probs=76.6

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .+.++|||+|||.++++++|+++|+.||.|.++.+.+++.++.++|||||+|.+.++|.+|++.|++..++|+.|+|.|+
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            34579999999999999999999999999999999999888999999999999999999999999999999999999998


Q ss_pred             cCC
Q 019811          219 TKG  221 (335)
Q Consensus       219 ~~~  221 (335)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>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=5.2e-18  Score=121.07  Aligned_cols=81  Identities=16%  Similarity=0.332  Sum_probs=74.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++..++   .+|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            4556889999999999999999999999999999999876   2489999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.77  E-value=9.2e-18  Score=123.05  Aligned_cols=90  Identities=53%  Similarity=0.928  Sum_probs=83.0

Q ss_pred             ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       135 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      .......++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34456678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEEccCCCCC
Q 019811          215 CNWATKGAGN  224 (335)
Q Consensus       215 v~~~~~~~~~  224 (335)
                      |.|+..+...
T Consensus        89 V~~a~~~~~~   98 (115)
T 2dgo_A           89 TNWATRKPPA   98 (115)
T ss_dssp             EEESSCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999876543

>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=99.77  E-value=7e-18  Score=122.91  Aligned_cols=84  Identities=19%  Similarity=0.362  Sum_probs=76.4

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhC------CccccC
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLN------GRHLFG  121 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~------~~~~~g  121 (335)
                      .+.+.++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+..|+      +..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            45567889999999999999999999999999999998764    46899999999999999999999      999999


Q ss_pred             ceeEEeeeccCCCc
Q 019811          122 QPIKVNWAYASGQR  135 (335)
Q Consensus       122 ~~l~v~~~~~~~~~  135 (335)
                      +.|+|.++.++...
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999876544

>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=99.77  E-value=4.7e-18  Score=120.20  Aligned_cols=81  Identities=22%  Similarity=0.236  Sum_probs=74.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHH----HHHhccCCceeEEEeecCC-CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQ----EVFSSTGPVEGCKLIRKDK-SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~----~~f~~~G~v~~v~~~~~~~-~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ..+.++|||+|||.++++++|+    ++|++||.|.+|++..++. +|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456789999999999999999    9999999999999987653 6899999999999999999999999999999999


Q ss_pred             eeccCC
Q 019811          128 WAYASG  133 (335)
Q Consensus       128 ~~~~~~  133 (335)
                      ++.+..
T Consensus        86 ~a~~~~   91 (96)
T 2dgx_A           86 LATGAS   91 (96)
T ss_dssp             ECCCSS
T ss_pred             EcCCCC
Confidence            997654

>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=99.76  E-value=4.5e-18  Score=129.69  Aligned_cols=81  Identities=25%  Similarity=0.387  Sum_probs=74.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~~  130 (335)
                      ++...+|||+||++.+|+++|+++|++||.|.+|++..+..+|||||+|.+.++|.+|++.|||..|.|  ++|+|.|+.
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            556678999999999999999999999999999999877677899999999999999999999999965  999999998


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      ++.
T Consensus       123 ~~~  125 (164)
T 1sjr_A          123 LTS  125 (164)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=3.1e-18  Score=121.77  Aligned_cols=83  Identities=24%  Similarity=0.481  Sum_probs=75.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      .+.++|||+|||.++++++|+++|+.||.|.+|++..++.       +|||||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4567899999999999999999999999999999987543       589999999999999999999999999999999


Q ss_pred             eeeccCCCcc
Q 019811          127 NWAYASGQRE  136 (335)
Q Consensus       127 ~~~~~~~~~~  136 (335)
                      .++.+.....
T Consensus        83 ~~a~~~~~~~   92 (98)
T 2cpf_A           83 RISERATKPA   92 (98)
T ss_dssp             ECSSCSSCCC
T ss_pred             EEccCCCCCC
Confidence            9997765543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.7e-18  Score=119.71  Aligned_cols=83  Identities=24%  Similarity=0.313  Sum_probs=75.1

Q ss_pred             CCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCcee
Q 019811           49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPI  124 (335)
Q Consensus        49 ~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l  124 (335)
                      ....+.+.++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A            8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            334566788999999999999999999999999999999988653    5899999999999999999999999999999


Q ss_pred             EEeeecc
Q 019811          125 KVNWAYA  131 (335)
Q Consensus       125 ~v~~~~~  131 (335)
                      +|.++..
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9999853

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.76  E-value=6e-19  Score=126.24  Aligned_cols=77  Identities=26%  Similarity=0.428  Sum_probs=71.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +...++|||+|||.++++++|+++|+.||.|.++++.  +++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY--PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe--cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            3456889999999999999999999999999999987  4568999999999999999999999999999999999864

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=6e-18  Score=119.62  Aligned_cols=86  Identities=34%  Similarity=0.454  Sum_probs=80.5

Q ss_pred             ccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       135 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      .....+.++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34556678999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEEccC
Q 019811          215 CNWATK  220 (335)
Q Consensus       215 v~~~~~  220 (335)
                      |.|++.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999864

>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=99.76  E-value=1e-17  Score=121.24  Aligned_cols=80  Identities=14%  Similarity=0.173  Sum_probs=73.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC-----ceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG-----QPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g-----~~l~v~  127 (335)
                      +...++|||+|||.++++++|+++|+.||.|.+|++..+   |||||+|.+.++|.+|++.||+..+.|     +.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~   88 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   88 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT---TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC---CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEE
Confidence            345788999999999999999999999999999999887   899999999999999999999999999     999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (108)
T 1x4c_A           89 VDGPRSPS   96 (108)
T ss_dssp             ESSCCSCC
T ss_pred             eCCCCCCC
Confidence            99876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.2e-18  Score=120.62  Aligned_cols=83  Identities=28%  Similarity=0.570  Sum_probs=75.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeE-EEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC-KLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v-~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .++++|||+|||.++++++|+++|+.||.|.++ ++..++    .+|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456889999999999999999999999999999 998763    368999999999999999999999999999999999


Q ss_pred             eccCCCcc
Q 019811          129 AYASGQRE  136 (335)
Q Consensus       129 ~~~~~~~~  136 (335)
                      +.++....
T Consensus        83 a~~~~~~~   90 (96)
T 1x5t_A           83 AFKKDSKG   90 (96)
T ss_dssp             SCCCCCCC
T ss_pred             ecccCCCC
Confidence            98766443

>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=99.76  E-value=7.3e-18  Score=120.11  Aligned_cols=86  Identities=27%  Similarity=0.349  Sum_probs=80.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.+
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            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987654

>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=99.76  E-value=4.7e-18  Score=117.52  Aligned_cols=78  Identities=28%  Similarity=0.473  Sum_probs=71.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +.+.++|||+|||.++++++|+++|++||.|.++++..++    .+|||||+|.+.++|.+|++.|||..+.|+.|+|.+
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            4567899999999999999999999999999999998763    368999999999999999999999999999999998


Q ss_pred             ec
Q 019811          129 AY  130 (335)
Q Consensus       129 ~~  130 (335)
                      +.
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.76  E-value=6.3e-18  Score=120.39  Aligned_cols=80  Identities=24%  Similarity=0.421  Sum_probs=73.6

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ...+.++|||+|||.++++++|+++|++||.|.+|++.++  +|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~--kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD--KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   88 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT--TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC--CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCC
Confidence            4556789999999999999999999999999999998765  58999999999999999999999999999999999976


Q ss_pred             CC
Q 019811          132 SG  133 (335)
Q Consensus       132 ~~  133 (335)
                      +.
T Consensus        89 ~~   90 (99)
T 2cpj_A           89 SA   90 (99)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.76  E-value=1.1e-17  Score=118.69  Aligned_cols=79  Identities=18%  Similarity=0.334  Sum_probs=72.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc--CceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF--GQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~~~  130 (335)
                      +.++++|||+|||.++++++|+++|++||.|.+|++..+  +|||||+|.+.++|.+|++.||+..+.  |+.|+|.++.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG--DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC--CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            445688999999999999999999999999999999776  679999999999999999999999999  9999999997


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      ++.
T Consensus        92 ~~~   94 (97)
T 1why_A           92 SGP   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=7.3e-18  Score=121.69  Aligned_cols=84  Identities=20%  Similarity=0.369  Sum_probs=75.8

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccc---cCcee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHL---FGQPI  124 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~---~g~~l  124 (335)
                      .+.+.++|||+|||.++++++|+++|++||.|.+|++..++    .+|||||+|.+.++|.+|++.||+..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            45567889999999999999999999999999999998864    468999999999999999999999887   89999


Q ss_pred             EEeeeccCCCc
Q 019811          125 KVNWAYASGQR  135 (335)
Q Consensus       125 ~v~~~~~~~~~  135 (335)
                      +|.++.+....
T Consensus        89 ~v~~a~~~~~~   99 (106)
T 2dgp_A           89 QVKPADSESRG   99 (106)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEECCccccc
Confidence            99999776543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.3e-18  Score=122.91  Aligned_cols=81  Identities=27%  Similarity=0.560  Sum_probs=74.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..++++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            45568899999999999999999999999999999988754    58999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +.++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            87654

>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=99.76  E-value=3.7e-18  Score=133.35  Aligned_cols=125  Identities=16%  Similarity=0.286  Sum_probs=80.1

Q ss_pred             EEEcCHHHHHHHHHHhCCcccc--CceeEEeeecc-----------------CCCccCCCCcceEEECCCCccccHHHHH
Q 019811           99 IHYFDRRSAAMAILSLNGRHLF--GQPIKVNWAYA-----------------SGQREDTSGHFNIFVGDLSPEVTDATLF  159 (335)
Q Consensus        99 v~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~~~~-----------------~~~~~~~~~~~~l~v~nlp~~~t~~~l~  159 (335)
                      .+|.+.++|..|+..+++....  |+.....+...                 .........+++|||+|||..+++++|.
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6889999999999888887665  55555544211                 0112223446789999999999999999


Q ss_pred             HHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCCC
Q 019811          160 ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGAG  223 (335)
Q Consensus       160 ~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~~  223 (335)
                      ++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|++..|.|+.|.|.|+..+..
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999988999999999999999999999999999999999999999977554

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=9.6e-18  Score=118.54  Aligned_cols=85  Identities=31%  Similarity=0.539  Sum_probs=80.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .++++|||+|||.++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45679999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 019811          219 TKGAG  223 (335)
Q Consensus       219 ~~~~~  223 (335)
                      ..+..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=6.6e-18  Score=119.62  Aligned_cols=86  Identities=31%  Similarity=0.654  Sum_probs=80.3

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceee-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDA-RVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      .++++|||+|||.++++++|+++|+.||.|..+ .+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356799999999999999999999999999999 9999988899999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 019811          218 ATKGAGN  224 (335)
Q Consensus       218 ~~~~~~~  224 (335)
                      +..+...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

>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=99.76  E-value=4.5e-18  Score=117.60  Aligned_cols=82  Identities=34%  Similarity=0.526  Sum_probs=77.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.|
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            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cc
Q 019811          218 AT  219 (335)
Q Consensus       218 ~~  219 (335)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.1e-17  Score=122.77  Aligned_cols=87  Identities=25%  Similarity=0.403  Sum_probs=76.8

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      .....+.++|||+|||.++++++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|++.+++ .|.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            3446677899999999999999999999999999999998864    468999999999999999999998 89999999


Q ss_pred             EeeeccCCCccC
Q 019811          126 VNWAYASGQRED  137 (335)
Q Consensus       126 v~~~~~~~~~~~  137 (335)
                      |.++........
T Consensus        90 V~~a~~~~~~~~  101 (116)
T 2cqd_A           90 VNLAYLGAKPRS  101 (116)
T ss_dssp             EEESTTTCCCCC
T ss_pred             EEEcccCCCccc
Confidence            999976554433

>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=99.76  E-value=5.9e-18  Score=119.80  Aligned_cols=82  Identities=27%  Similarity=0.603  Sum_probs=78.3

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      +++|||+|||..+++++|+++|+.||.|..+.+.+++.+|.++|||||+|.+.++|.+|++.|++..++|+.|+|.++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            47899999999999999999999999999999999988899999999999999999999999999999999999999977


Q ss_pred             CC
Q 019811          221 GA  222 (335)
Q Consensus       221 ~~  222 (335)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.76  E-value=5.5e-18  Score=119.97  Aligned_cols=80  Identities=31%  Similarity=0.458  Sum_probs=73.7

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ++++|||+|||.++++++|+++|+.||.|.++++..++    ++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.
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            35789999999999999999999999999999998774    36899999999999999999999999999999999997


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            6653

>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=99.75  E-value=7.8e-18  Score=119.16  Aligned_cols=76  Identities=20%  Similarity=0.352  Sum_probs=70.3

Q ss_pred             CCCcceEEEeCCCC-CCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ..++++|||+|||. ++++++|+++|+.||.|.++++.    +|||||+|.+.++|.+|+..|||..+.|+.|+|.++..
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC----SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            44578899999998 99999999999999999999883    68999999999999999999999999999999999865


Q ss_pred             C
Q 019811          132 S  132 (335)
Q Consensus       132 ~  132 (335)
                      +
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.5e-17  Score=118.65  Aligned_cols=85  Identities=18%  Similarity=0.364  Sum_probs=79.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+.+++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999997 88999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++.++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998754

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.75  E-value=8.1e-18  Score=119.81  Aligned_cols=77  Identities=25%  Similarity=0.376  Sum_probs=71.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCcee--------EEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG--------CKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      +...++|||+|||.++++++|+++|++||.|.+        +++..++.    +|||||+|.+.++|.+|++.|||..+.
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            455688999999999999999999999999999        99988753    589999999999999999999999999


Q ss_pred             CceeEEeee
Q 019811          121 GQPIKVNWA  129 (335)
Q Consensus       121 g~~l~v~~~  129 (335)
                      |+.|+|.++
T Consensus        90 g~~l~V~~A   98 (99)
T 2la6_A           90 GNPIKVSFA   98 (99)
T ss_dssp             SSBCEEEEC
T ss_pred             CcEEEEEec
Confidence            999999987

>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=99.75  E-value=5.5e-18  Score=116.59  Aligned_cols=77  Identities=23%  Similarity=0.513  Sum_probs=71.5

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +.+|||+|||.++++++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+
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            35799999999999999999999999999999987743    58999999999999999999999999999999999976


Q ss_pred             C
Q 019811          132 S  132 (335)
Q Consensus       132 ~  132 (335)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.4e-17  Score=118.55  Aligned_cols=85  Identities=22%  Similarity=0.448  Sum_probs=79.6

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.+
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            4556899999999999999999999999999999999998889999999999999999999998 999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +..+..
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            987654

>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=99.75  E-value=1e-17  Score=120.48  Aligned_cols=82  Identities=26%  Similarity=0.383  Sum_probs=74.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ...+.++|||+|||.++++++|+++|+.|| |.+|++..++     .+|||||+|.+.++|.+|+ .|++..+.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345668999999999999999999999999 9999998764     3689999999999999999 99999999999999


Q ss_pred             eeeccCCCc
Q 019811          127 NWAYASGQR  135 (335)
Q Consensus       127 ~~~~~~~~~  135 (335)
                      .++.++...
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999876544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.75  E-value=1.9e-17  Score=125.73  Aligned_cols=84  Identities=33%  Similarity=0.564  Sum_probs=76.6

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+...++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            345678999999999999999999999999999999998754    5899999999999999999999999999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.+...+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876544

>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=99.75  E-value=9.2e-18  Score=121.74  Aligned_cols=83  Identities=28%  Similarity=0.519  Sum_probs=75.7

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      .+...++|||+|||.++++++|+++|+.||.|.+|++..+  +|||||+|.+.++|.+|+..|+|..+.|+.|+|.|+.+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   98 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   98 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC--CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCC
Confidence            3456789999999999999999999999999999999877  68999999999999999999999999999999999987


Q ss_pred             CCCcc
Q 019811          132 SGQRE  136 (335)
Q Consensus       132 ~~~~~  136 (335)
                      .....
T Consensus        99 ~~~~~  103 (109)
T 1x4g_A           99 SPDMT  103 (109)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            66443

>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=99.75  E-value=9.4e-18  Score=121.18  Aligned_cols=81  Identities=32%  Similarity=0.571  Sum_probs=74.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +..+++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|++.|+|..+.|+.|+|.+
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            44568899999999999999999999999999999988753    58999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +.++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            87653

>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=99.75  E-value=7.5e-18  Score=116.45  Aligned_cols=76  Identities=24%  Similarity=0.445  Sum_probs=70.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh-CCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL-NGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l-~~~~~~g~~l~v~~~~  130 (335)
                      +...++|||+|||.++++++|+++|++||.|.++++.++  +|||||+|.+.++|.+|+..| +|..+.|++|+|.|++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~--kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR--QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG--GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC--CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            456688999999999999999999999999999999875  579999999999999999988 9999999999999873

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=119.93  Aligned_cols=87  Identities=32%  Similarity=0.463  Sum_probs=81.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            45668999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 019811          218 ATKGAGN  224 (335)
Q Consensus       218 ~~~~~~~  224 (335)
                      +......
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.75  E-value=1.3e-17  Score=122.27  Aligned_cols=87  Identities=28%  Similarity=0.466  Sum_probs=81.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |+..+..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9987654

>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=5.1e-18  Score=119.96  Aligned_cols=80  Identities=33%  Similarity=0.616  Sum_probs=73.4

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+...++|||+|||..+++++|+++|+.||.|.+|++..++.   +|||||+|.+.++|.+|++.||+..+.|+.|+|.+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            355678999999999999999999999999999999988753   58999999999999999999999999999999998


Q ss_pred             ecc
Q 019811          129 AYA  131 (335)
Q Consensus       129 ~~~  131 (335)
                      +..
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-17  Score=118.83  Aligned_cols=84  Identities=27%  Similarity=0.361  Sum_probs=78.7

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCcee--------eEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD--------ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      ......++|||+|||.++++++|+++|+.||.|..        +.+++++.+|.++|||||+|.+.++|.+|++.|++..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34556789999999999999999999999999999        9999998889999999999999999999999999999


Q ss_pred             eCCeeeEEEEcc
Q 019811          208 LGSRQIRCNWAT  219 (335)
Q Consensus       208 ~~g~~l~v~~~~  219 (335)
                      +.|+.|+|.+++
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999874

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.75  E-value=5.6e-18  Score=122.32  Aligned_cols=78  Identities=24%  Similarity=0.487  Sum_probs=72.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ....++|||+|||.++++++|+++|++||.|.+|++.    +|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            4566889999999999999999999999999999997    689999999999999999999999999999999999765


Q ss_pred             CC
Q 019811          133 GQ  134 (335)
Q Consensus       133 ~~  134 (335)
                      ..
T Consensus       104 ~~  105 (108)
T 2jvo_A          104 AK  105 (108)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>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=99.75  E-value=1.2e-17  Score=122.25  Aligned_cols=81  Identities=26%  Similarity=0.508  Sum_probs=74.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ....++|||+|||.++++++|+++|+.||.|.+|.+..++   .+|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            4567889999999999999999999999999999998865   4689999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .+..
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7654

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-17  Score=120.15  Aligned_cols=88  Identities=26%  Similarity=0.402  Sum_probs=81.9

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .++.....
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987654

>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=99.75  E-value=1e-17  Score=120.99  Aligned_cols=86  Identities=28%  Similarity=0.567  Sum_probs=80.6

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ....+.++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++.|++..++|+.|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEccCC
Q 019811          216 NWATKG  221 (335)
Q Consensus       216 ~~~~~~  221 (335)
                      .++..+
T Consensus       101 ~~a~~k  106 (108)
T 2jrs_A          101 GHVTER  106 (108)
T ss_dssp             ECSCSS
T ss_pred             EEcccC
Confidence            998765

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-17  Score=117.84  Aligned_cols=83  Identities=25%  Similarity=0.414  Sum_probs=78.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Ecc
Q 019811          217 WAT  219 (335)
Q Consensus       217 ~~~  219 (335)
                      |++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=3.8e-18  Score=119.62  Aligned_cols=79  Identities=16%  Similarity=0.284  Sum_probs=70.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCC--ceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCc----cccCc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGP--VEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGR----HLFGQ  122 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~--v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~----~~~g~  122 (335)
                      ...-.||||+|||+++|+++|+++|++||.  +.+|++.+++    ++|||||+|.+.++|.+|++.|||.    .+.|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            344578999999999999999999999995  6789988864    4689999999999999999999996    48899


Q ss_pred             eeEEeeecc
Q 019811          123 PIKVNWAYA  131 (335)
Q Consensus       123 ~l~v~~~~~  131 (335)
                      +|.|.|+.+
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999864

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=1.6e-17  Score=119.15  Aligned_cols=82  Identities=17%  Similarity=0.342  Sum_probs=74.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++++++|+++|+.|| |.+|++..++.    +|||||+|.+.++|.+|+ .||+..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            355678999999999999999999999997 99999998763    589999999999999999 899999999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.+....
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            99876543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.75  E-value=9e-18  Score=117.93  Aligned_cols=82  Identities=21%  Similarity=0.284  Sum_probs=74.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|.++++..+.  .+|||||+|.+.++|.+|++.|++..+.|+.|+|.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            3456889999999999999999999999999999998753  35899999999999999999999999999999999997


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            6543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=120.67  Aligned_cols=86  Identities=22%  Similarity=0.438  Sum_probs=80.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ....+++|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      |+..+.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            987653

>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=99.74  E-value=4e-18  Score=125.00  Aligned_cols=104  Identities=16%  Similarity=0.269  Sum_probs=92.4

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      +..+++|||+|||..+++++|+++|+.||.|..+.++++   +.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.|
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            345679999999999999999999999999999999865   45689999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcC
Q 019811          218 ATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG  287 (335)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G  287 (335)
                      +......                                           .+++...++++|.++|++||
T Consensus        82 a~~~~~~-------------------------------------------~~~~~~~~~~~l~~~~~~~g  108 (115)
T 3lqv_A           82 YNANRAF-------------------------------------------QKMDTKKKEEQLKLLKEKYG  108 (115)
T ss_dssp             CCHHHHT-------------------------------------------TTSCHHHHHHHHHHHHHHHC
T ss_pred             ecCChhh-------------------------------------------hhhhHhHhHHHHHHHHHHhC
Confidence            8653210                                           46778889999999999999

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=2.2e-17  Score=115.86  Aligned_cols=79  Identities=25%  Similarity=0.438  Sum_probs=72.7

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      +...++|||+|||.++++++|+++|+.||.|.++++.+    +||||+|.+.++|.+|+..|||..+.|+.|+|.++.++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~----~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   82 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK----DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR   82 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS----SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC----CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCC
Confidence            55678999999999999999999999999999999874    49999999999999999999999999999999999776


Q ss_pred             CCc
Q 019811          133 GQR  135 (335)
Q Consensus       133 ~~~  135 (335)
                      ...
T Consensus        83 ~~~   85 (92)
T 2dgt_A           83 LRT   85 (92)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

>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=99.74  E-value=1.9e-18  Score=120.71  Aligned_cols=81  Identities=16%  Similarity=0.255  Sum_probs=72.6

Q ss_pred             ceEEECCCCccccHHHHHHHhccCC--CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYP--SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+|||+|||.++++++|+++|+.||  .|.++.+++++.+|.++|||||+|.+.++|.+|++.|++..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=123.65  Aligned_cols=81  Identities=21%  Similarity=0.322  Sum_probs=72.3

Q ss_pred             CCcceEEEeCCCCCCCHHHHH----HHHhccCCceeEEEeec-CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQ----EVFSSTGPVEGCKLIRK-DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~----~~f~~~G~v~~v~~~~~-~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .++++|||+|||..+++++|+    ++|++||.|.+|.+..+ +++|||||+|.+.++|..|+..|||..+.|++|+|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            346789999999999999876    79999999999988664 4679999999999999999999999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +..+..
T Consensus       107 a~~~~~  112 (127)
T 2a3j_A          107 SETPQS  112 (127)
T ss_dssp             CCCCCH
T ss_pred             ccCcch
Confidence            976553

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=9.2e-18  Score=120.48  Aligned_cols=87  Identities=29%  Similarity=0.453  Sum_probs=81.1

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44566899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2dnm_A           89 VARYGRR   95 (103)
T ss_dssp             ECSSCCS
T ss_pred             ECCcCCC
Confidence            9987553

>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=99.74  E-value=2.8e-17  Score=118.41  Aligned_cols=86  Identities=22%  Similarity=0.398  Sum_probs=79.3

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC---eeeE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS---RQIR  214 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g---~~l~  214 (335)
                      ....++|||+|||.++++++|+++|+.||.|..+.+.+++ ++.++|||||+|.+.++|.+|+..|++..+.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            4557899999999999999999999999999999999986 78999999999999999999999999999988   9999


Q ss_pred             EEEccCCCCC
Q 019811          215 CNWATKGAGN  224 (335)
Q Consensus       215 v~~~~~~~~~  224 (335)
                      |.|+......
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-17  Score=115.61  Aligned_cols=78  Identities=27%  Similarity=0.528  Sum_probs=71.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      +.+.++|||+|||.++++++|+++|+.||.|.++++.+    +||||+|.+.++|.+|+..|||..+.|+.|+|.++.+.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~----~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK----DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS----SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            45678899999999999999999999999999999874    49999999999999999999999999999999999776


Q ss_pred             CC
Q 019811          133 GQ  134 (335)
Q Consensus       133 ~~  134 (335)
                      ..
T Consensus        82 ~~   83 (90)
T 2dnp_A           82 QK   83 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.9e-17  Score=120.98  Aligned_cols=84  Identities=21%  Similarity=0.289  Sum_probs=75.7

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCce--------eEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE--------GCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHL  119 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~--------~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~  119 (335)
                      .....++|||+|||.++++++|+++|+.||.|.        .|++..++    .+|||||+|.+.++|.+|++.|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            355678999999999999999999999999998        69998874    368999999999999999999999999


Q ss_pred             cCceeEEeeeccCCCc
Q 019811          120 FGQPIKVNWAYASGQR  135 (335)
Q Consensus       120 ~g~~l~v~~~~~~~~~  135 (335)
                      .|+.|+|.++..+...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999876544

>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=99.74  E-value=2.5e-17  Score=118.16  Aligned_cols=79  Identities=32%  Similarity=0.565  Sum_probs=72.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|++.    ++||||+|.+.++|.+|++.||+..+.|+.|+|.++.+.
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            3456889999999999999999999999999999986    459999999999999999999999999999999999766


Q ss_pred             CCc
Q 019811          133 GQR  135 (335)
Q Consensus       133 ~~~  135 (335)
                      ...
T Consensus        84 ~~~   86 (103)
T 2dgu_A           84 DQK   86 (103)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.74  E-value=7.8e-17  Score=119.67  Aligned_cols=85  Identities=20%  Similarity=0.267  Sum_probs=77.1

Q ss_pred             CCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           50 GFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        50 ~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      +.....+++|||+|||.++++++|+++|+.||.|.+|++..++   .+|||||+|.+.++|.+|++.|||..+.|+.|+|
T Consensus        29 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           29 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            3356778899999999999999999999999999999998865   4689999999999999999999999999999999


Q ss_pred             eeeccCCC
Q 019811          127 NWAYASGQ  134 (335)
Q Consensus       127 ~~~~~~~~  134 (335)
                      .++.....
T Consensus       109 ~~a~~~~~  116 (124)
T 2kt5_A          109 QLVASQID  116 (124)
T ss_dssp             EEECCTTC
T ss_pred             EEeCCCCC
Confidence            99976543

>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=99.74  E-value=2.2e-17  Score=120.24  Aligned_cols=88  Identities=23%  Similarity=0.348  Sum_probs=81.6

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeC
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT------GKWLG  209 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~------~~~~~  209 (335)
                      ......++|||+|||.++++++|+++|..||.|..+.+++++.++.++|||||+|.+.++|.+|+..++      +..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            344567899999999999999999999999999999999998889999999999999999999999999      99999


Q ss_pred             CeeeEEEEccCCCC
Q 019811          210 SRQIRCNWATKGAG  223 (335)
Q Consensus       210 g~~l~v~~~~~~~~  223 (335)
                      |+.|+|.|+..+..
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999987654

>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=99.74  E-value=2.3e-17  Score=120.76  Aligned_cols=85  Identities=32%  Similarity=0.485  Sum_probs=79.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999987 889999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +..+..
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            987553

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=2.9e-17  Score=117.87  Aligned_cols=87  Identities=26%  Similarity=0.527  Sum_probs=80.0

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+.++  ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34456789999999999999999999999999999999988  7889999999999999999999999999999999999


Q ss_pred             EEccCCCCC
Q 019811          216 NWATKGAGN  224 (335)
Q Consensus       216 ~~~~~~~~~  224 (335)
                      .|+..+...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2d9p_A           88 ALAQRKEER   96 (103)
T ss_dssp             EECSSCCCC
T ss_pred             EEecccccC
Confidence            999876543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.4e-17  Score=117.86  Aligned_cols=80  Identities=21%  Similarity=0.301  Sum_probs=73.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeE-EEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGC-KLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v-~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ....++|||+|||.++++++|+++|+.||.|.++ .+..++.++.|||+|.+.++|.+|+..|||..+.|++|+|.++.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            3456889999999999999999999999999999 588888777899999999999999999999999999999999976


Q ss_pred             C
Q 019811          132 S  132 (335)
Q Consensus       132 ~  132 (335)
                      +
T Consensus        92 ~   92 (96)
T 2e44_A           92 E   92 (96)
T ss_dssp             C
T ss_pred             c
Confidence            5

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.74  E-value=3.7e-18  Score=121.64  Aligned_cols=81  Identities=23%  Similarity=0.279  Sum_probs=77.4

Q ss_pred             CcceEEECCCCc------cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-ee
Q 019811          140 GHFNIFVGDLSP------EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS-RQ  212 (335)
Q Consensus       140 ~~~~l~v~nlp~------~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g-~~  212 (335)
                      .+++|||+|||.      ++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..|++..+.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            457999999999      99999999999999999999999999889999999999999999999999999999999 99


Q ss_pred             eEEEEccC
Q 019811          213 IRCNWATK  220 (335)
Q Consensus       213 l~v~~~~~  220 (335)
                      |+|.++.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999865

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=3e-17  Score=120.08  Aligned_cols=82  Identities=26%  Similarity=0.356  Sum_probs=74.4

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .....++|||+|||.++++++|+++|+.||.|.+|++..++.   +|||||+|.+.++|.+|++.||+..+.|+.|+|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            345578899999999999999999999999999999988754   57999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +....
T Consensus        91 a~~~~   95 (114)
T 2do0_A           91 DERAL   95 (114)
T ss_dssp             CSCCC
T ss_pred             cccCC
Confidence            86543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.4e-17  Score=119.38  Aligned_cols=86  Identities=41%  Similarity=0.596  Sum_probs=80.6

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45668999999999999999999999999999999999988889999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +..+..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=2.6e-17  Score=119.06  Aligned_cols=88  Identities=27%  Similarity=0.430  Sum_probs=81.2

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeee
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWD-QKTGRSRGFGFVSFRNQQDAQSAINDL-TGKWLGSRQI  213 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~g~~l  213 (335)
                      ......++|||+|||..+++++|+++|+.||.|..+.++++ +.++.++|||||+|.+.++|.+|+..| ++..+.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34456689999999999999999999999999999999988 678899999999999999999999999 9999999999


Q ss_pred             EEEEccCCCC
Q 019811          214 RCNWATKGAG  223 (335)
Q Consensus       214 ~v~~~~~~~~  223 (335)
                      .|.|+.....
T Consensus        90 ~v~~a~~~~~   99 (107)
T 2cph_A           90 VLEWADSEVT   99 (107)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987654

>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=99.74  E-value=1.4e-17  Score=121.02  Aligned_cols=82  Identities=27%  Similarity=0.508  Sum_probs=74.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|+..|+|..+.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4566889999999999999999999999999999998764    368999999999999999999999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.++..
T Consensus       103 a~~~~~  108 (110)
T 1oo0_B          103 CFVKGP  108 (110)
T ss_dssp             SEESSC
T ss_pred             cccCCC
Confidence            976553

>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=99.74  E-value=3.2e-18  Score=122.06  Aligned_cols=78  Identities=27%  Similarity=0.394  Sum_probs=69.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ....++|||+|||.++++++|+++|+.|| |.+|++..++     ++|||||+|.+.++|.+|+ .|+|..+.|+.|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            45678999999999999999999999999 9999998765     3699999999999999999 899999999999999


Q ss_pred             eeccC
Q 019811          128 WAYAS  132 (335)
Q Consensus       128 ~~~~~  132 (335)
                      ++.++
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98754

>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=99.74  E-value=3.7e-17  Score=119.84  Aligned_cols=84  Identities=20%  Similarity=0.325  Sum_probs=74.7

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCc----eeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPV----EGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v----~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..++++|||+|||.++|+++|+++|+.||.|    ..+.+...+++|||||+|.+.++|.+|+..|+|..+.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3457899999999999999999999999998    566666667789999999999999999999999999999999999


Q ss_pred             eccCCCcc
Q 019811          129 AYASGQRE  136 (335)
Q Consensus       129 ~~~~~~~~  136 (335)
                      +.+.....
T Consensus       102 a~~~~~~~  109 (115)
T 2cpx_A          102 GKNKKQRS  109 (115)
T ss_dssp             CCCCSCCC
T ss_pred             ccCCCCCC
Confidence            98765443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.1e-17  Score=118.30  Aligned_cols=71  Identities=14%  Similarity=0.201  Sum_probs=65.5

Q ss_pred             CCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcC--CCcccccCccccC
Q 019811          260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT--TQSSYLFGKQMKV  335 (335)
Q Consensus       260 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g--~~~~~~~g~~l~v  335 (335)
                      .+.++|||+|||+++++++|+++|++||  .|.++++.+++|+|||+|.+.++|.+|+..|++  .   .|+|++|+|
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG--~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~---~l~Gr~l~V   86 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFG--KVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTP---VLRGQPIYI   86 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHC--CEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCC---EETTEECCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC--CEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCc---eECCEEEEE
Confidence            3458999999999999999999999999  699999999999999999999999999998864  6   899999986

>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=99.74  E-value=9.2e-18  Score=122.81  Aligned_cols=81  Identities=23%  Similarity=0.481  Sum_probs=73.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .....++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+ .|||..|.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            34567899999999999999999999999999999998765    3689999999999999999 999999999999999


Q ss_pred             eeccCC
Q 019811          128 WAYASG  133 (335)
Q Consensus       128 ~~~~~~  133 (335)
                      ++.++.
T Consensus       100 ~a~~~~  105 (114)
T 2cq4_A          100 ASQAEK  105 (114)
T ss_dssp             EHHHHH
T ss_pred             ecCCCc
Confidence            986543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.74  E-value=1.2e-17  Score=125.23  Aligned_cols=81  Identities=16%  Similarity=0.273  Sum_probs=73.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCcee--EEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCc----cccCc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG--CKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGR----HLFGQ  122 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~--v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~----~~~g~  122 (335)
                      ....++|||+|||+++|+++|+++|++||.|..  |+++.++    ++|||||+|.+. +|.+|+..|||.    .+.|+
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            356688999999999999999999999999976  9998876    469999999999 999999999999    99999


Q ss_pred             eeEEeeeccCCC
Q 019811          123 PIKVNWAYASGQ  134 (335)
Q Consensus       123 ~l~v~~~~~~~~  134 (335)
                      .|+|.++.+...
T Consensus        99 ~l~V~~a~~~~~  110 (131)
T 2m2b_A           99 TINVEFAKGSKR  110 (131)
T ss_dssp             CCCCEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999977644

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.7e-17  Score=117.90  Aligned_cols=85  Identities=24%  Similarity=0.403  Sum_probs=78.1

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK---TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      .+.++|||+|||.++++++|+++|+.||.|..+.+.+++.   ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3557999999999999999999999999999999998865   5588999999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .++.....
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99977543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=119.28  Aligned_cols=81  Identities=25%  Similarity=0.358  Sum_probs=71.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+.+.++|||+|||.++++++|+++|+.||.|   ++..+   +.+|||||+|.+.++|.+|+..||+..+.|+.|+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            45667899999999999999999999999987   33333   4579999999999999999999999999999999999


Q ss_pred             eccCCCc
Q 019811          129 AYASGQR  135 (335)
Q Consensus       129 ~~~~~~~  135 (335)
                      +.++...
T Consensus        88 a~~~~~~   94 (101)
T 2fc9_A           88 QGPRGSP   94 (101)
T ss_dssp             CSSCCCC
T ss_pred             cCCCCCC
Confidence            9876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-17  Score=117.87  Aligned_cols=85  Identities=21%  Similarity=0.421  Sum_probs=79.6

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCce-eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCee----
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCS-DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQ----  212 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~-~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~----  212 (335)
                      ....++|||+|||.++++++|+++|+.||.|. .+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.    
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            34568999999999999999999999999999 9999999889999999999999999999999999999999999    


Q ss_pred             eEEEEccCCC
Q 019811          213 IRCNWATKGA  222 (335)
Q Consensus       213 l~v~~~~~~~  222 (335)
                      |+|.|+....
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999987653

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.73  E-value=1.1e-17  Score=124.73  Aligned_cols=87  Identities=32%  Similarity=0.453  Sum_probs=81.3

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ....+.++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34566789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 019811          216 NWATKGA  222 (335)
Q Consensus       216 ~~~~~~~  222 (335)
                      .|+..+.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9997754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.2e-17  Score=122.99  Aligned_cols=84  Identities=31%  Similarity=0.498  Sum_probs=78.2

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++.|++..++|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456689999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEcc
Q 019811          216 NWAT  219 (335)
Q Consensus       216 ~~~~  219 (335)
                      +|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9873

>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=99.73  E-value=2e-17  Score=120.20  Aligned_cols=86  Identities=20%  Similarity=0.400  Sum_probs=80.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ....+++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..++|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      |+..+.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            987654

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.73  E-value=3.1e-18  Score=119.67  Aligned_cols=78  Identities=21%  Similarity=0.219  Sum_probs=66.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccC--CceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTG--PVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G--~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      .+|||+|||.++|+++|+++|+.||  .|.++++..++    ++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
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            4699999999999999999999999  99999998875    35899999999999999999999999999999999987


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=6.2e-17  Score=115.19  Aligned_cols=78  Identities=33%  Similarity=0.571  Sum_probs=71.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcc--CCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSST--GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~--G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..+.++|||+|||.++++++|+++|+.|  |.|.++++.    +|||||+|.+.++|.+|+..|||..+.|+.|+|.++.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI----RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   87 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC----SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe----CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            4567899999999999999999999999  889988764    5799999999999999999999999999999999998


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      ++..
T Consensus        88 ~~~~   91 (99)
T 2cpd_A           88 PVDK   91 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=6e-17  Score=116.17  Aligned_cols=85  Identities=24%  Similarity=0.424  Sum_probs=78.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ...+.++|||+|||.++++++|+++|+.|| |..+.+++++.++.++|||||+|.+.++|.+|+ .|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345568999999999999999999999996 999999999888999999999999999999999 899999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      ++..+..
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9987553

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=117.15  Aligned_cols=76  Identities=24%  Similarity=0.297  Sum_probs=67.7

Q ss_pred             CCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       257 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ...+++++|||+|||+++++++|+++|++||  .|.++.+.++||+|||+|.+.++|.+|++.|+|.+. .++|++|.|
T Consensus        16 ~~~~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           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFG--PISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQI-YIAGHPAFV   91 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGS--CEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCE-EETTEEEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccC--CEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCc-eeCCcEEEE
Confidence            3445679999999999999999999999999  599999999999999999999999999999998822 388999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=128.27  Aligned_cols=78  Identities=24%  Similarity=0.260  Sum_probs=70.6

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccC--CceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTG--PVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G--~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...++|||+|||.++|+++|+++|+.||  .|.+|+++.++.    +|||||+|.+.++|.+|+..|||..|.|+.|+|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568899999999999999999999999  899999988753    5899999999999999999999999999999999


Q ss_pred             eecc
Q 019811          128 WAYA  131 (335)
Q Consensus       128 ~~~~  131 (335)
                      ++.+
T Consensus       133 ~a~~  136 (156)
T 3n9u_C          133 PATR  136 (156)
T ss_dssp             ECCH
T ss_pred             EcCC
Confidence            9854

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.4e-17  Score=118.80  Aligned_cols=78  Identities=18%  Similarity=0.147  Sum_probs=71.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ....++|||+|||.++|+++|+++|+.||.|.+|.+..++   ++|||||+|.+.++|.+|+. +++..+.|+.|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3456889999999999999999999999999999998864   57999999999999999998 8999999999999987


Q ss_pred             cc
Q 019811          130 YA  131 (335)
Q Consensus       130 ~~  131 (335)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            54

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.4e-17  Score=118.98  Aligned_cols=87  Identities=23%  Similarity=0.318  Sum_probs=80.8

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCce--------eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCS--------DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      .....++|||+|||.++++++|+++|+.||.|.        .+.+++++.++.++|||||+|.+.++|.+|+..|++..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            445678999999999999999999999999999        699999988899999999999999999999999999999


Q ss_pred             CCeeeEEEEccCCCC
Q 019811          209 GSRQIRCNWATKGAG  223 (335)
Q Consensus       209 ~g~~l~v~~~~~~~~  223 (335)
                      .|+.|+|.++..+..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999987654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.3e-17  Score=117.50  Aligned_cols=81  Identities=26%  Similarity=0.518  Sum_probs=73.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCce-eEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCce----
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE-GCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQP----  123 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~-~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~----  123 (335)
                      ..++++|||+|||.++++++|+++|++||.|. ++++..++.    +|||||+|.+.++|.+|++.|||..+.|+.    
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            45678999999999999999999999999999 999998753    489999999999999999999999999999    


Q ss_pred             eEEeeeccCC
Q 019811          124 IKVNWAYASG  133 (335)
Q Consensus       124 l~v~~~~~~~  133 (335)
                      |+|.|+.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999987554

>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=99.73  E-value=2.5e-17  Score=118.86  Aligned_cols=88  Identities=18%  Similarity=0.305  Sum_probs=81.1

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCee
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL---GSRQ  212 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~---~g~~  212 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3445668999999999999999999999999999999999988899999999999999999999999999987   8999


Q ss_pred             eEEEEccCCCC
Q 019811          213 IRCNWATKGAG  223 (335)
Q Consensus       213 l~v~~~~~~~~  223 (335)
                      |.|.++..+..
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999987553

>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=99.73  E-value=1.1e-17  Score=121.53  Aligned_cols=82  Identities=17%  Similarity=0.258  Sum_probs=74.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHH---HHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQ---EVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~---~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      .....++|||+|||.++++++|+   ++|++||.|.+|++..++.       +|||||+|.+.++|.+|++.|||..+.|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34456789999999999999999   9999999999999987642       4799999999999999999999999999


Q ss_pred             ceeEEeeeccCC
Q 019811          122 QPIKVNWAYASG  133 (335)
Q Consensus       122 ~~l~v~~~~~~~  133 (335)
                      +.|+|.++.++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999997665

>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=99.73  E-value=3.2e-17  Score=116.52  Aligned_cols=84  Identities=20%  Similarity=0.299  Sum_probs=78.3

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|.+|++.|++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34557899999999999999999999999999998888888899999999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8653

>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=99.73  E-value=2.1e-17  Score=114.97  Aligned_cols=83  Identities=19%  Similarity=0.360  Sum_probs=76.5

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGR-SRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~-~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..++|||+|||.++++++|+++|+.||.|..+.+++++.++. ++|+|||+|.+.++|.+|+..|++..++|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            346899999999999999999999999999999998876555 8999999999999999999999999999999999999


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.73  E-value=2.2e-17  Score=116.80  Aligned_cols=79  Identities=19%  Similarity=0.334  Sum_probs=70.9

Q ss_pred             CCCcceEEEeCCCC-CCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ..+.++|||+|||. .+++++|+++|+.||.|.+|++.    +|||||+|.+.++|.+|+..|+|..+.|+.|+|.++..
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   82 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSS   82 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE----TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCc
Confidence            45678899999998 99999999999999999999984    68999999999999999999999999999999999976


Q ss_pred             CCCc
Q 019811          132 SGQR  135 (335)
Q Consensus       132 ~~~~  135 (335)
                      ....
T Consensus        83 ~~~~   86 (96)
T 2kvi_A           83 NARP   86 (96)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            5543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.72  E-value=4.3e-17  Score=123.69  Aligned_cols=88  Identities=26%  Similarity=0.446  Sum_probs=81.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EccCCCCC
Q 019811          217 WATKGAGN  224 (335)
Q Consensus       217 ~~~~~~~~  224 (335)
                      ++..+...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.72  E-value=2.7e-18  Score=127.71  Aligned_cols=82  Identities=18%  Similarity=0.356  Sum_probs=77.3

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+ .|++..++|+.|+|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3579999999999999999999999999999999999888999999999999999999999 799999999999999987


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      ...
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.72  E-value=2.9e-17  Score=116.01  Aligned_cols=83  Identities=25%  Similarity=0.449  Sum_probs=77.2

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|+++|+.||.|..+.+.+++. +.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            345568999999999999999999999999999999999865 8899999999999999999999999999999999999


Q ss_pred             EccC
Q 019811          217 WATK  220 (335)
Q Consensus       217 ~~~~  220 (335)
                      ++..
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=9.4e-18  Score=119.51  Aligned_cols=79  Identities=16%  Similarity=0.163  Sum_probs=72.8

Q ss_pred             CCcceEEEeCCCC------CCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccC-c
Q 019811           54 STCRSVYVGNIHT------QVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFG-Q  122 (335)
Q Consensus        54 ~~~~~v~v~nlp~------~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g-~  122 (335)
                      ...++|||+|||.      ++++++|+++|++||.|.+|++..++.    +|||||+|.+.++|.+|++.|||..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4568899999999      999999999999999999999988763    6999999999999999999999999999 9


Q ss_pred             eeEEeeeccC
Q 019811          123 PIKVNWAYAS  132 (335)
Q Consensus       123 ~l~v~~~~~~  132 (335)
                      .|+|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998653

>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=99.72  E-value=2.6e-17  Score=116.98  Aligned_cols=80  Identities=15%  Similarity=0.213  Sum_probs=71.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ....++|||+|||.++++++|+++|+.||.|.++.++.++    .+|||||+|.+.++|.+|++.|||..|.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4456789999999999999999999999999887777654    358999999999999999999999999999999999


Q ss_pred             eccC
Q 019811          129 AYAS  132 (335)
Q Consensus       129 ~~~~  132 (335)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8644

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.72  E-value=4.2e-17  Score=124.02  Aligned_cols=81  Identities=28%  Similarity=0.473  Sum_probs=73.1

Q ss_pred             CCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCcee
Q 019811           49 PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPI  124 (335)
Q Consensus        49 ~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l  124 (335)
                      .+....+.++|||+|||.++++++|+++|++||.|.++++..++    .+|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus        56 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             SCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34456678899999999999999999999999999999998763    46999999999999999999999999999999


Q ss_pred             EEeee
Q 019811          125 KVNWA  129 (335)
Q Consensus       125 ~v~~~  129 (335)
                      +|.++
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99875

>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=99.72  E-value=2.4e-17  Score=115.94  Aligned_cols=80  Identities=31%  Similarity=0.521  Sum_probs=70.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCC-ceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCC-ccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNG-RHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~-v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~-~~~~g~~l~v~~~~  130 (335)
                      +...++|||+|||.++|+++|+++|++||. |..+.+.   ++|||||+|.+.++|.+|++.||| ..+.|+.|+|.++.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~   81 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   81 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc---CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEcc
Confidence            345678999999999999999999999999 6666653   358999999999999999999999 99999999999998


Q ss_pred             cCCCc
Q 019811          131 ASGQR  135 (335)
Q Consensus       131 ~~~~~  135 (335)
                      ++..+
T Consensus        82 ~~~~~   86 (93)
T 2cqh_A           82 SKKLR   86 (93)
T ss_dssp             CCCCC
T ss_pred             Ccccc
Confidence            76543

>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=99.72  E-value=6.3e-17  Score=116.25  Aligned_cols=85  Identities=26%  Similarity=0.463  Sum_probs=78.5

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKT-GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ...+.++|||+|||.++++++|+++|+.|| |..+.+++++.+ +.++|||||+|.+.++|.+|+ .|++..+.|+.|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345568999999999999999999999999 999999999877 899999999999999999999 89999999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .++..+..
T Consensus        89 ~~a~~~~~   96 (104)
T 1wi8_A           89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987654

>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=99.72  E-value=3e-17  Score=118.64  Aligned_cols=78  Identities=21%  Similarity=0.301  Sum_probs=72.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..+.++|||+|||..+++++|+++|+.||.|.+|++..++   .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            4567889999999999999999999999999999999875   3589999999999999999999999999999999987


Q ss_pred             c
Q 019811          130 Y  130 (335)
Q Consensus       130 ~  130 (335)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.72  E-value=1.4e-16  Score=114.31  Aligned_cols=87  Identities=29%  Similarity=0.455  Sum_probs=78.5

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+++++.  .++|||||+|.+.++|.+|+..|++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3445668999999999999999999999999999999998853  38999999999999999999999999999999999


Q ss_pred             EEccCCCCC
Q 019811          216 NWATKGAGN  224 (335)
Q Consensus       216 ~~~~~~~~~  224 (335)
                      .++..+...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999876543

>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=99.72  E-value=5.4e-17  Score=117.33  Aligned_cols=82  Identities=27%  Similarity=0.370  Sum_probs=77.5

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ...+.++|||+|||..+++++|+++|+.||.|..+.+++++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            44567899999999999999999999999999999999997 88999999999999999999999999999999999999


Q ss_pred             Ecc
Q 019811          217 WAT  219 (335)
Q Consensus       217 ~~~  219 (335)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            975

>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=99.72  E-value=3e-17  Score=113.91  Aligned_cols=77  Identities=21%  Similarity=0.361  Sum_probs=69.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++++++|+++|++||.|.++++..++.    +|||||+|.+.++|.+|++ +++..+.|+.|+|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            356678999999999999999999999999999999988753    5899999999999999995 58889999999998


Q ss_pred             ee
Q 019811          128 WA  129 (335)
Q Consensus       128 ~~  129 (335)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=3.4e-17  Score=117.71  Aligned_cols=86  Identities=38%  Similarity=0.771  Sum_probs=79.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhcc-CCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-eCCeeeE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSV-YPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW-LGSRQIR  214 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~-~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~-~~g~~l~  214 (335)
                      .....++|||+|||.++++++|+++|+. ||.|..+.+++++ ++.++|||||+|.+.++|.+|+..|++.. +.|+.|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456689999999999999999999999 9999999999997 88999999999999999999999999999 9999999


Q ss_pred             EEEccCCCC
Q 019811          215 CNWATKGAG  223 (335)
Q Consensus       215 v~~~~~~~~  223 (335)
                      |.++..+..
T Consensus        84 v~~a~~~~~   92 (104)
T 2dhg_A           84 LSVAIPKAS   92 (104)
T ss_dssp             CCBCCCCCS
T ss_pred             EEEccCCCc
Confidence            999976553

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1.6e-17  Score=118.71  Aligned_cols=76  Identities=26%  Similarity=0.493  Sum_probs=71.3

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ++|||+|||.++++++|+++|+.||.|..+.+.++     ++|||||+|.+.++|.+|+..|++..+.|+.|+|.++...
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            47999999999999999999999999999999865     6889999999999999999999999999999999999876


Q ss_pred             C
Q 019811          222 A  222 (335)
Q Consensus       222 ~  222 (335)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.72  E-value=3.3e-17  Score=118.53  Aligned_cols=82  Identities=21%  Similarity=0.391  Sum_probs=70.4

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++++++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|+..+ +..+.|+.|+|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            45567889999999999999999999999999999998864    3689999999999999999876 599999999999


Q ss_pred             eeccCCC
Q 019811          128 WAYASGQ  134 (335)
Q Consensus       128 ~~~~~~~  134 (335)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9976543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=3.5e-17  Score=117.85  Aligned_cols=84  Identities=20%  Similarity=0.394  Sum_probs=75.8

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+.. ++..|.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            456778999999999999999999999999999999998753    48999999999999999988 9999999999999


Q ss_pred             eeccCCCcc
Q 019811          128 WAYASGQRE  136 (335)
Q Consensus       128 ~~~~~~~~~  136 (335)
                      ++.++....
T Consensus        91 ~a~~~~~~~   99 (105)
T 2dh8_A           91 PCTPRGMQP   99 (105)
T ss_dssp             CSCCSSCCT
T ss_pred             EccCCCCCC
Confidence            998765443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-16  Score=116.13  Aligned_cols=86  Identities=26%  Similarity=0.332  Sum_probs=78.8

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|..||.|..+.+++++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34556899999999999999999999999999999999986 58899999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      ++.....
T Consensus        90 ~a~~~~~   96 (114)
T 2do0_A           90 MDERALP   96 (114)
T ss_dssp             ECSCCCC
T ss_pred             EcccCCC
Confidence            9876443

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=3.2e-16  Score=114.70  Aligned_cols=79  Identities=16%  Similarity=0.264  Sum_probs=70.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCe-EEEEEcCHHHHHHHHHHhCCccccC--ceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY-GFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~-afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~  129 (335)
                      ++....|||+|||+.+++++|+++|++||.|.+|++...  .|| |||+|.+.++|..|++.|||..|.|  ++|+|.++
T Consensus        22 ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~--~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES--SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            455566889999999999999999999999999999763  486 9999999999999999999999987  68999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7654

>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=99.71  E-value=4.9e-17  Score=113.36  Aligned_cols=80  Identities=21%  Similarity=0.400  Sum_probs=76.2

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||.++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+ .+++..+.|+.|+|.++..
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            468999999999999999999999999999999999888999999999999999999999 8999999999999999876


Q ss_pred             C
Q 019811          221 G  221 (335)
Q Consensus       221 ~  221 (335)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.4e-16  Score=112.81  Aligned_cols=80  Identities=26%  Similarity=0.324  Sum_probs=71.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      .+.+.++|||+||  ++++++|+++|++||.|.+|++.  +.+|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.+
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~   86 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD--PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   86 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSS
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec--CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCC
Confidence            3456789999996  89999999999999999999884  5668999999999999999999999999999999999977


Q ss_pred             CCCc
Q 019811          132 SGQR  135 (335)
Q Consensus       132 ~~~~  135 (335)
                      +...
T Consensus        87 ~~~~   90 (97)
T 1x5p_A           87 QPML   90 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.71  E-value=5.9e-17  Score=112.42  Aligned_cols=81  Identities=28%  Similarity=0.475  Sum_probs=75.1

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998889999999999999999999996 58889999999998


Q ss_pred             Ec
Q 019811          217 WA  218 (335)
Q Consensus       217 ~~  218 (335)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=7.2e-17  Score=116.02  Aligned_cols=83  Identities=23%  Similarity=0.434  Sum_probs=75.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhc-cCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCcc-ccCceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSS-TGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRH-LFGQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~-~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~-~~g~~l~v~  127 (335)
                      +.+.++|||+|||.++++++|+++|+. ||.|.+|++..++   ++|||||+|.+.++|.+|++.|++.. +.|+.|+|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            456688999999999999999999999 9999999998875   35899999999999999999999999 999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99766543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=9e-17  Score=117.89  Aligned_cols=85  Identities=34%  Similarity=0.517  Sum_probs=79.1

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..+++ .+.|+.|+|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            445668999999999999999999999999999999999988899999999999999999999999998 8999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++....
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            997654

>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=99.71  E-value=1.2e-16  Score=115.91  Aligned_cols=77  Identities=35%  Similarity=0.621  Sum_probs=70.9

Q ss_pred             CCCcceEEEeCCCCC-CCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ....++|||+|||.+ +++++|+++|++||.|.+|++    .+|||||+|.+.++|.+|++.|++..+.|+.|+|.++..
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            345689999999999 999999999999999999998    568999999999999999999999999999999999975


Q ss_pred             CC
Q 019811          132 SG  133 (335)
Q Consensus       132 ~~  133 (335)
                      ..
T Consensus       100 ~~  101 (110)
T 1wf1_A          100 PK  101 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.71  E-value=2.7e-17  Score=110.73  Aligned_cols=69  Identities=17%  Similarity=0.193  Sum_probs=65.7

Q ss_pred             CCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       262 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +.-|+|+||++.+++++|+++|.+||  .|.++++..++|+|||+|.+.++|.+|++.|||.   .++||+|+|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G--~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~---~l~gr~I~V   75 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHG--PLVSFHPYLNQGIALCKYTTREEANKAQMALNNC---VLANTTIFA   75 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHS--CEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTE---EETTEEEEE
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhC--CEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCC---EECCcEEEE
Confidence            46799999999999999999999999  5999999999999999999999999999999999   999999975

>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=99.71  E-value=3.8e-17  Score=118.58  Aligned_cols=78  Identities=17%  Similarity=0.224  Sum_probs=71.2

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ...++|||+|||.++++++|+++|++||.|.+|.+..  .+|||||+|.+.++|.+|+..|||..+.|+.|+|.|+....
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE--GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS--SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC--CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            3467899999999999999999999999999998864  55799999999999999999999999999999999997543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.6e-17  Score=117.42  Aligned_cols=81  Identities=9%  Similarity=0.113  Sum_probs=75.3

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++|+++|.++|+.||.|.++.+++++. +.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34557999999999999999999999999999999999976 8999999999999999999998 899999999999998


Q ss_pred             ccC
Q 019811          218 ATK  220 (335)
Q Consensus       218 ~~~  220 (335)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            754

>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=99.71  E-value=5.7e-17  Score=120.82  Aligned_cols=82  Identities=27%  Similarity=0.533  Sum_probs=74.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|++.|||..|.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4557889999999999999999999999999999998764    368999999999999999999999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.+...
T Consensus        99 a~~~~~  104 (126)
T 3ex7_B           99 CFVRGP  104 (126)
T ss_dssp             SEESSS
T ss_pred             ecCCCC
Confidence            976654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.71  E-value=4.5e-17  Score=125.37  Aligned_cols=81  Identities=20%  Similarity=0.302  Sum_probs=76.6

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCC--CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYP--SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..++|||+|||.++++++|+++|+.||  .|..+.+++|+.+|.++|||||+|.+.++|.+|+..|++..++|+.|.|.+
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            347999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 019811          218 ATK  220 (335)
Q Consensus       218 ~~~  220 (335)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            865

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=8.3e-18  Score=116.22  Aligned_cols=78  Identities=19%  Similarity=0.271  Sum_probs=71.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +.+.++|||+|||.++++++|+++|+.||.|.++++..++    ++|||||+|.+.++|.+|++.|||..+.|+.+++.+
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            3457889999999999999999999999999999998764    368999999999999999999999999999999887


Q ss_pred             ec
Q 019811          129 AY  130 (335)
Q Consensus       129 ~~  130 (335)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.71  E-value=3.2e-17  Score=115.84  Aligned_cols=82  Identities=21%  Similarity=0.318  Sum_probs=75.7

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.++
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            34579999999999999999999999999999999998888999999999999999999999999999999999999987


Q ss_pred             cC
Q 019811          219 TK  220 (335)
Q Consensus       219 ~~  220 (335)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            54

>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=99.71  E-value=1.2e-16  Score=114.66  Aligned_cols=85  Identities=25%  Similarity=0.548  Sum_probs=77.4

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|+++|+.||.|..+.+++++.  .++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            345668999999999999999999999999999999998853  368999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |+..+..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqi_A           89 WATTPSS   95 (103)
T ss_dssp             ECCCTTC
T ss_pred             ECCCCcc
Confidence            9987654

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.5e-16  Score=114.11  Aligned_cols=82  Identities=16%  Similarity=0.212  Sum_probs=72.8

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+.  ++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            345668899999999999999999999999999999988753    5899999999999999997  4789999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99876543

>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=99.71  E-value=3.8e-17  Score=117.52  Aligned_cols=83  Identities=29%  Similarity=0.553  Sum_probs=78.5

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|++..+.|+.|+|.++.
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            34789999999999999999999999999999999998889999999999999999999999999999999999999997


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      ...
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            654

>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=99.71  E-value=3.8e-17  Score=119.34  Aligned_cols=80  Identities=10%  Similarity=0.056  Sum_probs=72.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCc-eeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPV-EGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v-~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++|+++|+++|+.||.| .+|+++.++   .+|||||+|.+.++|.+|+.. |+..|.|+.|.|.
T Consensus        11 ~~~~~~~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           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            45667899999999999999999999999999 889998765   468999999999999999976 9999999999999


Q ss_pred             eeccC
Q 019811          128 WAYAS  132 (335)
Q Consensus       128 ~~~~~  132 (335)
                      ++...
T Consensus        90 ~a~~~   94 (114)
T 2cpy_A           90 VVTLE   94 (114)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98653

>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=99.71  E-value=4.8e-17  Score=116.00  Aligned_cols=75  Identities=20%  Similarity=0.217  Sum_probs=66.6

Q ss_pred             CCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          258 NNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       258 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..+++++|||+|||+++++++|+++|++||  .|..+.+.+++|+|||+|.+.++|.+|+..|++... .++|++|+|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG--~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~-~i~Gr~l~V   85 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFG--TICYVMMMPFKRQALVEFENIDSAKECVTFAADVPV-YIAGQQAFF   85 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTS--CEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCC-BSSSSBCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCC--CEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCc-eECCEEEEE
Confidence            345668999999999999999999999999  589999999999999999999999999999876511 599999875

>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=99.71  E-value=4.6e-17  Score=113.51  Aligned_cols=77  Identities=25%  Similarity=0.436  Sum_probs=71.2

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++++++|+++|+.||.|.++++..++    ++|||||+|.+.++|.+|+ .+||..+.|+.|+|.++.
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            35789999999999999999999999999999998764    3689999999999999999 999999999999999986


Q ss_pred             cC
Q 019811          131 AS  132 (335)
Q Consensus       131 ~~  132 (335)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
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=99.71  E-value=1.6e-16  Score=111.12  Aligned_cols=82  Identities=17%  Similarity=0.345  Sum_probs=76.6

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.| .|..+.++++ .+|.++|+|||+|.+.++|.+|+. +++..++|+.|.|.+
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            4456799999999999999999999999 9999999999 788999999999999999999999 999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +..+.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            97754

>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=99.71  E-value=2.1e-17  Score=116.74  Aligned_cols=77  Identities=16%  Similarity=0.222  Sum_probs=69.2

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||.++++++|+++|++||.|.+++++.++    .+|||||+|.+.++|.+|++.||+..+.|+.|+|.++
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            345889999999999999999999999999888887754    3589999999999999999999999999999999987


Q ss_pred             c
Q 019811          130 Y  130 (335)
Q Consensus       130 ~  130 (335)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.71  E-value=3e-17  Score=116.47  Aligned_cols=81  Identities=19%  Similarity=0.421  Sum_probs=72.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHH----HHHhccCCceeEEEeec-CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQ----EVFSSTGPVEGCKLIRK-DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~----~~f~~~G~v~~v~~~~~-~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ..++++|||+|||.++++++|+    ++|++||.|.+|++... +++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456889999999999999999    99999999999988743 346899999999999999999999999999999999


Q ss_pred             eeccCC
Q 019811          128 WAYASG  133 (335)
Q Consensus       128 ~~~~~~  133 (335)
                      ++.+..
T Consensus        85 ~a~~~~   90 (97)
T 1nu4_A           85 YAKTDS   90 (97)
T ss_dssp             ECSSCC
T ss_pred             EccCCC
Confidence            997654

>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=99.71  E-value=8e-18  Score=150.88  Aligned_cols=85  Identities=20%  Similarity=0.456  Sum_probs=79.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+.++|||+|||..+|+++|.++|..||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|++..|.|+.|.|.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34557999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +....
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            97654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.71  E-value=4.5e-17  Score=117.11  Aligned_cols=80  Identities=19%  Similarity=0.221  Sum_probs=71.7

Q ss_pred             CCCcceEEEeCCCCCC------CHHHHHHHHhccCCceeEEEeec--CCCCeEEEEEcCHHHHHHHHHHhCCccccCc-e
Q 019811           53 PSTCRSVYVGNIHTQV------TEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQ-P  123 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~------t~~~l~~~f~~~G~v~~v~~~~~--~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~-~  123 (335)
                      ...+++|||+|||..+      ++++|+++|++||.|.+|++.+.  +++|||||+|.+.++|.+|+..|||..+.|+ +
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            4456889999999999      78999999999999999998743  3479999999999999999999999999998 9


Q ss_pred             eEEeeeccC
Q 019811          124 IKVNWAYAS  132 (335)
Q Consensus       124 l~v~~~~~~  132 (335)
                      |+|.++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999998644

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.70  E-value=7e-17  Score=116.83  Aligned_cols=85  Identities=31%  Similarity=0.393  Sum_probs=75.6

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+++++.+|.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3455689999999999999999999999999999999999888999999999999999999999976 589999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++..+.
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            997654

>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=3.4e-17  Score=123.15  Aligned_cols=84  Identities=24%  Similarity=0.375  Sum_probs=75.8

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .+.+.++|||+|||.++|+++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+..|+|..+.|+.|+|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            35567889999999999999999999999999999998764    46899999999999999999999999999999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      ++.+...+
T Consensus       123 ~a~~~~~~  130 (135)
T 2lea_A          123 MARYGRPP  130 (135)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99766543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.3e-18  Score=115.96  Aligned_cols=81  Identities=23%  Similarity=0.443  Sum_probs=75.8

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .++++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.+++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45679999999999999999999999999999999999888999999999999999999999999999999999987765


Q ss_pred             c
Q 019811          219 T  219 (335)
Q Consensus       219 ~  219 (335)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=8.7e-17  Score=113.63  Aligned_cols=81  Identities=20%  Similarity=0.205  Sum_probs=74.6

Q ss_pred             CCcceEEECCCCccccHHHHH----HHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          139 SGHFNIFVGDLSPEVTDATLF----ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      ...++|||+|||.++++++|+    ++|+.||.|.++.+++++.+   +|||||+|.+.++|.+|+..|++..+.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            455799999999999999999    99999999999999988654   88999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 019811          215 CNWATKGA  222 (335)
Q Consensus       215 v~~~~~~~  222 (335)
                      |.++....
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.5e-16  Score=108.07  Aligned_cols=74  Identities=19%  Similarity=0.346  Sum_probs=65.7

Q ss_pred             cce-EEEeCCCCCCCHHH----HHHHHhccC-CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           56 CRS-VYVGNIHTQVTEPL----LQEVFSSTG-PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        56 ~~~-v~v~nlp~~~t~~~----l~~~f~~~G-~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +.| |||+|||..+++++    |+++|++|| .|.+|      ..|+|||.|.+.++|.+|++.|+|..+.|++|+|.++
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tgG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A   81 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFT   81 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CTTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESS
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ecCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEec
Confidence            445 99999999999988    558999995 99888      2389999999999999999999999999999999999


Q ss_pred             ccCCCc
Q 019811          130 YASGQR  135 (335)
Q Consensus       130 ~~~~~~  135 (335)
                      ..++..
T Consensus        82 ~~~sd~   87 (96)
T 2diu_A           82 PKNREL   87 (96)
T ss_dssp             CCSCCC
T ss_pred             CCCcce
Confidence            876643

>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=99.70  E-value=6.7e-17  Score=120.46  Aligned_cols=88  Identities=22%  Similarity=0.418  Sum_probs=81.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|.++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             EccCCCCC
Q 019811          217 WATKGAGN  224 (335)
Q Consensus       217 ~~~~~~~~  224 (335)
                      |+......
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99776543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.70  E-value=1.1e-16  Score=112.37  Aligned_cols=83  Identities=27%  Similarity=0.351  Sum_probs=76.8

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+.++  ++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
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            345679999999999999999999999999999999874  678999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +....
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            97754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.3e-16  Score=111.68  Aligned_cols=79  Identities=19%  Similarity=0.272  Sum_probs=72.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +...++|||+|||.++++++|+++|+.| .|.+|++..+..   +|||||+|.+.++|.+|+. +||..+.|+.|+|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            4567889999999999999999999999 899999988732   5899999999999999999 9999999999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.70  E-value=1.2e-16  Score=117.42  Aligned_cols=80  Identities=25%  Similarity=0.432  Sum_probs=72.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCe-EEEEEcCHHHHHHHHHHhCCccccC--ceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY-GFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~-afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~  129 (335)
                      ++....|||+||++.+|+++|+++|++||.|.+|++..+. +|+ |||+|.+.++|.+|++.|||..|.|  ++|+|.|+
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            4566778999999999999999999999999999887754 566 9999999999999999999999998  89999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      +...
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            7654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=5.7e-17  Score=116.74  Aligned_cols=86  Identities=30%  Similarity=0.397  Sum_probs=80.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            345668999999999999999999999999999999999988899999999999999999999998 9999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      ++..+..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            9877653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.70  E-value=2.6e-17  Score=110.83  Aligned_cols=75  Identities=31%  Similarity=0.545  Sum_probs=71.6

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      +|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++ +++..++|+.|.|.++
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            48999999999999999999999999999999998889999999999999999999998 9999999999999875

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.3e-17  Score=117.82  Aligned_cols=83  Identities=17%  Similarity=0.383  Sum_probs=74.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +...++|||+|||.++++++|+++|+.||.|.+|++..++    .+|||||+|.+.++|.+|+.. ++..|.|+.|+|.+
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            4456899999999999999999999999999999998864    368999999999999999987 99999999999999


Q ss_pred             eccCCCcc
Q 019811          129 AYASGQRE  136 (335)
Q Consensus       129 ~~~~~~~~  136 (335)
                      +.++....
T Consensus       103 a~~~~~~~  110 (116)
T 1x4b_A          103 AVAREESG  110 (116)
T ss_dssp             CSSCCCCC
T ss_pred             CCCCccCC
Confidence            98766543

>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=99.70  E-value=6.7e-17  Score=114.36  Aligned_cols=80  Identities=14%  Similarity=0.161  Sum_probs=71.5

Q ss_pred             CCCCcceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeee
Q 019811          137 DTSGHFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG--KWLGSRQI  213 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~g~~l  213 (335)
                      ...++++|||+|||. ++++++|+++|++||.|.++.++++      +|+|||+|.+.++|..|++.|++  ..+.|+.|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            445678999999999 9999999999999999999999854      47999999999999999998885  45999999


Q ss_pred             EEEEccCCC
Q 019811          214 RCNWATKGA  222 (335)
Q Consensus       214 ~v~~~~~~~  222 (335)
                      +|.|+....
T Consensus        85 ~V~~a~~~~   93 (102)
T 1x4d_A           85 RVHLSQKYK   93 (102)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCCC
Confidence            999998654

>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=99.70  E-value=2.9e-16  Score=112.59  Aligned_cols=86  Identities=23%  Similarity=0.350  Sum_probs=78.6

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+.  ++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            344566899999999999999999999999999999999998889999999999999999999998  577999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .++..+..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqg_A           88 KLPNSKQS   95 (103)
T ss_dssp             ECCCTTCC
T ss_pred             EecCCCCc
Confidence            99987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.70  E-value=3e-17  Score=123.08  Aligned_cols=85  Identities=21%  Similarity=0.387  Sum_probs=78.9

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCcee--eEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCC
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD--ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK----WLGS  210 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~--~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~----~~~g  210 (335)
                      ....+++|||+|||+++++++|+++|+.||.|..  +++++|+.+|.++|||||+|.+. +|.+|+..|++.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456689999999999999999999999999977  99999988999999999999999 999999999999    9999


Q ss_pred             eeeEEEEccCCC
Q 019811          211 RQIRCNWATKGA  222 (335)
Q Consensus       211 ~~l~v~~~~~~~  222 (335)
                      +.|.|.++....
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999999997754

>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=99.70  E-value=2.5e-17  Score=117.40  Aligned_cols=83  Identities=28%  Similarity=0.483  Sum_probs=74.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ-KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      .....++|||+|||.++++++|+++|+.|| |.++.+++++ .+|.++|||||+|.+.++|.+|+ .|++..++|+.|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345568999999999999999999999999 9999999987 58899999999999999999999 89999999999999


Q ss_pred             EEccCC
Q 019811          216 NWATKG  221 (335)
Q Consensus       216 ~~~~~~  221 (335)
                      .++..+
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            998764

>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=99.70  E-value=4.8e-17  Score=116.94  Aligned_cols=80  Identities=38%  Similarity=0.642  Sum_probs=73.5

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||.++++++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            3467899999999999999999999999999999988753    589999999999999999999999999999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .+..
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            7654

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.5e-17  Score=115.74  Aligned_cols=78  Identities=21%  Similarity=0.319  Sum_probs=68.9

Q ss_pred             CCcceEEE--eCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccc-----cCceeEE
Q 019811           54 STCRSVYV--GNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHL-----FGQPIKV  126 (335)
Q Consensus        54 ~~~~~v~v--~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~-----~g~~l~v  126 (335)
                      .++++|||  +||+.++++++|+++|++||.|.+|.+..  .+|||||+|.+.++|.+|++.|||..+     .|++|.|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~--~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v  100 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL  100 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT--TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEE
Confidence            34678999  77999999999999999999999998865  368999999999999999999999988     6889999


Q ss_pred             eeeccCC
Q 019811          127 NWAYASG  133 (335)
Q Consensus       127 ~~~~~~~  133 (335)
                      .++...+
T Consensus       101 ~~a~~~p  107 (114)
T 2cq2_A          101 NFVEKVQ  107 (114)
T ss_dssp             EEESCCC
T ss_pred             EecccCc
Confidence            9886443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.70  E-value=1.8e-16  Score=117.72  Aligned_cols=85  Identities=25%  Similarity=0.343  Sum_probs=79.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ....+++|||+|||..+++++|+++|+.||.|..+.+.+++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34556899999999999999999999999999999999997 88999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++....
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            997754

>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=1.7e-16  Score=113.83  Aligned_cols=81  Identities=12%  Similarity=0.106  Sum_probs=71.4

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCcee-EEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG-CKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~-v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .....++|||+|||+++|+++|+++|+.||.|.+ |.+..+   +.+|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            3456788999999999999999999999999987 877765   3469999999999999999987 9999999999999


Q ss_pred             eeccCC
Q 019811          128 WAYASG  133 (335)
Q Consensus       128 ~~~~~~  133 (335)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            886543

>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=2.7e-16  Score=114.99  Aligned_cols=81  Identities=17%  Similarity=0.343  Sum_probs=72.2

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccc--------c
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHL--------F  120 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~--------~  120 (335)
                      ...+.++|||+|||.++++++|+++|+.||.|.++++..++.   +|||||+|.+.++|.+|++.|||..+        .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            345668899999999999999999999999999999988753   58999999999999999999999999        5


Q ss_pred             CceeEEeeeccC
Q 019811          121 GQPIKVNWAYAS  132 (335)
Q Consensus       121 g~~l~v~~~~~~  132 (335)
                      +++|.|.|+.+.
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            778899888643

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.4e-17  Score=114.50  Aligned_cols=81  Identities=14%  Similarity=0.199  Sum_probs=71.4

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ..+...++|||+|||+++|+++|+++|+.||.+ +|+++.++.   +|||||+|.+.++|.+|+ .+|+..+.|+.|+|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~   87 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEE
Confidence            345667899999999999999999999999965 999988753   589999999999999999 579999999999999


Q ss_pred             eeccCC
Q 019811          128 WAYASG  133 (335)
Q Consensus       128 ~~~~~~  133 (335)
                      ++....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            886544

>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=3.1e-16  Score=111.07  Aligned_cols=82  Identities=13%  Similarity=0.172  Sum_probs=72.5

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeee
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL--TGKWLGSRQI  213 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~g~~l  213 (335)
                      ....++++|||+|||..+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|++.+  ++..+.|+.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            34456689999999999999999999999999999988743      789999999999999999976  5678999999


Q ss_pred             EEEEccCCCC
Q 019811          214 RCNWATKGAG  223 (335)
Q Consensus       214 ~v~~~~~~~~  223 (335)
                      .|.|+..+..
T Consensus        84 ~V~~a~~~~~   93 (101)
T 2cq1_A           84 YIQYSNHKEL   93 (101)
T ss_dssp             EEEECSCSSC
T ss_pred             EEEEcCcccC
Confidence            9999987554

>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=99.69  E-value=2e-16  Score=122.42  Aligned_cols=86  Identities=24%  Similarity=0.398  Sum_probs=80.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||..+++++|.++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+..|++..|.|+.|+|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +.....
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            987554

>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=99.69  E-value=1.2e-16  Score=115.89  Aligned_cols=81  Identities=23%  Similarity=0.348  Sum_probs=72.6

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCC-ceeEEEe-ec----CCCCeEEEEEcCHHHHHHHHHHhC--CccccCceeE
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLI-RK----DKSSYGFIHYFDRRSAAMAILSLN--GRHLFGQPIK  125 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~-v~~v~~~-~~----~~~g~afv~f~~~~~A~~a~~~l~--~~~~~g~~l~  125 (335)
                      .+.++|||+|||.++++++|+++|+.||. |.++.+. .+    +++|||||+|.+.++|.+|++.|+  +..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45688999999999999999999999998 9999987 44    356899999999999999999996  5899999999


Q ss_pred             EeeeccCCC
Q 019811          126 VNWAYASGQ  134 (335)
Q Consensus       126 v~~~~~~~~  134 (335)
                      |.|+.++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=3.1e-17  Score=112.10  Aligned_cols=72  Identities=21%  Similarity=0.286  Sum_probs=65.0

Q ss_pred             cceEEEeCCCCCC------CHHHHHHHHhccCCceeEEEeec--CCCCeEEEEEcCHHHHHHHHHHhCCccccCc-eeEE
Q 019811           56 CRSVYVGNIHTQV------TEPLLQEVFSSTGPVEGCKLIRK--DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQ-PIKV  126 (335)
Q Consensus        56 ~~~v~v~nlp~~~------t~~~l~~~f~~~G~v~~v~~~~~--~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~-~l~v  126 (335)
                      +++|||+|||..+      ++++|+++|++||.|.++++.+.  +++|||||+|.+.++|.+|++.|||..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3689999999999      78999999999999999998743  3479999999999999999999999999999 8876


Q ss_pred             e
Q 019811          127 N  127 (335)
Q Consensus       127 ~  127 (335)
                      .
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.69  E-value=1.4e-16  Score=115.58  Aligned_cols=96  Identities=22%  Similarity=0.408  Sum_probs=83.4

Q ss_pred             cCceeEEeeeccCCCccCCCCcceEEECCCCcc-ccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHH
Q 019811          120 FGQPIKVNWAYASGQREDTSGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS  198 (335)
Q Consensus       120 ~g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~  198 (335)
                      .|..+.+..+............++|||+|||.. +++++|+++|+.||.|..+.+        ++|||||+|.+.++|.+
T Consensus         6 ~g~~~~~~~s~~~~~~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~   77 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARA   77 (110)
T ss_dssp             CSCCCCCCCCCSCCSCCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHH
T ss_pred             CCcccccccCCCCCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHH
Confidence            466777777766555555566689999999999 999999999999999999988        46899999999999999


Q ss_pred             HHHHhCCceeCCeeeEEEEccCCCC
Q 019811          199 AINDLTGKWLGSRQIRCNWATKGAG  223 (335)
Q Consensus       199 a~~~l~~~~~~g~~l~v~~~~~~~~  223 (335)
                      |+..|++..+.|+.|+|.++.....
T Consensus        78 A~~~l~g~~~~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           78 AVLGENGRVLAGQTLDINMAGEPKP  102 (110)
T ss_dssp             HHHHHTTCEETTEECCEEESCCCCS
T ss_pred             HHHHcCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999999976443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.69  E-value=4.5e-17  Score=109.63  Aligned_cols=71  Identities=14%  Similarity=0.291  Sum_probs=65.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +|||+|||.++++++|+++|++||.|.++++..++    ++|||||+|.+.++|.+|++ +++..+.|+.|+|.++
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            49999999999999999999999999999998765    36899999999999999997 9999999999999875

>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=8.8e-17  Score=118.01  Aligned_cols=78  Identities=14%  Similarity=0.083  Sum_probs=71.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCC---ceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGP---VEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~---v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      +...++|||+|||+++|+++|+++|+.||.   |.+|++..++.   +|||||+|.+.++|.+|++ +|+..+.|+.|+|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            456788999999999999999999999998   89999987653   5899999999999999998 9999999999999


Q ss_pred             eeecc
Q 019811          127 NWAYA  131 (335)
Q Consensus       127 ~~~~~  131 (335)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98743

>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=1.4e-16  Score=115.27  Aligned_cols=84  Identities=30%  Similarity=0.476  Sum_probs=76.7

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.||.|..+.+.+++  +.++|||||+|.+.++|.+|+..|++..++|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344566899999999999999999999999999999999884  348999999999999999999999999999999999


Q ss_pred             EEccCC
Q 019811          216 NWATKG  221 (335)
Q Consensus       216 ~~~~~~  221 (335)
                      .++..+
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            998764

>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=99.69  E-value=7.9e-17  Score=111.91  Aligned_cols=77  Identities=13%  Similarity=0.198  Sum_probs=70.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ...++|||+|||.++++++|+++|++| .|.++++.  +++|||||+|.+.++|.+|++.|||..+.|++|+|.++....
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD--RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE--GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe--CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            356789999999999999999999999 99999884  667899999999999999999999999999999999986543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=3.7e-17  Score=110.67  Aligned_cols=76  Identities=33%  Similarity=0.475  Sum_probs=72.6

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|+|||+|.+.++|.+|+..++ ..+.|+.|.|+++
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            379999999999999999999999999999999998889999999999999999999999988 9999999999986

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=6.6e-17  Score=114.41  Aligned_cols=81  Identities=16%  Similarity=0.257  Sum_probs=71.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|..+ .....++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            4567899999999999999999999999998777 233345789999999999999999999999999999999999765


Q ss_pred             CC
Q 019811          133 GQ  134 (335)
Q Consensus       133 ~~  134 (335)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=114.51  Aligned_cols=82  Identities=17%  Similarity=0.432  Sum_probs=70.9

Q ss_pred             CCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           51 FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        51 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ..+.+.++|||+|||.++++++|+++|+.|+   .++++.++    .+|||||+|.+.++|.+|++.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3456678899999999999999999999874   55666654    3589999999999999999999999999999999


Q ss_pred             eeeccCCCc
Q 019811          127 NWAYASGQR  135 (335)
Q Consensus       127 ~~~~~~~~~  135 (335)
                      .++.++...
T Consensus        87 ~~a~~~~~~   95 (102)
T 2fc8_A           87 DWAKPKGEG   95 (102)
T ss_dssp             EECCCCCSS
T ss_pred             EEecCCCCC
Confidence            999876654

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.4e-16  Score=113.43  Aligned_cols=84  Identities=23%  Similarity=0.425  Sum_probs=75.7

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|.+|++.|++..+.|+.|+|.
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            3455689999999999999999999999999999998644   4678999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |+.....
T Consensus        95 ~a~~~~~  101 (109)
T 1x4a_A           95 FPRSGRG  101 (109)
T ss_dssp             CCCCCCC
T ss_pred             EcccCCC
Confidence            9977543

>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=99.69  E-value=2e-16  Score=114.79  Aligned_cols=81  Identities=12%  Similarity=0.171  Sum_probs=72.4

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeeeEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG--KWLGSRQIRC  215 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~g~~l~v  215 (335)
                      ..++++|||+|||+++++++|+++|++||.|.++.++++      +|||||+|++.++|.+|++.+++  ..+.|+.|+|
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            445689999999999999999999999999999999854      68999999999999999998874  6899999999


Q ss_pred             EEccCCCCC
Q 019811          216 NWATKGAGN  224 (335)
Q Consensus       216 ~~~~~~~~~  224 (335)
                      .|+..+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999775543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=4.9e-17  Score=110.08  Aligned_cols=72  Identities=22%  Similarity=0.446  Sum_probs=67.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ++|||+|||.++++++|+++|++||.|.++.+..++    ++|||||+|.+.++|.+|++.++ ..+.|+.|+|.++
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            479999999999999999999999999999998765    36899999999999999999998 9999999999886

>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=99.68  E-value=1.7e-16  Score=109.57  Aligned_cols=72  Identities=29%  Similarity=0.552  Sum_probs=67.0

Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhh-cCCCcccccCccccC
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG-NTTQSSYLFGKQMKV  335 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l-~g~~~~~~~g~~l~v  335 (335)
                      ....++|||+|||.++++++|+++|+.||  .+..+.+.+++|+|||+|.+.++|.+|+..| +|.   .++|++|+|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G--~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~---~~~g~~l~v   81 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFG--EIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKL---IVNGRRLNV   81 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTS--CEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTC---EETTEECCE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCC--CEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCe---eECCCEEEE
Confidence            34558999999999999999999999999  5999999999999999999999999999998 999   999999975

>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=99.68  E-value=1.4e-16  Score=115.68  Aligned_cols=85  Identities=15%  Similarity=0.221  Sum_probs=77.0

Q ss_pred             CCCcceEEECCCCccccHHHHH---HHhccCCCceeeEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 019811          138 TSGHFNIFVGDLSPEVTDATLF---ACFSVYPSCSDARVMWDQKTG---RSRGFGFVSFRNQQDAQSAINDLTGKWLGSR  211 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~---~~f~~~g~v~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~  211 (335)
                      ....++|||+|||.++++++|+   ++|+.||.|..+.+.++..++   .++|||||+|.+.++|.+|+..|++..++|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3455799999999999999999   999999999999999886643   5669999999999999999999999999999


Q ss_pred             eeEEEEccCCC
Q 019811          212 QIRCNWATKGA  222 (335)
Q Consensus       212 ~l~v~~~~~~~  222 (335)
                      .|+|.|+..+.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998765

>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=99.68  E-value=2e-17  Score=115.56  Aligned_cols=77  Identities=30%  Similarity=0.493  Sum_probs=68.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ++|||+|||.++++++|+++|+.||.|.++++..++    ++|||||+|.+.+ |.+|+..|||..+.|+.|+|.++.+.
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            579999999999999999999999999999998764    3689999999999 99999999999999999999998765


Q ss_pred             CC
Q 019811          133 GQ  134 (335)
Q Consensus       133 ~~  134 (335)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.7e-16  Score=115.03  Aligned_cols=85  Identities=22%  Similarity=0.357  Sum_probs=77.8

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCC-ceeeEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeeeE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPS-CSDARVM-WDQKTGRSRGFGFVSFRNQQDAQSAINDLT--GKWLGSRQIR  214 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~-v~~~~~~-~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~g~~l~  214 (335)
                      .+.++|||+|||.++++++|+++|..||. |..+.++ .++.++.++|||||+|.+.++|.+|+..|+  +..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45679999999999999999999999998 9999998 787788999999999999999999999996  5899999999


Q ss_pred             EEEccCCCC
Q 019811          215 CNWATKGAG  223 (335)
Q Consensus       215 v~~~~~~~~  223 (335)
                      |.|+.....
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987553

>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=99.68  E-value=8.4e-17  Score=115.45  Aligned_cols=74  Identities=16%  Similarity=0.203  Sum_probs=65.6

Q ss_pred             CCCCCeEEEcCCCcc-cCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          259 NPQYTTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..++++|||+|||++ +++++|+++|+.||  .|.++.+.+++|+|||+|.+.++|.+|+..|++... .|+||+|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG--~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~-~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYG--KIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL-WFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTS--CCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCC-CSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcC--CEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCc-eECCEEEEE
Confidence            345689999999998 99999999999999  588999999999999999999999999998865411 699999975

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.6e-16  Score=115.40  Aligned_cols=83  Identities=28%  Similarity=0.443  Sum_probs=78.0

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||.++++++|+++|..||.|..+.+++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            347999999999999999999999999999999999988899999999999999999999987 9999999999999998


Q ss_pred             CCCC
Q 019811          220 KGAG  223 (335)
Q Consensus       220 ~~~~  223 (335)
                      .+..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=3.5e-16  Score=110.11  Aligned_cols=79  Identities=20%  Similarity=0.254  Sum_probs=68.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCC-CeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~-g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ....++|||+|||.++++++|+++|+.||.|.+|  +.++.+ .||||+|.+.++|.+|+. |+|..+.|+.|+|.++.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            3456789999999999999999999999999987  333322 299999999999999999 999999999999998865


Q ss_pred             CCC
Q 019811          132 SGQ  134 (335)
Q Consensus       132 ~~~  134 (335)
                      +..
T Consensus        82 ~~~   84 (94)
T 2e5g_A           82 KEF   84 (94)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            543

>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=99.68  E-value=1.2e-16  Score=118.57  Aligned_cols=79  Identities=14%  Similarity=0.145  Sum_probs=68.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      .....++|||+|||+++|+++|+++|+.||.|.++.++.+.    .+|||||+|.+.++|.+|+. +|+..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34566899999999999999999999999999874444432    35899999999999999998 99999999999999


Q ss_pred             eecc
Q 019811          128 WAYA  131 (335)
Q Consensus       128 ~~~~  131 (335)
                      ++..
T Consensus       100 ~a~~  103 (124)
T 1wel_A          100 PITK  103 (124)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8854

>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=99.68  E-value=4.2e-16  Score=120.59  Aligned_cols=82  Identities=24%  Similarity=0.434  Sum_probs=75.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+..||+..|.|+.|+|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999988753    47999999999999999999999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            976543

>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=99.68  E-value=4e-16  Score=114.08  Aligned_cols=83  Identities=18%  Similarity=0.483  Sum_probs=76.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--------C
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL--------G  209 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~--------~  209 (335)
                      ....++|||+|||.++++++|+++|+.||.|..+.+++++ ++.++|||||+|.+.++|.+|+..|++..+        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3456899999999999999999999999999999999997 889999999999999999999999999998        5


Q ss_pred             CeeeEEEEccCC
Q 019811          210 SRQIRCNWATKG  221 (335)
Q Consensus       210 g~~l~v~~~~~~  221 (335)
                      ++.|.|.|+.++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999998754

>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=99.68  E-value=2e-17  Score=115.57  Aligned_cols=80  Identities=28%  Similarity=0.464  Sum_probs=73.7

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ++|||+|||.++++++|+++|+.||.|.++.+.+++.++.++|||||+|.+.+ |.+|+..|++..++|+.|+|.++...
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            47999999999999999999999999999999999888999999999999999 99999999999999999999998775


Q ss_pred             C
Q 019811          222 A  222 (335)
Q Consensus       222 ~  222 (335)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.68  E-value=1e-16  Score=114.58  Aligned_cols=80  Identities=16%  Similarity=0.287  Sum_probs=69.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEee----cCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~----~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +...++|||+|||.++++++|+++|+.||.|.+ .++.    .+++|||||+|.+.++|.+|++ |||..+.|+.|+|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345688999999999999999999999998877 3333    3457999999999999999998 999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.++..
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            976543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.68  E-value=2.1e-16  Score=120.10  Aligned_cols=82  Identities=34%  Similarity=0.527  Sum_probs=76.8

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             Ec
Q 019811          217 WA  218 (335)
Q Consensus       217 ~~  218 (335)
                      |+
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2e-16  Score=113.75  Aligned_cols=77  Identities=14%  Similarity=0.210  Sum_probs=69.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ....++|||+|||+++|+++|+++|+.| .|.+|+|..++   ++|||||+|.+.++|.+|+ .+|+..+.|+.|.|..+
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            3456789999999999999999999999 88899998764   4799999999999999999 69999999999999877


Q ss_pred             cc
Q 019811          130 YA  131 (335)
Q Consensus       130 ~~  131 (335)
                      ..
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            43

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.9e-16  Score=115.61  Aligned_cols=83  Identities=19%  Similarity=0.253  Sum_probs=76.6

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCc-eeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSC-SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v-~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      .....++|||+|||.++++++|+++|+.||.| ..+.+++++ ++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34556899999999999999999999999999 899999997 889999999999999999999986 999999999999


Q ss_pred             EEccCC
Q 019811          216 NWATKG  221 (335)
Q Consensus       216 ~~~~~~  221 (335)
                      .++..+
T Consensus        89 ~~a~~~   94 (114)
T 2cpy_A           89 HVVTLE   94 (114)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998654

>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=99.67  E-value=2.2e-16  Score=123.26  Aligned_cols=83  Identities=27%  Similarity=0.523  Sum_probs=74.1

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||..+++++|+++|+.||.|..|.+..++.    +|||||+|.+.++|.+|+..|||..|.|+.|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567899999999999999999999999999999998753    58999999999999999999999999999999999


Q ss_pred             eccCCCc
Q 019811          129 AYASGQR  135 (335)
Q Consensus       129 ~~~~~~~  135 (335)
                      +......
T Consensus       149 a~~~~~~  155 (165)
T 1rk8_A          149 CFVKGPK  155 (165)
T ss_dssp             SEECC--
T ss_pred             ecCCCCC
Confidence            9776543

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.3e-16  Score=116.60  Aligned_cols=80  Identities=26%  Similarity=0.348  Sum_probs=76.2

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+ .|++..+.|+.|.|.++..
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            478999999999999999999999999999999999888999999999999999999999 8999999999999999865


Q ss_pred             C
Q 019811          221 G  221 (335)
Q Consensus       221 ~  221 (335)
                      +
T Consensus       104 ~  104 (114)
T 2cq4_A          104 E  104 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=6.7e-16  Score=110.23  Aligned_cols=83  Identities=23%  Similarity=0.352  Sum_probs=74.1

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|   .++++ .++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567899999999999999999999999977   45555 578899999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |+..+..
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9987643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=113.27  Aligned_cols=83  Identities=17%  Similarity=0.251  Sum_probs=75.1

Q ss_pred             CCCcceEEECCCCccc------cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 019811          138 TSGHFNIFVGDLSPEV------TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSR  211 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~  211 (335)
                      ...+++|||+|||..+      ++++|+++|+.||.|..+.++  +.+|.++|||||+|.+.++|.+|+..|+|..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3446799999999999      889999999999999999888  35789999999999999999999999999999998


Q ss_pred             -eeEEEEccCCC
Q 019811          212 -QIRCNWATKGA  222 (335)
Q Consensus       212 -~l~v~~~~~~~  222 (335)
                       .|+|.++....
T Consensus        90 ~~l~V~~a~~~~  101 (105)
T 2nlw_A           90 HTFRVNLFTDFD  101 (105)
T ss_dssp             CEEEEECSCCCC
T ss_pred             ceEEEEEcchHh
Confidence             99999987543

>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=1.5e-16  Score=119.05  Aligned_cols=78  Identities=14%  Similarity=0.082  Sum_probs=71.2

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCC---ceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGP---VEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~---v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      .+...++|||+|||+++|+++|+++|+.||.   |.+|++..++   ++|||||+|.+.++|.+|++ +|+..+.|+.|+
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            3556788999999999999999999999999   8899998865   35899999999999999998 999999999999


Q ss_pred             Eeeec
Q 019811          126 VNWAY  130 (335)
Q Consensus       126 v~~~~  130 (335)
                      |.++.
T Consensus       119 V~~a~  123 (136)
T 2hgl_A          119 VFKSH  123 (136)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            98874

>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=99.67  E-value=3.9e-16  Score=111.27  Aligned_cols=82  Identities=16%  Similarity=0.214  Sum_probs=74.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||+++++++|+++|+.||. ..+.+++++ ++.++|||||+|.+.++|.+|+. +++..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            445679999999999999999999999995 499999997 89999999999999999999995 799999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87654

>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=2.3e-16  Score=118.04  Aligned_cols=81  Identities=16%  Similarity=0.243  Sum_probs=75.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCC---ceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPS---CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      ....++|||+|||+++|+++|+++|+.||.   |..+.+++++. |.++|||||+|.+.++|.+|+. +++..++|+.|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            445679999999999999999999999999   89999999976 8999999999999999999999 999999999999


Q ss_pred             EEEccC
Q 019811          215 CNWATK  220 (335)
Q Consensus       215 v~~~~~  220 (335)
                      |.++..
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            999754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1e-15  Score=109.53  Aligned_cols=85  Identities=29%  Similarity=0.513  Sum_probs=76.3

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ......++|||+|||.++++++|+++|+.|   ..+.+++++.++.++|||||+|.+.++|.+|+..|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345567899999999999999999999977   36778888788899999999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .|+..+..
T Consensus        87 ~~a~~~~~   94 (102)
T 2fc8_A           87 DWAKPKGE   94 (102)
T ss_dssp             EECCCCCS
T ss_pred             EEecCCCC
Confidence            99987653

>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=99.67  E-value=5.3e-16  Score=111.25  Aligned_cols=83  Identities=22%  Similarity=0.253  Sum_probs=75.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCcee-eEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSD-ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ....++|||+|||.++++++|+++|..||.|.. +.++++ .++.++|||||+|.+.++|.+|+.. ++..++|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            345689999999999999999999999999987 888888 7889999999999999999999997 9999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987643

>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=99.67  E-value=1.1e-16  Score=115.41  Aligned_cols=79  Identities=9%  Similarity=0.010  Sum_probs=71.5

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCC---ceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGP---VEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~---v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|++..++   ++|||||+|.+.++|.+|+. +++..+.|+.|+
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3456788999999999999999999999998   8999998764   46899999999999999998 999999999999


Q ss_pred             Eeeecc
Q 019811          126 VNWAYA  131 (335)
Q Consensus       126 v~~~~~  131 (335)
                      |.++.+
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            998754

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.67  E-value=3.8e-16  Score=114.64  Aligned_cols=81  Identities=15%  Similarity=0.232  Sum_probs=75.2

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCC---ceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPS---CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      ....++|||+|||+++++++|+++|+.||.   |..+.+++++. |.++|||||+|.+.++|.+|+. +++..++|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345678999999999999999999999998   89999999876 8999999999999999999999 999999999999


Q ss_pred             EEEccC
Q 019811          215 CNWATK  220 (335)
Q Consensus       215 v~~~~~  220 (335)
                      |.++..
T Consensus        92 V~~a~~   97 (118)
T 2db1_A           92 VFKSHR   97 (118)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            999854

>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=99.67  E-value=2.2e-16  Score=112.27  Aligned_cols=72  Identities=36%  Similarity=0.604  Sum_probs=67.4

Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..+.++|||+|||.++++++|+++|+.||  .|..+.+.+++|+|||+|.+.++|.+|+..|+|.   .|+|++|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~---~~~g~~l~v   83 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM---PLRGKQLRV   83 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTC--CCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTC---CBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcC--CeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCC---EeCCceEEE
Confidence            34568999999999999999999999999  5889999999999999999999999999999999   999999875

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.66  E-value=2.7e-16  Score=116.21  Aligned_cols=82  Identities=18%  Similarity=0.239  Sum_probs=73.3

Q ss_pred             CCCcceEEECCCCccccHHHHH----HHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          138 TSGHFNIFVGDLSPEVTDATLF----ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      ..++++|||+|||+.+++++|+    ++|+.||.|.++.+.   .++.++|||||+|.+.++|..|+..|+|..+.|+.|
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            3456799999999999999876    699999999998775   357889999999999999999999999999999999


Q ss_pred             EEEEccCCC
Q 019811          214 RCNWATKGA  222 (335)
Q Consensus       214 ~v~~~~~~~  222 (335)
                      +|.|+..+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999997654

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.66  E-value=2.9e-16  Score=114.71  Aligned_cols=76  Identities=14%  Similarity=0.203  Sum_probs=66.3

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCce-----eEEee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQP-----IKVNW  128 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~-----l~v~~  128 (335)
                      ...++|||+|||.++++++|+++|+.||.|.+|.+..+   |||||+|.+.++|.+|++.|||..|.|+.     ++|..
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~   90 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   90 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC---CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEecc
Confidence            34678999999999999999999999999999999877   89999999999999999999999999998     66666


Q ss_pred             eccC
Q 019811          129 AYAS  132 (335)
Q Consensus       129 ~~~~  132 (335)
                      ..+.
T Consensus        91 ~~~~   94 (115)
T 3beg_B           91 DGPR   94 (115)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            5443

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=9.3e-16  Score=106.99  Aligned_cols=78  Identities=23%  Similarity=0.452  Sum_probs=72.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+.        ++||||+|.+.++|.+|+..|++..+.|+.|+|.+
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            4566899999999999999999999999999999887        57999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +..+..
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.66  E-value=7e-16  Score=109.24  Aligned_cols=71  Identities=23%  Similarity=0.400  Sum_probs=66.5

Q ss_pred             CCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCccccc--CccccC
Q 019811          260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLF--GKQMKV  335 (335)
Q Consensus       260 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~--g~~l~v  335 (335)
                      .+.++|||+|||.++++++|+++|+.||  .|..+.+..++|+|||+|.+.++|.+|+..|||.   .++  |++|+|
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G--~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~---~~~~~g~~l~V   87 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFG--SIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF---PLGGPDRRLRV   87 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTS--CEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTC---BCSSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCC---EeCCCCcEEEE
Confidence            4458999999999999999999999999  5999999999999999999999999999999999   899  999875

>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=99.66  E-value=1.9e-16  Score=117.46  Aligned_cols=82  Identities=24%  Similarity=0.398  Sum_probs=75.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +++..++|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3455899999999999999999999999999987677777789999999999999999999999 999999999999999


Q ss_pred             ccC
Q 019811          218 ATK  220 (335)
Q Consensus       218 ~~~  220 (335)
                      +..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            865

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.66  E-value=4.5e-16  Score=115.60  Aligned_cols=79  Identities=28%  Similarity=0.416  Sum_probs=72.1

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++++++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|+ .|+|..|.|+.|+|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            46899999999999999999999999999999998764    3689999999999999999 899999999999999987


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      ....
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            5443

>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=99.66  E-value=3.5e-16  Score=108.51  Aligned_cols=73  Identities=25%  Similarity=0.521  Sum_probs=67.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcc----C-------CceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSST----G-------PVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~----G-------~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      ..+.++|||+|||.++++++|+++|+.|    |       .|.++++.++  +|||||+|.+.++|.+|+ .|||..+.|
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~--kg~afV~f~~~~~a~~A~-~l~g~~~~g   79 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD--KNFAFLEFRSVDETTQAM-AFDGIIFQG   79 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS--SSEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC--CcEEEEEcCCHHHHHHHH-hcCCCEECC
Confidence            3467899999999999999999999999    8       8999988765  689999999999999999 999999999


Q ss_pred             ceeEEee
Q 019811          122 QPIKVNW  128 (335)
Q Consensus       122 ~~l~v~~  128 (335)
                      +.|+|..
T Consensus        80 ~~l~V~r   86 (87)
T 2hzc_A           80 QSLKIRR   86 (87)
T ss_dssp             EECEEEC
T ss_pred             eEEEEeC
Confidence            9999974

>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=99.66  E-value=4.4e-16  Score=108.09  Aligned_cols=76  Identities=22%  Similarity=0.338  Sum_probs=62.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccc--cCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHL--FGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~--~g~~l~v~~~~  130 (335)
                      +.+..+|||+|||.++|+++|+++|++||.|.+|++..+ ++|||||+|.+.++|.+    +++..+  .|+.|.|.++.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            445678999999999999999999999999999999875 67999999999999973    455544  58999999887


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      ++.
T Consensus        83 ~k~   85 (89)
T 3d2w_A           83 PKH   85 (89)
T ss_dssp             ---
T ss_pred             CCC
Confidence            554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.65  E-value=2.9e-16  Score=113.08  Aligned_cols=79  Identities=13%  Similarity=0.068  Sum_probs=71.2

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCC-CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYP-SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ...++|||+|||+++++++|+++|+.|| .|..+.+..+    .++|||||+|.+.++|.+|++.|++..+.|+.|+|.+
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 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3457999999999999999999999999 8999887532    5789999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8653

>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=99.65  E-value=7.4e-17  Score=121.03  Aligned_cols=123  Identities=14%  Similarity=0.095  Sum_probs=73.9

Q ss_pred             CeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCCCccCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEe
Q 019811           95 SYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVM  174 (335)
Q Consensus        95 g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~  174 (335)
                      ++||.+|..++.+..++..+... +.|...--.... ..........++|||+|||+++|+++|+++|+.|| +..+.++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~-~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~   78 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGD-SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIE   78 (139)
T ss_dssp             ---------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCC-cccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEE
Confidence            46788888888777666554332 233222111111 11122334557999999999999999999999999 7799999


Q ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          175 WDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       175 ~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      +++. +.++|||||+|.+.++|.+|+ .+++..++|+.|.|.++....
T Consensus        79 ~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           79 IGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             CSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             ECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            9965 899999999999999999999 789999999999999987654

>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=99.65  E-value=2e-16  Score=115.91  Aligned_cols=87  Identities=22%  Similarity=0.360  Sum_probs=75.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..++++|||+|||.++++++|+++|..||.|..+.+..+..++.++|||||+|.+.++|.+|+..|++..+.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34568999999999999999999999999986554443334788999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 019811          218 ATKGAGN  224 (335)
Q Consensus       218 ~~~~~~~  224 (335)
                      +..+...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876543

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=1.6e-15  Score=109.61  Aligned_cols=80  Identities=21%  Similarity=0.204  Sum_probs=73.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-----ee
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS-----RQ  212 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g-----~~  212 (335)
                      ....++|||+|||.++++++|+++|..||.|..+.++.+       |||||+|.+.++|.+|++.|++..+.|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            345689999999999999999999999999999999854       799999999999999999999999999     99


Q ss_pred             eEEEEccCCCCC
Q 019811          213 IRCNWATKGAGN  224 (335)
Q Consensus       213 l~v~~~~~~~~~  224 (335)
                      |+|.++..+...
T Consensus        85 i~V~~a~~~~~~   96 (108)
T 1x4c_A           85 IRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEESSCCSCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999876543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=1.3e-16  Score=108.98  Aligned_cols=72  Identities=17%  Similarity=0.314  Sum_probs=66.9

Q ss_pred             ceEEECCCCccc------cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-eeE
Q 019811          142 FNIFVGDLSPEV------TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSR-QIR  214 (335)
Q Consensus       142 ~~l~v~nlp~~~------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~-~l~  214 (335)
                      ++|||+|||..+      ++++|+++|+.||.|.++.+.  +.+|.++|||||+|.+.++|.+|+..|+|..+.|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      789999999999999999887  35788999999999999999999999999999999 887


Q ss_pred             E
Q 019811          215 C  215 (335)
Q Consensus       215 v  215 (335)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.65  E-value=4.8e-16  Score=110.99  Aligned_cols=70  Identities=30%  Similarity=0.510  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       261 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..++|||+|||.++++++|+++|+.||  .|.++++.+++|+|||+|.+.++|.+|+..|+|.   .++|++|+|
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G--~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~---~~~g~~l~V   95 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFG--FILDFKHYPEKGCCFIKYDTHEQAAVCIVALANF---PFQGRNLRT   95 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTS--CCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTC---EETTEECCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCC--CEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCC---eECCeEEEE
Confidence            358999999999999999999999999  5889999999999999999999999999999999   999999986

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=2.1e-15  Score=105.66  Aligned_cols=79  Identities=22%  Similarity=0.366  Sum_probs=72.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+.+        +||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            345668999999999999999999999999999998873        399999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      ++..+..
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9977543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1e-15  Score=108.41  Aligned_cols=80  Identities=23%  Similarity=0.387  Sum_probs=71.9

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||..+++++|+++|+.||.|. +.++.+    .++|||||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            44567999999999999999999999999997 666644    6789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +..+.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.65  E-value=8.9e-16  Score=120.76  Aligned_cols=82  Identities=20%  Similarity=0.262  Sum_probs=74.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+..+++|||+|||.++++++|+++|+.||.|.+|.+..++   ++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45667899999999999999999999999999999998864   468999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            86543

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.64  E-value=1.7e-16  Score=106.74  Aligned_cols=71  Identities=17%  Similarity=0.300  Sum_probs=65.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +|||+|||.++++++|+++|++||.|.++.+..++    ++|||||+|.+.++|.+|++ +++..+.|+.|+|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999998754    46899999999999999997 4899999999999864

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.64  E-value=1.1e-16  Score=107.62  Aligned_cols=75  Identities=24%  Similarity=0.474  Sum_probs=70.9

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      +|||+|||.++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++. ++..+.|+.|.|.++
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            589999999999999999999999999999999988899999999999999999999984 889999999999875

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=8.7e-17  Score=114.89  Aligned_cols=83  Identities=29%  Similarity=0.466  Sum_probs=75.2

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.||.|.. .++.+..++.++|||||+|.+.++|.+|++ |++..+.|+.|+|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345689999999999999999999999999888 566676778899999999999999999998 999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +..+.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            97654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.64  E-value=1.2e-15  Score=110.07  Aligned_cols=78  Identities=21%  Similarity=0.446  Sum_probs=71.8

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+.        +|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34566899999999999999999999999999999887        6799999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      |+....
T Consensus        99 ~a~~~~  104 (108)
T 2jvo_A           99 YSKLPA  104 (108)
T ss_dssp             SCSCCC
T ss_pred             EecCCC
Confidence            987754

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.1e-15  Score=110.64  Aligned_cols=80  Identities=21%  Similarity=0.528  Sum_probs=73.4

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||..+++++|+++|+.||.|..+.+.++      +|||||+|.+.++|.+|+..|++..+.|+.|+|.|
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            345679999999999999999999999999999999854      78999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      +.....
T Consensus        96 a~~~~~  101 (109)
T 1x4g_A           96 GKESPD  101 (109)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987653

>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=8.7e-16  Score=110.39  Aligned_cols=78  Identities=19%  Similarity=0.254  Sum_probs=72.0

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||+++++++|+++|+.| .|..+.+++++. |.++|+|||+|.+.++|.+|+ .+++..++|+.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            34789999999999999999999999 899999999865 899999999999999999999 689999999999998875


Q ss_pred             C
Q 019811          220 K  220 (335)
Q Consensus       220 ~  220 (335)
                      .
T Consensus        92 ~   92 (109)
T 2dnn_A           92 E   92 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.64  E-value=3.5e-16  Score=108.65  Aligned_cols=79  Identities=22%  Similarity=0.273  Sum_probs=66.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ..+++|||+|||.++++++|+++|+.||.|.+|++..+ ++|||||+|.+.++|++|..  ....+.|+.|.|.++.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCC
Confidence            45688999999999999999999999999999998876 67999999999999976432  1344589999999987665


Q ss_pred             Cc
Q 019811          134 QR  135 (335)
Q Consensus       134 ~~  135 (335)
                      ..
T Consensus        80 ~~   81 (88)
T 1wf0_A           80 NS   81 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.64  E-value=3.2e-16  Score=113.02  Aligned_cols=81  Identities=19%  Similarity=0.268  Sum_probs=75.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCC---ceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPS---CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~---v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      ....++|||+|||.++++++|+++|+.||.   |..+.+++++. |.++|||||+|.+.++|.+|+. +++..++|+.|.
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            455679999999999999999999999887   89999999976 8999999999999999999999 999999999999


Q ss_pred             EEEccC
Q 019811          215 CNWATK  220 (335)
Q Consensus       215 v~~~~~  220 (335)
                      |.++..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            999865

>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=99.64  E-value=5.3e-16  Score=112.51  Aligned_cols=69  Identities=14%  Similarity=0.161  Sum_probs=65.6

Q ss_pred             CCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       262 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .++|||+|||.++++++|+++|++||  .|..|.+.+++|+|||+|.+.++|.+|+..|||.   .|+|++|+|
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~---~~~g~~l~V   78 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFG--SLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS---KFHHVPLYL   78 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTS--CEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTC---BSSSSBCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcC--CEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCC---EECCeEEEE
Confidence            37899999999999999999999999  5899999999999999999999999999999999   999999875

>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=99.63  E-value=1.9e-15  Score=106.81  Aligned_cols=77  Identities=22%  Similarity=0.396  Sum_probs=70.4

Q ss_pred             CCCCcceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          137 DTSGHFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ....+++|||+|||. ++++++|+++|+.||.|..+.+.        +|||||+|.+.++|.+|+..|++..++|+.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345668999999998 99999999999999999999873        689999999999999999999999999999999


Q ss_pred             EEccCC
Q 019811          216 NWATKG  221 (335)
Q Consensus       216 ~~~~~~  221 (335)
                      .++..+
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998764

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.63  E-value=4.1e-16  Score=110.53  Aligned_cols=82  Identities=23%  Similarity=0.367  Sum_probs=74.2

Q ss_pred             CCCcceEEECCCCccccHHHHH----HHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          138 TSGHFNIFVGDLSPEVTDATLF----ACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~----~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      ..++++|||+|||.++++++|+    ++|+.||.|..+.+.+   ++.++|||||+|.+.++|.+|+..|++..+.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3456899999999999999999    9999999999998873   46778999999999999999999999999999999


Q ss_pred             EEEEccCCC
Q 019811          214 RCNWATKGA  222 (335)
Q Consensus       214 ~v~~~~~~~  222 (335)
                      +|.|+....
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999997754

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.63  E-value=5.2e-16  Score=127.33  Aligned_cols=81  Identities=16%  Similarity=0.267  Sum_probs=76.3

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCC--CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYP--SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g--~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..++|||+|||.++++++|+++|+.||  .|..+.|++++.++.++|||||+|.+.++|.+|+..|++..|.|+.|+|.+
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            456899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 019811          218 ATK  220 (335)
Q Consensus       218 ~~~  220 (335)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            854

>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=99.63  E-value=8.6e-16  Score=117.03  Aligned_cols=81  Identities=26%  Similarity=0.393  Sum_probs=70.8

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCcee--------EEEee-cCCCCeEEEEEcCHHHHHHHHHHhCCccccCcee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG--------CKLIR-KDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPI  124 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~--------v~~~~-~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l  124 (335)
                      .++++|||+|||.++|+++|+++|+.||.|.+        +.+.. .+++|||||+|.+.++|.+|+..|||..+.|+.|
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            45688999999999999999999999999876        33333 4567999999999999999999999999999999


Q ss_pred             EEeeeccCCC
Q 019811          125 KVNWAYASGQ  134 (335)
Q Consensus       125 ~v~~~~~~~~  134 (335)
                      +|.++.....
T Consensus       123 ~V~~a~~~~~  132 (143)
T 3egn_A          123 VVQFARSARP  132 (143)
T ss_dssp             EEEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999976544

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=2.1e-15  Score=105.19  Aligned_cols=78  Identities=28%  Similarity=0.478  Sum_probs=71.5

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.+.+        +||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345668999999999999999999999999999998873        389999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++....
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            997754

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.63  E-value=8.7e-16  Score=110.44  Aligned_cols=80  Identities=15%  Similarity=0.198  Sum_probs=72.1

Q ss_pred             ceEEECCC----CccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HhCCce
Q 019811          142 FNIFVGDL----SPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN----QQD----AQSAIN--DLTGKW  207 (335)
Q Consensus       142 ~~l~v~nl----p~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~----~~~----a~~a~~--~l~~~~  207 (335)
                      ..|||+||    |+.+++++|+++|+.||+|.++.++.|+.+|.++|||||+|.+    .++    |.+|+.  .+++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999996    322    788888  789999


Q ss_pred             eCCeeeEEEEccCC
Q 019811          208 LGSRQIRCNWATKG  221 (335)
Q Consensus       208 ~~g~~l~v~~~~~~  221 (335)
                      ++|+.|+|.+....
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987653

>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=99.62  E-value=3.4e-15  Score=106.89  Aligned_cols=80  Identities=21%  Similarity=0.366  Sum_probs=72.2

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.||.|..+.++        ++||||+|.+.++|.+|+..|++..+.|+.|.|.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456799999999999999999999999999999886        34899999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 019811          218 ATKGAGNN  225 (335)
Q Consensus       218 ~~~~~~~~  225 (335)
                      +.......
T Consensus        80 a~~~~~~~   87 (103)
T 2dgu_A           80 AKPPDQKR   87 (103)
T ss_dssp             CCCCCCCC
T ss_pred             cCCCcccc
Confidence            98765433

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=1.2e-15  Score=107.93  Aligned_cols=81  Identities=16%  Similarity=0.338  Sum_probs=72.6

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||..+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34556899999999999999999999999988766     2467889999999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++..+.
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            997654

>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=99.62  E-value=3e-16  Score=117.72  Aligned_cols=80  Identities=14%  Similarity=0.118  Sum_probs=69.7

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+...++|||+|||+++|+++|+++|+.|| |.+|+|+.++   ++|||||+|.+.++|.+|+ .+|+..+.|+.|.|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            445678899999999999999999999999 6699998764   4689999999999999999 7899999999999998


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +....
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            86544

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.41  E-value=3.9e-17  Score=119.83  Aligned_cols=83  Identities=23%  Similarity=0.319  Sum_probs=74.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCcee--------EEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG--------CKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~--------v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|.+        |++..++    .+|||||+|.+.++|.+|+..|||..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345688999999999999999999999999988        8887763    3689999999999999999999999999


Q ss_pred             CceeEEeeeccCCCc
Q 019811          121 GQPIKVNWAYASGQR  135 (335)
Q Consensus       121 g~~l~v~~~~~~~~~  135 (335)
                      |+.|+|.++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999776543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.61  E-value=2.2e-15  Score=118.46  Aligned_cols=83  Identities=25%  Similarity=0.354  Sum_probs=77.9

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ...+++|||+|||..+++++|+++|+.||.|..+.+..++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4456899999999999999999999999999999999987 889999999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      +...
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8763

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=2e-15  Score=106.58  Aligned_cols=78  Identities=23%  Similarity=0.382  Sum_probs=70.5

Q ss_pred             CCCcceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          138 TSGHFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       138 ~~~~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ..++++|||+|||. .+++++|+++|+.||.|..+.+.        +|||||+|.+.++|.+|+..|++..+.|+.|+|.
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            34568999999998 99999999999999999999884        6799999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      ++.....
T Consensus        79 ~a~~~~~   85 (96)
T 2kvi_A           79 VSSSNAR   85 (96)
T ss_dssp             EEECCCC
T ss_pred             EcCcCCC
Confidence            9977543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=8.7e-15  Score=103.97  Aligned_cols=78  Identities=23%  Similarity=0.330  Sum_probs=70.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccC--CCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~--g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ....++|||+|||.++++++|+++|+.|  |.|..+.+.        +|||||+|.+.++|.+|+..|++..+.|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3456899999999999999999999999  888888664        569999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .|+..+..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987543

>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=99.61  E-value=2.8e-15  Score=105.23  Aligned_cols=79  Identities=25%  Similarity=0.408  Sum_probs=69.7

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCC-ceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceeCCeeeEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPS-CSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG-KWLGSRQIRC  215 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~-v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~-~~~~g~~l~v  215 (335)
                      ....++|||+|||.++++++|+++|+.||. |..+.+.       ++|||||+|.+.++|.+|+..|++ ..+.|+.|+|
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            345679999999999999999999999999 6655552       468999999999999999999999 9999999999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .|+..+..
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99987543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.61  E-value=6.6e-16  Score=110.48  Aligned_cols=81  Identities=25%  Similarity=0.457  Sum_probs=75.5

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||+|||.++++++|+++|+.||.|..+.+++++ ++.++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            345799999999999999999999999999999999997 88999999999999999999998  999999999999998


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      ..+.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            7654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.41  E-value=4.4e-17  Score=119.54  Aligned_cols=85  Identities=28%  Similarity=0.370  Sum_probs=79.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCcee--------eEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSD--------ARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      .+.++|||+|||.++++++|+++|+.||.|..        +.+++++.++.++|||||+|.+.++|.+|+..|++..+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            45679999999999999999999999999998        8899888888999999999999999999999999999999


Q ss_pred             eeeEEEEccCCCC
Q 019811          211 RQIRCNWATKGAG  223 (335)
Q Consensus       211 ~~l~v~~~~~~~~  223 (335)
                      +.|+|.++..+..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987643

>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=99.61  E-value=1.3e-15  Score=111.97  Aligned_cols=78  Identities=15%  Similarity=0.116  Sum_probs=68.1

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCce--eEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE--GCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~--~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      .+...++|||+|||+++|+++|+++|+.| .|.  +|++..++   ++|||||+|.+.++|.+|++ +++..+.|+.|.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            44567889999999999999999999999 566  88888764   47999999999999999997 4789999999999


Q ss_pred             eeecc
Q 019811          127 NWAYA  131 (335)
Q Consensus       127 ~~~~~  131 (335)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88753

>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=99.61  E-value=9.4e-15  Score=106.16  Aligned_cols=82  Identities=18%  Similarity=0.201  Sum_probs=70.9

Q ss_pred             CCCCcceEEEeCCCCCCC-----------HHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           52 DPSTCRSVYVGNIHTQVT-----------EPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t-----------~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      .+.++++|+|+||.....           +++|+++|++||.|.+|.+.....+|||||+|.+.++|.+|+..|||..+.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            466789999999944332           689999999999999997744446899999999999999999999999999


Q ss_pred             CceeEEeeeccCC
Q 019811          121 GQPIKVNWAYASG  133 (335)
Q Consensus       121 g~~l~v~~~~~~~  133 (335)
                      |++|+|.++.+..
T Consensus        91 gr~l~v~~a~~~~  103 (112)
T 2dit_A           91 GRQITAQAWDGTT  103 (112)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CcEEEEEEeCCCC
Confidence            9999999987654

>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=99.61  E-value=8e-15  Score=111.79  Aligned_cols=80  Identities=19%  Similarity=0.184  Sum_probs=71.6

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eeeEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS--RQIRCN  216 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~  216 (335)
                      .....|||+||++.+++++|+++|++||.|.++.+..+    .++|+|||+|.+.++|.+|++.|+|..|.|  +.|+|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34467899999999999999999999999999998643    357899999999999999999999999965  999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      |++.+.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            998764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.4e-14  Score=102.43  Aligned_cols=79  Identities=23%  Similarity=0.311  Sum_probs=71.2

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|+  ++++++|+++|+.||.|..+.+.      .++|||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456689999996  89999999999999999999885      567899999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |+..+..
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9977654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.1e-15  Score=112.19  Aligned_cols=77  Identities=14%  Similarity=0.111  Sum_probs=67.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCc----eeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPV----EGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v----~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      ....++|||+|||+++|+++|+++|+.||.|    .+|++..+.   ++|||||+|.+.++|.+|++. |+..+.|+.|.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            3456789999999999999999999999975    689988764   358999999999999999985 99999999999


Q ss_pred             Eeeec
Q 019811          126 VNWAY  130 (335)
Q Consensus       126 v~~~~  130 (335)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98764

>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=99.60  E-value=2e-15  Score=104.65  Aligned_cols=71  Identities=23%  Similarity=0.439  Sum_probs=65.1

Q ss_pred             CCCeEEEcCCCcccCHHHHHHHhhhc----CCe-----eeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCc
Q 019811          261 QYTTVYVGNLAPEVTQLDLHRHFHSL----GAG-----VIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGK  331 (335)
Q Consensus       261 ~~~~l~v~nlp~~~t~~~l~~~f~~~----G~~-----~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~  331 (335)
                      +.++|||+|||.++++++|+++|+.|    |..     .+.++.+.+++|+|||+|.+.++|.+|+ .|||.   .++|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~---~~~g~   80 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGI---IFQGQ   80 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTC---EETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCC---EECCe
Confidence            34899999999999999999999999    711     4889999999999999999999999999 99999   99999


Q ss_pred             cccC
Q 019811          332 QMKV  335 (335)
Q Consensus       332 ~l~v  335 (335)
                      +|+|
T Consensus        81 ~l~V   84 (87)
T 2hzc_A           81 SLKI   84 (87)
T ss_dssp             ECEE
T ss_pred             EEEE
Confidence            9975

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=3.6e-15  Score=107.00  Aligned_cols=78  Identities=17%  Similarity=0.250  Sum_probs=69.7

Q ss_pred             CCCcceEEE--CCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-----CC
Q 019811          138 TSGHFNIFV--GDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL-----GS  210 (335)
Q Consensus       138 ~~~~~~l~v--~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~-----~g  210 (335)
                      ..++++|||  +||+.++++++|+++|++||.|..+.++.      .+|||||+|.+.++|.+|++.|||..+     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345678999  77999999999999999999999987762      378999999999999999999999988     78


Q ss_pred             eeeEEEEccCC
Q 019811          211 RQIRCNWATKG  221 (335)
Q Consensus       211 ~~l~v~~~~~~  221 (335)
                      +.|.|.|+..-
T Consensus        96 ~~l~v~~a~~~  106 (114)
T 2cq2_A           96 ITLYLNFVEKV  106 (114)
T ss_dssp             EECEEEEESCC
T ss_pred             cEEEEEecccC
Confidence            99999998753

>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=99.60  E-value=1.7e-15  Score=124.24  Aligned_cols=77  Identities=21%  Similarity=0.216  Sum_probs=70.4

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccC--CceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTG--PVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G--~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..++|||+|||.++|+++|+++|+.||  .|.+|+|+.++    ++|||||+|.+.++|.+|++.||+..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  99999999875    358999999999999999999999999999999998


Q ss_pred             ecc
Q 019811          129 AYA  131 (335)
Q Consensus       129 ~~~  131 (335)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            853

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.9e-15  Score=110.98  Aligned_cols=80  Identities=23%  Similarity=0.214  Sum_probs=72.4

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCc----eeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSC----SDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v----~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      ...++|||+|||+++|+++|+++|+.||.|    ..+.++++ .+|+++|||||+|.+.++|.+|+.. ++..++|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            345799999999999999999999999875    68999988 5889999999999999999999985 99999999999


Q ss_pred             EEEccC
Q 019811          215 CNWATK  220 (335)
Q Consensus       215 v~~~~~  220 (335)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            988754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.60  E-value=5.4e-15  Score=105.53  Aligned_cols=79  Identities=22%  Similarity=0.259  Sum_probs=69.2

Q ss_pred             CCCcceEEEeCCCC-----CCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHhCCccccCc
Q 019811           53 PSTCRSVYVGNIHT-----QVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQ  122 (335)
Q Consensus        53 ~~~~~~v~v~nlp~-----~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~  122 (335)
                      +.++++|+|+|+..     +-++++|++.|++||.|.+|++..++     ++|+|||+|.+.++|.+|+..|||..+.|+
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            34678899999963     23789999999999999999998753     469999999999999999999999999999


Q ss_pred             eeEEeeecc
Q 019811          123 PIKVNWAYA  131 (335)
Q Consensus       123 ~l~v~~~~~  131 (335)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999854

>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=99.59  E-value=5.5e-15  Score=102.50  Aligned_cols=76  Identities=20%  Similarity=0.246  Sum_probs=70.0

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||.++++++|+++|+.| .|..+.+.      .++|||||+|.+.++|.+|+..|++..+.|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            45789999999999999999999999 99999884      568999999999999999999999999999999999986


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.59  E-value=1.7e-15  Score=108.34  Aligned_cols=79  Identities=20%  Similarity=0.420  Sum_probs=71.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ....++|||+|||.++++++|+++|+.||.|.++++..++   .+|||||+|.+.++|.+|+.  ++..+.|+.|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            3456889999999999999999999999999999999875   35899999999999999997  899999999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      ..+.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            7554

>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=99.59  E-value=3.2e-15  Score=109.16  Aligned_cols=68  Identities=24%  Similarity=0.315  Sum_probs=62.6

Q ss_pred             CCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCcccc
Q 019811          261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMK  334 (335)
Q Consensus       261 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~  334 (335)
                      ..++|||+|||+++++++|+++|+.||  .|..+.+..+ |+|||+|.+.++|.+|++.|||.   .|+|++|+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G--~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~---~~~gr~~~   82 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAG--DVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNT---KFRSHEGE   82 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGS--CEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTC---BCCCTTSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC--CeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCC---EECCcEee
Confidence            348899999999999999999999999  5999999887 99999999999999999999999   99999854

>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=99.59  E-value=1.5e-15  Score=115.70  Aligned_cols=85  Identities=22%  Similarity=0.343  Sum_probs=73.2

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEE-----eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCee
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARV-----MWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQ  212 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~-----~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~  212 (335)
                      ..++++|||+|||.++++++|+++|+.||.|..+.+     ++...++.++|||||+|.+.++|.+|+..|++..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            345679999999999999999999999999877411     111246789999999999999999999999999999999


Q ss_pred             eEEEEccCCC
Q 019811          213 IRCNWATKGA  222 (335)
Q Consensus       213 l~v~~~~~~~  222 (335)
                      |.|.|+....
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=9.3e-15  Score=99.30  Aligned_cols=75  Identities=17%  Similarity=0.144  Sum_probs=66.4

Q ss_pred             eEEECCCCccccHHH----HHHHhccCC-CceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          143 NIFVGDLSPEVTDAT----LFACFSVYP-SCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~----l~~~f~~~g-~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      .|||+|||..+++++    |+++|++|| .|.+|       ++   |+|||+|.+.++|.+|++.|+|..+.|+.|+|.|
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            499999999999988    558999994 99888       23   8999999999999999999999999999999999


Q ss_pred             ccCCCCCCCC
Q 019811          218 ATKGAGNNED  227 (335)
Q Consensus       218 ~~~~~~~~~~  227 (335)
                      ++........
T Consensus        81 A~~~sd~~~~   90 (96)
T 2diu_A           81 TPKNRELCET   90 (96)
T ss_dssp             SCCSCCCCCC
T ss_pred             cCCCcceeEe
Confidence            9887655443

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=3.9e-15  Score=105.21  Aligned_cols=79  Identities=15%  Similarity=0.231  Sum_probs=71.1

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceee-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDA-RVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ...++|||+|||.++++++|+++|+.||.|..+ .++.++.+    +.|||+|.+.++|.+|+..|++..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            446799999999999999999999999999999 47766443    3499999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9875

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.59  E-value=1.2e-14  Score=106.76  Aligned_cols=79  Identities=19%  Similarity=0.210  Sum_probs=70.3

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--eeeEEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGF-GFVSFRNQQDAQSAINDLTGKWLGS--RQIRCN  216 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~  216 (335)
                      .-..|||+||++.+|+++|+++|++||.|.++.+..+     .+|+ |||+|.+.++|.+|++.|+|..+.|  +.|+|.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            3356889999999999999999999999999988753     2566 9999999999999999999999987  999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |++....
T Consensus       102 ~ak~~~l  108 (130)
T 3zzy_A          102 FSKLTSL  108 (130)
T ss_dssp             ECSCSSC
T ss_pred             ecCCCce
Confidence            9987653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=8.5e-15  Score=102.94  Aligned_cols=78  Identities=19%  Similarity=0.338  Sum_probs=68.6

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||+|||.++++++|+++|+.||.|..+  +.++.++.   ||||+|.+.++|.+|+. |++..+.|+.|.|.++
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            345799999999999999999999999999987  44544544   99999999999999999 9999999999999987


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      ..+.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6543

>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=99.59  E-value=2.1e-14  Score=128.74  Aligned_cols=80  Identities=20%  Similarity=0.404  Sum_probs=73.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+.++|||+|||..+|+++|.++|+.||.|..|+|+.++    .+|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999998764    4689999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7543

>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=99.58  E-value=2.3e-15  Score=110.74  Aligned_cols=80  Identities=20%  Similarity=0.241  Sum_probs=72.0

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCce--eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCS--DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~--~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ....++|||+|||+++|+++|+++|+.| .|.  .+.+++++. |.++|||||+|.+.++|.+|+.. ++..++|+.|.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            3455789999999999999999999999 677  899999876 89999999999999999999984 779999999999


Q ss_pred             EEccC
Q 019811          216 NWATK  220 (335)
Q Consensus       216 ~~~~~  220 (335)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88754

>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=99.58  E-value=1.4e-14  Score=115.59  Aligned_cols=117  Identities=9%  Similarity=0.060  Sum_probs=91.6

Q ss_pred             CHHHHHHHHHHh--CCccccCceeEEeeeccCCCcc------CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEe
Q 019811          103 DRRSAAMAILSL--NGRHLFGQPIKVNWAYASGQRE------DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVM  174 (335)
Q Consensus       103 ~~~~A~~a~~~l--~~~~~~g~~l~v~~~~~~~~~~------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~  174 (335)
                      +.+.+..|+...  ....+.+...+|......+.+.      .....++|||+|||.++++++|.++|+.||.|..+.++
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            567777787766  4555566656665553222111      11235789999999999999999999999999999999


Q ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          175 WDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       175 ~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ++. ++.++|+|||+|.+.++|.+|+..+ +..+.|+.|.|.+...-
T Consensus       143 ~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          143 RTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             ECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             ECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            885 5889999999999999999999865 45999999999987653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.58  E-value=1.7e-14  Score=102.92  Aligned_cols=82  Identities=13%  Similarity=0.179  Sum_probs=72.2

Q ss_pred             CCcceEEECCCCc-----cccHHHHHHHhccCCCceeeEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCee
Q 019811          139 SGHFNIFVGDLSP-----EVTDATLFACFSVYPSCSDARVMWDQKT-GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQ  212 (335)
Q Consensus       139 ~~~~~l~v~nlp~-----~~t~~~l~~~f~~~g~v~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~  212 (335)
                      .++++|+|.|+..     +-++++|+++|++||.|.++.+++++.+ +.++|+|||+|.+.++|.+|+..|||..+.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4567899999963     2378999999999999999999988653 578999999999999999999999999999999


Q ss_pred             eEEEEccC
Q 019811          213 IRCNWATK  220 (335)
Q Consensus       213 l~v~~~~~  220 (335)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999854

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.57  E-value=5.3e-15  Score=120.54  Aligned_cols=79  Identities=23%  Similarity=0.447  Sum_probs=71.1

Q ss_pred             CCCcceEEEeCCCCCC---------CHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccc----
Q 019811           53 PSTCRSVYVGNIHTQV---------TEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHL----  119 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~---------t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~----  119 (335)
                      ....++|||+|||..+         ++++|+++|++||.|.+|+++.+  +|||||.|.+.++|+.|++.|+|..+    
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~--kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~  208 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES--KNCGFVKFKYQANAEFAKEAMSNQTLLLPS  208 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG--GTEEEEEESSHHHHHHHHHHHTTCCCCCTT
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC--CCEEEEEeCCHHHHHHHHHHhCCCEEeccc
Confidence            4567899999999998         79999999999999999999865  58999999999999999999999999    


Q ss_pred             --------cCceeEEeeeccCC
Q 019811          120 --------FGQPIKVNWAYASG  133 (335)
Q Consensus       120 --------~g~~l~v~~~~~~~  133 (335)
                              .|+.|.|.|+...+
T Consensus       209 ~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          209 DKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             STTGGGGGGSCCCEEEECC---
T ss_pred             cccccccCCCCEEEEEEccCCC
Confidence                    89999999997654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=8e-15  Score=106.94  Aligned_cols=73  Identities=21%  Similarity=0.282  Sum_probs=60.8

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec-------CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK-------DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~-------~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      ...++|||+|||.++++++|+++|++||.|. +.++.+       +++|||||+|.+.++|.+|++.|+  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568899999999999999999999999998 767654       347999999999999999999883  255666665


Q ss_pred             eee
Q 019811          127 NWA  129 (335)
Q Consensus       127 ~~~  129 (335)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=2.6e-14  Score=104.57  Aligned_cols=76  Identities=14%  Similarity=0.132  Sum_probs=67.5

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--eeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGF-GFVSFRNQQDAQSAINDLTGKWLGS--RQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~~  218 (335)
                      ..|||+||+..+++++|+++|++||.|.++.+...      .|+ |||+|.+.++|..|+..|+|..|.|  +.|+|.|+
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            35689999999999999999999999999988642      275 9999999999999999999999977  68999999


Q ss_pred             cCCCC
Q 019811          219 TKGAG  223 (335)
Q Consensus       219 ~~~~~  223 (335)
                      +.+..
T Consensus       100 k~~~l  104 (124)
T 2e5i_A          100 RPTRL  104 (124)
T ss_dssp             SCSCC
T ss_pred             cCCcc
Confidence            87653

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.54  E-value=2.3e-14  Score=99.36  Aligned_cols=76  Identities=25%  Similarity=0.321  Sum_probs=62.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce--eCCeeeEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKW--LGSRQIRC  215 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~--~~g~~l~v  215 (335)
                      ....++|||+|||.++++++|+++|++||.|.++.++++     ++|||||+|.+.++|.+    +++..  +.|+.|.|
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            345679999999999999999999999999999998853     68999999999999983    45544  56999999


Q ss_pred             EEccCCC
Q 019811          216 NWATKGA  222 (335)
Q Consensus       216 ~~~~~~~  222 (335)
                      .++.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9987654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=3.9e-14  Score=103.22  Aligned_cols=77  Identities=19%  Similarity=0.369  Sum_probs=66.6

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKT---GRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ...++|||+|||.++++++|+++|+.||.|. +.++.+..+   |.++|||||+|.+.++|.+|++.|+  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4567899999999999999999999999999 778877666   6899999999999999999999883  367777766


Q ss_pred             EEc
Q 019811          216 NWA  218 (335)
Q Consensus       216 ~~~  218 (335)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            644

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.53  E-value=2.2e-14  Score=103.20  Aligned_cols=74  Identities=15%  Similarity=0.167  Sum_probs=65.4

Q ss_pred             ceEEEeCC----CCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcC----HHH----HHHHHH--HhCCcc
Q 019811           57 RSVYVGNI----HTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFD----RRS----AAMAIL--SLNGRH  118 (335)
Q Consensus        57 ~~v~v~nl----p~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~----~~~----A~~a~~--~l~~~~  118 (335)
                      ..|||+||    |+.+++.+|+++|+.||.|.++.++.|+.    +|||||+|.+    +++    |.+|+.  .++|..
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            56999999    99999999999999999999999999875    4899999996    444    788888  789999


Q ss_pred             ccCceeEEeeec
Q 019811          119 LFGQPIKVNWAY  130 (335)
Q Consensus       119 ~~g~~l~v~~~~  130 (335)
                      |.|++|+|..-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999998764

>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=99.51  E-value=3.2e-14  Score=98.65  Aligned_cols=77  Identities=26%  Similarity=0.322  Sum_probs=65.3

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+++|||+|||.++++++|+++|+.||.|..+.++++     ++|||||+|.+.++|.++..  ....+.|+.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            4579999999999999999999999999999998743     68899999999999976432  2345689999999987


Q ss_pred             CCCC
Q 019811          220 KGAG  223 (335)
Q Consensus       220 ~~~~  223 (335)
                      ++..
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.50  E-value=8.8e-14  Score=99.28  Aligned_cols=78  Identities=13%  Similarity=0.168  Sum_probs=68.1

Q ss_pred             CCcceEEEeCC--CCCCC--------HHHHHHHHhccCCceeEEEeecC------CCCeEEEEEcCHHHHHHHHHHhCCc
Q 019811           54 STCRSVYVGNI--HTQVT--------EPLLQEVFSSTGPVEGCKLIRKD------KSSYGFIHYFDRRSAAMAILSLNGR  117 (335)
Q Consensus        54 ~~~~~v~v~nl--p~~~t--------~~~l~~~f~~~G~v~~v~~~~~~------~~g~afv~f~~~~~A~~a~~~l~~~  117 (335)
                      .+++.|.|.|+  |.++.        +++|++.|++||.|.+|+|.+++      ++|+|||+|.+.++|.+|+..|||.
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            35788999998  44443        47899999999999999998764      4699999999999999999999999


Q ss_pred             cccCceeEEeeecc
Q 019811          118 HLFGQPIKVNWAYA  131 (335)
Q Consensus       118 ~~~g~~l~v~~~~~  131 (335)
                      .+.|+.|+|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999998753

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.49  E-value=9.9e-14  Score=110.69  Aligned_cols=77  Identities=18%  Similarity=0.154  Sum_probs=68.7

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++.++.   .+|||||+|.+.++|.+|+..+ +..+.|+.|.|.+...
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            35889999999999999999999999999999998754   3589999999999999999765 4589999999998765


Q ss_pred             C
Q 019811          132 S  132 (335)
Q Consensus       132 ~  132 (335)
                      .
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.48  E-value=1.5e-13  Score=99.99  Aligned_cols=77  Identities=17%  Similarity=0.200  Sum_probs=66.9

Q ss_pred             CcceEEEeCCC--CCC---CHHHHHHHHhccCCceeEEEeecCC--------CCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           55 TCRSVYVGNIH--TQV---TEPLLQEVFSSTGPVEGCKLIRKDK--------SSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        55 ~~~~v~v~nlp--~~~---t~~~l~~~f~~~G~v~~v~~~~~~~--------~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      ++++|+|+|+-  .++   -+++|++.|++||.|.+|+|..++.        +|++||+|.+.++|.+|+..|||..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            46789999984  333   3799999999999999999988642        3899999999999999999999999999


Q ss_pred             ceeEEeeecc
Q 019811          122 QPIKVNWAYA  131 (335)
Q Consensus       122 ~~l~v~~~~~  131 (335)
                      +.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998753

>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=99.48  E-value=2.8e-13  Score=97.80  Aligned_cols=78  Identities=17%  Similarity=0.197  Sum_probs=68.2

Q ss_pred             CCCcceEEEeCCCCCCC----------HHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCc
Q 019811           53 PSTCRSVYVGNIHTQVT----------EPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQ  122 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t----------~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~  122 (335)
                      +.+++.|.|.|+=..-.          +++|++.|++||.|.+|.+.++..+|++||+|.+.++|.+|++.|||..|.|+
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            45678899999743221          46889999999999999998877789999999999999999999999999999


Q ss_pred             eeEEeeec
Q 019811          123 PIKVNWAY  130 (335)
Q Consensus       123 ~l~v~~~~  130 (335)
                      .|+|.++.
T Consensus        84 ~i~v~~~~   91 (114)
T 3s6e_A           84 MITAAYVP   91 (114)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEEc
Confidence            99999874

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.47  E-value=1.1e-13  Score=112.89  Aligned_cols=71  Identities=27%  Similarity=0.429  Sum_probs=66.0

Q ss_pred             CCCCeEEEcCCCccc---------CHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccc--
Q 019811          260 PQYTTVYVGNLAPEV---------TQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL--  328 (335)
Q Consensus       260 ~~~~~l~v~nlp~~~---------t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~--  328 (335)
                      ..+++|||+||+..+         ++++|+++|+.||  .|.+|++..++|+|||+|.+.++|..|+..|+|.   .|  
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG--~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~---~l~~  206 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLG--DIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQ---TLLL  206 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTS--CEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTC---CCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccC--CEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCC---EEec
Confidence            355899999999998         7999999999999  6999999999999999999999999999999999   88  


Q ss_pred             ----------cCccccC
Q 019811          329 ----------FGKQMKV  335 (335)
Q Consensus       329 ----------~g~~l~v  335 (335)
                                +|+.|+|
T Consensus       207 ~~~~e~~~~~~gr~L~V  223 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLV  223 (240)
T ss_dssp             TTSTTGGGGGGSCCCEE
T ss_pred             cccccccccCCCCEEEE
Confidence                      8998875

>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=99.46  E-value=2.4e-13  Score=96.99  Aligned_cols=81  Identities=17%  Similarity=0.165  Sum_probs=69.9

Q ss_pred             CcceEEECCC--Cccc--------cHHHHHHHhccCCCceeeEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          140 GHFNIFVGDL--SPEV--------TDATLFACFSVYPSCSDARVMWDQKT--GRSRGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       140 ~~~~l~v~nl--p~~~--------t~~~l~~~f~~~g~v~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      ++++|.|.|+  |..+        .+++|++.|++||.|.++.+++++.+  +.++|++||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5678899998  3332        35799999999999999999988654  3578999999999999999999999999


Q ss_pred             eCCeeeEEEEccC
Q 019811          208 LGSRQIRCNWATK  220 (335)
Q Consensus       208 ~~g~~l~v~~~~~  220 (335)
                      ++||.|.|.|...
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999754

>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=1.2e-12  Score=94.91  Aligned_cols=82  Identities=21%  Similarity=0.343  Sum_probs=69.9

Q ss_pred             CCCCcceEEECCCCccc-----------cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          137 DTSGHFNIFVGDLSPEV-----------TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~-----------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      .+.++++|+|.||....           ++++|+++|++||.|..+.+ .++   .++|+|||+|.+.++|.+|+..|+|
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            44567899999994332           26899999999999999965 443   4799999999999999999999999


Q ss_pred             ceeCCeeeEEEEccCCC
Q 019811          206 KWLGSRQIRCNWATKGA  222 (335)
Q Consensus       206 ~~~~g~~l~v~~~~~~~  222 (335)
                      ..+.|+.|.|.++....
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999987654

>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=99.45  E-value=4.4e-13  Score=97.43  Aligned_cols=81  Identities=11%  Similarity=0.249  Sum_probs=70.0

Q ss_pred             CcceEEECCCCc--cc---cHHHHHHHhccCCCceeeEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 019811          140 GHFNIFVGDLSP--EV---TDATLFACFSVYPSCSDARVMWDQK----TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS  210 (335)
Q Consensus       140 ~~~~l~v~nlp~--~~---t~~~l~~~f~~~g~v~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g  210 (335)
                      ++++|+|.|+-.  ++   .+++|++.|++||.|.++.|++++.    ++.++|++||+|.+.++|.+|+..|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            457899999842  22   3789999999999999999998864    34577999999999999999999999999999


Q ss_pred             eeeEEEEccC
Q 019811          211 RQIRCNWATK  220 (335)
Q Consensus       211 ~~l~v~~~~~  220 (335)
                      |.|.|.|...
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-12  Score=91.53  Aligned_cols=76  Identities=17%  Similarity=0.271  Sum_probs=64.5

Q ss_pred             cceEEEeCCC-------CCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           56 CRSVYVGNIH-------TQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        56 ~~~v~v~nlp-------~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .++|.|.-.+       .++++++|+++|++||.|.+|.+. .+++|||||+|.+.++|..|++.+++  +.|++|+|.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~   86 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISW   86 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEEC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEE
Confidence            5568887665       458999999999999999999987 46679999999999999999987544  6799999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.+...
T Consensus        87 a~~~~~   92 (100)
T 2d9o_A           87 LEGQPQ   92 (100)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            876653

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.42  E-value=1.8e-13  Score=97.57  Aligned_cols=72  Identities=22%  Similarity=0.426  Sum_probs=63.2

Q ss_pred             ECCCCccccHHHHHHHh------------ccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          146 VGDLSPEVTDATLFACF------------SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       146 v~nlp~~~t~~~l~~~f------------~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      +.||+..+++++|.+.|            ++||.|.++.+.++.. +.++|+|||+|.+.++|.+|+..|+|..++|+.|
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            55777777777766665            9999999999998754 7889999999999999999999999999999999


Q ss_pred             EEEEc
Q 019811          214 RCNWA  218 (335)
Q Consensus       214 ~v~~~  218 (335)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.40  E-value=9.5e-14  Score=98.99  Aligned_cols=69  Identities=22%  Similarity=0.370  Sum_probs=59.8

Q ss_pred             EeCCCCCCCHHHHHHHH------------hccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           61 VGNIHTQVTEPLLQEVF------------SSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        61 v~nlp~~~t~~~l~~~f------------~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      +.|||..+++++|++.|            ++||.|.+|++.++.   ++|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            45666777777776666            999999999998865   469999999999999999999999999999999


Q ss_pred             Eeee
Q 019811          126 VNWA  129 (335)
Q Consensus       126 v~~~  129 (335)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.39  E-value=9e-13  Score=113.27  Aligned_cols=76  Identities=24%  Similarity=0.394  Sum_probs=65.4

Q ss_pred             CCCcceEEEeC--CCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc---Cc--eeE
Q 019811           53 PSTCRSVYVGN--IHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF---GQ--PIK  125 (335)
Q Consensus        53 ~~~~~~v~v~n--lp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~---g~--~l~  125 (335)
                      ..++++|||+|  |+.++|+++|+++|++||.|.+|.+..  ++|||||+|.+.++|++|++.|||..+.   |+  .+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~--~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT--TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            45678899999  578999999999999999999987754  5689999999999999999999999884   44  577


Q ss_pred             Eeeec
Q 019811          126 VNWAY  130 (335)
Q Consensus       126 v~~~~  130 (335)
                      +.++.
T Consensus        93 ~~~~~   97 (345)
T 3tht_A           93 LNFVE   97 (345)
T ss_dssp             EEECS
T ss_pred             EEEee
Confidence            77763

>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=99.32  E-value=9.2e-12  Score=89.78  Aligned_cols=78  Identities=13%  Similarity=0.170  Sum_probs=66.2

Q ss_pred             CCcceEEECCCCcc----------ccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          139 SGHFNIFVGDLSPE----------VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       139 ~~~~~l~v~nlp~~----------~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      .++++|.|.|+-..          -.+++|++.|++||.|.++.+.++    ..+|++||+|.+.++|.+|+..|||..+
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 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN----SAQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT----CTTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC----CCcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            45678888888332          235789999999999999988755    2589999999999999999999999999


Q ss_pred             CCeeeEEEEccC
Q 019811          209 GSRQIRCNWATK  220 (335)
Q Consensus       209 ~g~~l~v~~~~~  220 (335)
                      +|+.|.|.|+..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999854

>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=99.30  E-value=5e-12  Score=108.63  Aligned_cols=62  Identities=23%  Similarity=0.310  Sum_probs=57.6

Q ss_pred             CCCCeEEEcC--CCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          260 PQYTTVYVGN--LAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       260 ~~~~~l~v~n--lp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      .++++|||+|  |+..+|+++|+++|++||  .|.+|.+..+||||||+|.+.++|.+|++.|||.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G--~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~   79 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCG--LVDALLMPPNKPYSFARYRTTEESKRAYVTLNGK   79 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTS--CEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcC--CeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            4558999999  578999999999999999  5888999889999999999999999999999999

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=5.3e-11  Score=83.63  Aligned_cols=65  Identities=14%  Similarity=0.233  Sum_probs=57.5

Q ss_pred             ccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          151 PEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       151 ~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      ..+++++|+++|++||.|..+.++     +.++|||||+|.+.++|..|+..++  .+.|+.|+|.|+....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCC
Confidence            578999999999999999999887     3678999999999999999999744  4689999999987654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.17  E-value=1.2e-10  Score=83.84  Aligned_cols=74  Identities=14%  Similarity=0.106  Sum_probs=65.6

Q ss_pred             CCcceEEEeCCCCC-CCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcC-HHHHHHHHHHh--CCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFD-RRSAAMAILSL--NGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~-~~~A~~a~~~l--~~~~~~g~~l~v~~~  129 (335)
                      ...+.|+|+||+.+ +++++|+++|+.||.|..|.+..+..  .|||.|.+ ..+|..|+..+  ++..|.|..+++...
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~--tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK--EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS--EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC--EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            34578999999999 99999999999999999999988776  69999999 89999999998  478888888877654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=1.7e-10  Score=83.19  Aligned_cols=72  Identities=18%  Similarity=0.147  Sum_probs=63.5

Q ss_pred             CCCCCCeEEEcCCCcc-cCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCC-HHHHHHHHHhhc--CCCcccccCccc
Q 019811          258 NNPQYTTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYST-HAEAALAIQMGN--TTQSSYLFGKQM  333 (335)
Q Consensus       258 ~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~-~~~a~~A~~~l~--g~~~~~~~g~~l  333 (335)
                      ..++++.|+|+||+.+ ++.++|+++|+.||  .|.+|.+.++...|||+|.+ ..+|..|+..|+  |.   .|.|..+
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G--~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~---~i~g~~~   88 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHG--EIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNL---QLRNKEV   88 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSC--CEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCB---CTTSSSE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcC--CEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCc---EEeCcEE
Confidence            4456689999999999 99999999999999  69999999999999999999 899999999995  55   7877665


Q ss_pred             c
Q 019811          334 K  334 (335)
Q Consensus       334 ~  334 (335)
                      +
T Consensus        89 ~   89 (121)
T 1owx_A           89 T   89 (121)
T ss_dssp             E
T ss_pred             E
Confidence            4

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.14  E-value=1.9e-10  Score=77.39  Aligned_cols=71  Identities=20%  Similarity=0.303  Sum_probs=60.8

Q ss_pred             cceEEEeCCCC----CCCH----HHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           56 CRSVYVGNIHT----QVTE----PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        56 ~~~v~v~nlp~----~~t~----~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      ..||+|.-.+.    .+-.    .+|.+.|.+||.|..+++..++    +||+|.+.++|.+|++ |||..+.|+.|+|.
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~----~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK----MWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS----EEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC----EEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            45688887762    3333    6789999999999999998876    9999999999999997 99999999999999


Q ss_pred             eecc
Q 019811          128 WAYA  131 (335)
Q Consensus       128 ~~~~  131 (335)
                      ..++
T Consensus        82 lkt~   85 (91)
T 2dnr_A           82 LKSP   85 (91)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            8864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=5.4e-10  Score=75.23  Aligned_cols=69  Identities=20%  Similarity=0.247  Sum_probs=57.5

Q ss_pred             CCCCCeEEEcCCCc----ccCH----HHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccC
Q 019811          259 NPQYTTVYVGNLAP----EVTQ----LDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFG  330 (335)
Q Consensus       259 ~~~~~~l~v~nlp~----~~t~----~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g  330 (335)
                      .|+..||+|.-.+.    +..+    .+|.+.|+.||  .+..+++..++  +||+|.+.++|.+|++ |+|.   .++|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G--~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~---~v~G   75 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFG--EVILIRFVEDK--MWVTFLEGSSALNVLS-LNGK---ELLN   75 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTC--CEEEEEECSSS--EEEEESSHHHHHHGGG-GTTC---EETT
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCC--CeEEEEEecCC--EEEEECChHHHHHHHh-cCCe---EeCC
Confidence            34557888887662    3333    57899999999  69999999875  8999999999999998 9999   9999


Q ss_pred             ccccC
Q 019811          331 KQMKV  335 (335)
Q Consensus       331 ~~l~v  335 (335)
                      |.|+|
T Consensus        76 r~LkV   80 (91)
T 2dnr_A           76 RTITI   80 (91)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            99986

>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=98.93  E-value=1.5e-09  Score=73.38  Aligned_cols=71  Identities=15%  Similarity=0.172  Sum_probs=60.6

Q ss_pred             CcceEEEeCCCCC-----CCH----HHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           55 TCRSVYVGNIHTQ-----VTE----PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        55 ~~~~v~v~nlp~~-----~t~----~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      +..||+|.-++.+     +-.    .+|.+.|..||.|..+++..++    +||+|.+.++|.+|++ |||..+.|+.|+
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~----~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ----MLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE----EEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc----EEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            3457999988742     322    5688999999999999998887    9999999999999998 999999999999


Q ss_pred             Eeeec
Q 019811          126 VNWAY  130 (335)
Q Consensus       126 v~~~~  130 (335)
                      |.+..
T Consensus        89 V~~k~   93 (95)
T 1ufw_A           89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            98753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.93  E-value=2.6e-09  Score=73.53  Aligned_cols=68  Identities=15%  Similarity=0.126  Sum_probs=65.2

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhc-----CCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSL-----GAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~-----G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ++|-+-|||+.+++..|+.+.+++     |  .+..+.+..+.+.|+|+|.|...|.+|.-.|+|.   .|.||+|+|
T Consensus        22 rtiaL~~ipDtvndarIr~lve~~~~i~~g--~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~---ef~gr~Lr~   94 (117)
T 2l9w_A           22 TLICLFPLSDKVSPSLICQFLQEEIHINEK--DIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGS---QFQGKVIRS   94 (117)
T ss_dssp             SCEEEECCCTTCCHHHHHHHHHHHTCCCTT--TCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSE---EETTEEEEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHhhhhccCcc--ceeEEEEecCCCceEEEEccchhhHHHHhhcCCe---eecCeEEEe
Confidence            789999999999999999999999     8  5999999999999999999999999999999999   999999985

>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=98.93  E-value=8.5e-10  Score=74.59  Aligned_cols=70  Identities=21%  Similarity=0.301  Sum_probs=58.4

Q ss_pred             CCCCCCeEEEcCCCcc-----cCH----HHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccc
Q 019811          258 NNPQYTTVYVGNLAPE-----VTQ----LDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYL  328 (335)
Q Consensus       258 ~~~~~~~l~v~nlp~~-----~t~----~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~  328 (335)
                      ..|+..||+|.-++..     ..+    .+|.+.|+.||  .+..+++..++  +||+|.+.++|.+|++ |+|.   .+
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G--~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~---~v   82 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYG--TIVLVRINQGQ--MLVTFADSHSALSVLD-VDGM---KV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHS--CCSEEEEETTE--EEEECSCSHHHHHHHH-GGGS---EE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCC--CEEEEEEecCc--EEEEEcChHHHHHHHh-cCCe---ee
Confidence            4456688999888642     223    46889999999  58888998875  9999999999999998 9999   99


Q ss_pred             cCccccC
Q 019811          329 FGKQMKV  335 (335)
Q Consensus       329 ~g~~l~v  335 (335)
                      +||.|+|
T Consensus        83 ~Gr~L~V   89 (95)
T 1ufw_A           83 KGRAVKI   89 (95)
T ss_dssp             TTEEEEE
T ss_pred             CCeEEEE
Confidence            9999986

>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=98.86  E-value=7.1e-09  Score=84.68  Aligned_cols=68  Identities=13%  Similarity=0.247  Sum_probs=60.9

Q ss_pred             ccHHHHHHHhccCCCceeeEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          153 VTDATLFACFSVYPSCSDARVMWDQK----TGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       153 ~t~~~l~~~f~~~g~v~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      -.+++|.+.|++||.|.++.+.++..    ++.++|++||+|.+.++|.+|+..|+|+.+.||.|.+.|...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            35789999999999999999986643    347899999999999999999999999999999999999754

>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=98.73  E-value=2.3e-08  Score=81.66  Aligned_cols=75  Identities=17%  Similarity=0.163  Sum_probs=61.6

Q ss_pred             cceEEEeCCC-----CCCCHHHHHHHHhccCCceeEEEeecC--------CCCeEEEEEcCHHHHHHHHHHhCCccccCc
Q 019811           56 CRSVYVGNIH-----TQVTEPLLQEVFSSTGPVEGCKLIRKD--------KSSYGFIHYFDRRSAAMAILSLNGRHLFGQ  122 (335)
Q Consensus        56 ~~~v~v~nlp-----~~~t~~~l~~~f~~~G~v~~v~~~~~~--------~~g~afv~f~~~~~A~~a~~~l~~~~~~g~  122 (335)
                      +..+.+.|+-     .+-.+++|++.|++||.|.++++.++.        .+|++||+|.+.++|.+|+..|||..+.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            3445555542     123468999999999999999997542        348999999999999999999999999999


Q ss_pred             eeEEeeec
Q 019811          123 PIKVNWAY  130 (335)
Q Consensus       123 ~l~v~~~~  130 (335)
                      .|.+.++.
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.65  E-value=2e-07  Score=64.23  Aligned_cols=73  Identities=16%  Similarity=0.208  Sum_probs=66.4

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcc-----CCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSST-----GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~-----G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..++|-+-|||..++...|+.+.++|     |.+..|.+..+-.  =|+|+|.+...|.+|...|+|..|.|++|++.-.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~--GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN--GAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT--EEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC--ceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            46789999999999999999999999     9999998877764  5999999999999999999999999999998643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.51  E-value=2e-06  Score=58.91  Aligned_cols=89  Identities=19%  Similarity=0.285  Sum_probs=71.9

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhc---c--CCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSS---T--GPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~---~--G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +..++|.|.|||.++.++.|.-+|+.   .  |+|.+++...    +-|+|.|.+.+.|++.+.. ....+.+.+|.|..
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~----~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P   80 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG----CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRP   80 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET----TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC----CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEc
Confidence            34578999999999999999999987   2  4888888755    4699999999999999853 36788889999987


Q ss_pred             eccCCCccCCCCcceEEECCCCcccc
Q 019811          129 AYASGQREDTSGHFNIFVGDLSPEVT  154 (335)
Q Consensus       129 ~~~~~~~~~~~~~~~l~v~nlp~~~t  154 (335)
                      ..+..       ..++++.+|++.++
T Consensus        81 ~~~~~-------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           81 APPRA-------PARLLLQGLPPGTS   99 (104)
T ss_dssp             CCCCC-------CCCCCCCSCCCCCC
T ss_pred             CCCCC-------cceEeeecCCCCCC
Confidence            65443       35788999988754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.16  E-value=1.5e-05  Score=54.50  Aligned_cols=67  Identities=22%  Similarity=0.263  Sum_probs=55.7

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhh---cCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHS---LGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~---~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .+|.|.|||++++++.|.-+|++   -|...+..+....  +.|+|+|.+...|.+.++.- .+   .|+|..|.|
T Consensus         9 ~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~-~H---~L~~~~LsV   78 (104)
T 2dhx_A            9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQA-DH---ELHGAQLSL   78 (104)
T ss_dssp             CEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCS-CC---BSSSSBCEE
T ss_pred             cEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCC-cc---eecCeEEEE
Confidence            78999999999999999999997   4667899998887  79999999999999998652 23   466666543

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.08  E-value=8.8e-06  Score=55.99  Aligned_cols=74  Identities=18%  Similarity=0.208  Sum_probs=63.2

Q ss_pred             cceEEEeCCCCCC-C----HHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           56 CRSVYVGNIHTQV-T----EPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        56 ~~~v~v~nlp~~~-t----~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..+|+|.||+.++ .    .+.++++|..|+++......+.-.  -..|.|.++++|.+|...|++..+.|+.+++.++.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR--Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK--RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT--EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce--EEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            3569999999876 3    257789999999998877776654  48999999999999999999999999999999886


Q ss_pred             c
Q 019811          131 A  131 (335)
Q Consensus       131 ~  131 (335)
                      +
T Consensus        83 ~   83 (104)
T 1wey_A           83 T   83 (104)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.08  E-value=6.4e-06  Score=56.69  Aligned_cols=68  Identities=16%  Similarity=0.113  Sum_probs=58.9

Q ss_pred             CeEEEcCCCccc-CH----HHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          263 TTVYVGNLAPEV-TQ----LDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       263 ~~l~v~nlp~~~-t~----~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ++|+|.||+.++ ..    +.++++|..|+  ........++=....|.|.+.++|.+|...||+.   .|+|++|+|
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~--~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~---~f~g~~~r~   78 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYD--KDTTFQYFKSFKRVRINFSNPLSAADARLRLHKT---EFLGKEMKL   78 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTC--SSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTS---EETTEECEE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhC--cCcceeecCcceEEEEEeCChHHHHHHHHHhccc---eecCceeEE
Confidence            789999998876 22    56789999998  4677788888778899999999999999999999   999999875

>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=98.02  E-value=3.3e-05  Score=52.13  Aligned_cols=59  Identities=15%  Similarity=0.224  Sum_probs=48.0

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN  115 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~  115 (335)
                      .+.....++| +.|..+...||.++|+.||.| .|+-+.+.   .|||.|.+++.|..|+..+.
T Consensus        12 ~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT---sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           12 QPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT---SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT---EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC---eEEEEecCHHHHHHHHHhcc
Confidence            3445566677 999999999999999999976 45555555   59999999999999998753

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.84  E-value=6.6e-05  Score=50.82  Aligned_cols=65  Identities=12%  Similarity=0.215  Sum_probs=54.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC------CCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK------SSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~------~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      ..|-|++||+.+|++++.+.+..+..+........+.      ..-|||.|.+.+++....+.++|..|.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            4689999999999999999999988776555554432      2579999999999999999999988864

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.83  E-value=0.00021  Score=48.32  Aligned_cols=54  Identities=20%  Similarity=0.264  Sum_probs=45.9

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      ..++| ++|..+...||..+|+.||.+.|..|.    .-.|||.|.+.+.|..|+..++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wid----DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID----DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEE----TTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEEEEEEc----CCeEEEEecCHHHHHHHHHhcc
Confidence            55666 999999999999999999965555543    5689999999999999998774

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.55  E-value=0.00027  Score=47.83  Aligned_cols=64  Identities=11%  Similarity=0.225  Sum_probs=52.3

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc--------cceEEEEeCCHHHHHHHHHhhcCCCcccccCc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--------KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGK  331 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~--------~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~  331 (335)
                      ..|.|++||+++|++++.+.+....  .+....+..+        ...|||.|.+.+++..-.+.++|+   .|-+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~--~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~---~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMP--EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGY---VFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCC--CEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTC---EEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcc--cceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCc---EEEcC
Confidence            4699999999999999999999887  3545544332        257999999999999999999999   66543

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.48  E-value=0.00096  Score=47.28  Aligned_cols=74  Identities=16%  Similarity=0.087  Sum_probs=59.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC-ceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG-QPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g-~~l~v~~~~  130 (335)
                      ....+.|.|-+.|... .+.|...|++||.|.+...  ....++..|.|.+..+|++||. .||..+.| -.|-|.+..
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~--~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM--SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE--CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc--CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            3446779999999985 7889999999999988765  3345799999999999999995 69998874 556666543

>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=97.39  E-value=0.00017  Score=48.93  Aligned_cols=53  Identities=15%  Similarity=0.212  Sum_probs=44.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN  115 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~  115 (335)
                      .++| +.|..+...||.++|+.||.| .|+-+.+.   .|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT---sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT---SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT---EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC---eEEEEecCHHHHHHHHHhcc
Confidence            3555 999999999999999999955 45555555   59999999999999998764

>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=97.30  E-value=0.00035  Score=47.34  Aligned_cols=54  Identities=19%  Similarity=0.265  Sum_probs=44.5

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      ..++| ++|..+...||..+|+.||+   ..|+... ...|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg---v~I~Wid-DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN---IQISWID-DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE---EEEEEEE-TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC---EEEEEEc-CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 99999999999999999985   3444433 5689999999999999998774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.23  E-value=0.0018  Score=45.90  Aligned_cols=62  Identities=16%  Similarity=0.133  Sum_probs=52.1

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGK  331 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~  331 (335)
                      +.|.|-++|+.. .+.|...|++||  .|.+........+..|+|.+..+|.+|+. .||.   .|+|.
T Consensus        25 ~wVtVFGFp~~~-~~~VL~~F~~~G--~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~---ii~g~   86 (119)
T 1wwh_A           25 TWVTVFGFPQAS-ASYILLQFAQYG--NILKHVMSNTGNWMHIRYQSKLQARKALS-KDGR---IFGES   86 (119)
T ss_dssp             GEEEEECCCGGG-HHHHHHHHHTTS--CEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTC---EETTT
T ss_pred             CEEEEECCCHHH-HHHHHHHHHhhC--cEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCe---EecCC
Confidence            678888999885 667889999999  58887776677899999999999999995 4888   77654

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.17  E-value=0.00042  Score=47.15  Aligned_cols=66  Identities=12%  Similarity=0.168  Sum_probs=49.2

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC------CCCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD------KSSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~------~~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      +..|-||.||+.+|++++.+.++.+-.+........+      .-.-|||.|.+.++.....+..+|..|.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            4569999999999999988888765443222211111      11469999999999999999999988864

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.88  E-value=0.0014  Score=47.02  Aligned_cols=72  Identities=21%  Similarity=0.187  Sum_probs=54.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCcee-EEEee------------c-----CCCCeEEEEEcCHHHHHHHHHHhCCcc
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEG-CKLIR------------K-----DKSSYGFIHYFDRRSAAMAILSLNGRH  118 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~-v~~~~------------~-----~~~g~afv~f~~~~~A~~a~~~l~~~~  118 (335)
                      ..|.|-+.|.+. ...+.+.|++||.|.+ +...+            .     ...++..|.|.+..+|.+|+. .||..
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            348899997776 6788899999999866 21111            0     023588999999999999995 69999


Q ss_pred             ccCceeEEeeec
Q 019811          119 LFGQPIKVNWAY  130 (335)
Q Consensus       119 ~~g~~l~v~~~~  130 (335)
                      |.|..|-|.+..
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999877777664

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=96.75  E-value=0.00043  Score=66.37  Aligned_cols=10  Identities=30%  Similarity=0.275  Sum_probs=4.8

Q ss_pred             CCHHHHHHHH
Q 019811           68 VTEPLLQEVF   77 (335)
Q Consensus        68 ~t~~~l~~~f   77 (335)
                      .+...+.+++
T Consensus       132 ~~~~~l~~~~  141 (727)
T 4b8c_D          132 CTKQALMEMA  141 (727)
T ss_dssp             CCCHHHHHHH
T ss_pred             cchhhhhhhh
Confidence            3444455554

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.64  E-value=0.0026  Score=43.28  Aligned_cols=68  Identities=15%  Similarity=0.183  Sum_probs=49.8

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG--RSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      +-+|.|+.||+.+||+++.+.++..-.+.....+....+.  .....|||.|.+.++...-.+.++|..+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            3579999999999999999888776444333332211111  1234589999999999999999999876

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.62  E-value=0.0014  Score=58.42  Aligned_cols=55  Identities=15%  Similarity=0.236  Sum_probs=41.7

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHH
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL  112 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~  112 (335)
                      .|+|+|. .|..+++.+|.++|++||+|.++.+..++. -||.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-eEEEEEeCCHHHHHHHHh
Confidence            4789998 799999999999999999999987765443 599999999999987653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.59  E-value=0.0067  Score=54.05  Aligned_cols=54  Identities=11%  Similarity=0.190  Sum_probs=41.6

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccc-eEEEEeCCHHHHHHHHHh
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG-FGFVRYSTHAEAALAIQM  319 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g-~afV~f~~~~~a~~A~~~  319 (335)
                      ++|+|. .|...++.+|.++|+.||  .|.++.+.+++| +|.|+|.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g--~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFG--PINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGS--CCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcC--CcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            789997 799999999999999999  588888888876 899999999998877643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.14  E-value=0.02  Score=41.14  Aligned_cols=63  Identities=17%  Similarity=0.292  Sum_probs=45.3

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEe-------------------cccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ-------------------RDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~-------------------~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      ..|.|-+.|+..+ ..|.+.|++||. .++++...                   ....+..|+|++..+|.+|+ .-||.
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~-IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~   84 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGT-ILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGA   84 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSC-BCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTC
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhce-EeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCe
Confidence            4577778866554 457789999994 22322211                   13568899999999999999 55888


Q ss_pred             CcccccCc
Q 019811          324 QSSYLFGK  331 (335)
Q Consensus       324 ~~~~~~g~  331 (335)
                         .|+|.
T Consensus        85 ---ii~G~   89 (132)
T 3p3d_A           85 ---VFNGV   89 (132)
T ss_dssp             ---EETTE
T ss_pred             ---EeCcE
Confidence               88886

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.66  E-value=0.24  Score=45.06  Aligned_cols=57  Identities=14%  Similarity=0.173  Sum_probs=46.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN  115 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~  115 (335)
                      .....++|+ +|..+...+|.+.|+.||.+ +|+.+.+.   .|||.|.+.+.|..++..++
T Consensus       438 ~R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt---~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          438 KRDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT---SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             CGGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS---EEEEECSCHHHHHHHHHHHT
T ss_pred             CcCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC---eEEEEECCHHHHHHHHHHHH
Confidence            344566776 99999999999999999966 55444443   69999999999999998875

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=89.20  E-value=1.6  Score=39.61  Aligned_cols=57  Identities=19%  Similarity=0.248  Sum_probs=45.2

Q ss_pred             CCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       262 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      ...++|+ +|..+...+|.+.|+.||.   .+|+.. +...|||.|.+.+.|..++..++..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~---v~V~wi-ddt~a~V~~~~~~~a~~~l~~~~~~  496 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN---IQISWI-DDTSAFVSLSQPEQVQIAVNTSKYA  496 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC---CEEEEC-SSSEEEEECSCHHHHHHHHHHHTTC
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC---EEEEEE-cCCeEEEEECCHHHHHHHHHHHHhC
Confidence            3556665 9999999999999999994   344443 3568999999999999999988544

---

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	335
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-23
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-17
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-05
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-19
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-17
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-17
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-17
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-17
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-16
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-16
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-16
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-16
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-16
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-16
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-15
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-15
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-15
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-15
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-15
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-15
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-14
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-14
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-13
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-14
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-14
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.002
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	7e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	7e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	6e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.004
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-11
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	4e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-11
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	8e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	7e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-04
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:) 4e-10
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:) 3e-09
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:) 8e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-10
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	9e-10
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	4e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	7e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.001
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-08
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-05
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	3e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	5e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	7e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-04

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 93.9 bits (232), Expect = 1e-23
 Identities = 30/175 (17%), Positives = 61/175 (34%), Gaps = 7/175 (4%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYG---FIHYFDRRSAA 108
           +P   R +++G +  + T+  L+  F   G +  C ++R   +          +      
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 109 MAILSLNGRHLFGQPIKVNWA---YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVY 165
            A ++     + G+ ++   A     S +         IFVG +  +  +  L   F  Y
Sbjct: 62  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121

Query: 166 PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
                  +M D+ +G+ RGF FV+F +       +       +         A  
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALS 175

>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 = 75.0 bits (183), Expect = 8e-17
 Identities = 41/196 (20%), Positives = 69/196 (35%), Gaps = 38/196 (19%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYT 263
             K  G         ++                                           
Sbjct: 69  PHKVDGRVVEPKRAVSREDSQRPGAH------------------------------LTVK 98

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQM 319
            ++VG +  +  +  L  +F   G   + E+   R     +GF FV +  H      +  
Sbjct: 99  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

Query: 320 GNTTQSSYLFGKQMKV 335
              T    + G   +V
Sbjct: 159 KYHT----VNGHNCEV 170

>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 = 51.5 bits (122), Expect = 1e-08
 Identities = 17/93 (18%), Positives = 34/93 (36%), Gaps = 5/93 (5%)

Query: 51  FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRS 106
               T + ++VG I     E  L++ F   G +E  +++    S     + F+ + D  S
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQREDTS 139
               +       + G   +V  A +  +    S
Sbjct: 152 VDKIV-IQKYHTVNGHNCEVRKALSKQEMASAS 183

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (97), Expect = 3e-05
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQ------RDKGFGFVRYSTHAEAA 314
           Q   +++G L+ E T   L  HF     G + +  V       R +GFGFV Y+T  E  
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQ--WGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 315 LAIQMGNTTQSSYLFGKQM 333
            A+          +   + 
Sbjct: 63  AAMNARPHKVDGRVVEPKR 81

>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 = 83.0 bits (205), Expect = 8e-21
 Identities = 25/78 (32%), Positives = 44/78 (56%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           +++VGDL P+VT+A L+  FS        RV  D  T RS G+ +V+F+   DA+ A++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 203 LTGKWLGSRQIRCNWATK 220
           +    +  + +R  W+ +
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.6 bits (178), Expect = 5e-17
 Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILS 113
           S+YVG++H  VTE +L E FS  GP+   ++ R   +     Y ++++     A  A+ +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 114 LNGRHLFGQPIKVNWA 129
           +N   + G+P+++ W+
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
           ++YVG+L P+VT+  L+  F   G      V  ++  +R  G+ +V +   A+A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 320 GNTTQSSYLFGKQMKV 335
            N      + GK +++
Sbjct: 62  MNFD---VIKGKPVRI 74

>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 = 78.5 bits (193), Expect = 4e-19
 Identities = 20/81 (24%), Positives = 36/81 (44%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G L   + D  +    + +       ++ D  TG S+G+ F  + +      AI  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 204 TGKWLGSRQIRCNWATKGAGN 224
            G  LG +++    A+ GA N
Sbjct: 64  NGMQLGDKKLLVQRASVGAKN 84

>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 = 61.6 bits (149), Expect = 5e-13
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +++G +   + +  ++E+ +S GP++   L++   +     Y F  Y D      AI  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 115 NGRHLFGQPIKVNWAYASGQ 134
           NG  L  + + V  A    +
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 7/75 (9%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMG 320
           +++G L   +    +     S G      +         KG+ F  Y        AI   
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 321 NTTQSSYLFGKQMKV 335
           N  Q   L  K++ V
Sbjct: 64  NGMQ---LGDKKLLV 75

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.0 bits (184), Expect = 1e-17
 Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK-TGRSRGFGFVSFRNQQDAQSAIN 201
            I V ++  +     +   FS +      R+      TG  RGFGFV F  +QDA+ A N
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 202 DLT-GKWLGSRQIRCNWATK 220
            L     L  R++   WA  
Sbjct: 70  ALCHSTHLYGRRLVLEWADS 89

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.4 bits (167), Expect = 2e-15
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 6/83 (7%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSA 107
             T   + V NI  Q  +  ++E+FS+ G ++  +L +K   +     +GF+ +  ++ A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 108 AMAILSL-NGRHLFGQPIKVNWA 129
             A  +L +  HL+G+ + + WA
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWA 87

>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 = 56.1 bits (135), Expect = 7e-11
 Identities = 17/87 (19%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-----KGFGFVRYS 308
           + P+     + + V N+  +  Q ++   F + G      +  +       +GFGFV + 
Sbjct: 1   QVPKKQTT-SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 59

Query: 309 THAEAALAIQMGNTTQSSYLFGKQMKV 335
           T  +A  A        S++L+G+++ +
Sbjct: 60  TKQDAKKAFN--ALCHSTHLYGRRLVL 84

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 1e-17
 Identities = 25/92 (27%), Positives = 45/92 (48%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G   + +    ++VG L  +V++  L+  F       +  +  D+ TG+ +G+GFV F +
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWATKGAGN 224
           ++DA  AI  +    L  + IR N A+    N
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNKN 92

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 3e-15
 Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 4/90 (4%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDR 104
           P  + +   +VYVG +  +V+EPLL E+F   GPV    + +   +     YGF+ +   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQ 134
             A  AI  ++   L+G+PI+VN A A  +
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHA 311
                Q  TVYVG L  +V++  L   F   G  V   +   R      G+GFV + +  
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
           +A  AI++ +  +   L+GK ++V
Sbjct: 63  DADYAIKIMDMIK---LYGKPIRV 83

>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 = 74.6 bits (183), Expect = 1e-17
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG+LS   T+  ++  FS         +  D+    + GF FV + ++ DA++A+  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQ 229
            G  L  R IR +W    AG  E +Q
Sbjct: 70  NGTRLDDRIIRTDWD---AGFKEGRQ 92

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.1 bits (161), Expect = 2e-14
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR----KDKSSYGFIHYFDRRSAAMAIL 112
            ++YVGN+    TE  + E+FS +G ++   +      K    + F+ Y+ R  A  A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 113 SLNGRHLFGQPIKVNWAYASGQRE 136
            +NG  L  + I+ +W   +G +E
Sbjct: 68  YINGTRLDDRIIRTDW--DAGFKE 89

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEV----RVQRDKGFGFVRYSTHAEAALAIQ 318
            T+YVGNL+   T+  ++  F   G      +      +   GF FV Y + A+A  A++
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 319 MGNTTQSSYLFGKQMKV 335
             N T+   L  + ++ 
Sbjct: 68  YINGTR---LDDRIIRT 81

>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 = 73.5 bits (180), Expect = 2e-17
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS + T   L   F  +    +  VM D  T RSRGFGFV+F +Q      +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 204 TGKWLGSRQIRCNWA 218
           +   L S+ I    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.5 bits (149), Expect = 5e-13
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAI 111
           C+ +++G +  Q T+  L+E F   G V+ C ++R   +     +GF+ + D+      +
Sbjct: 1   CK-MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59

Query: 112 LSLNGRHLFGQPIKVNWAY 130
            + +   L  + I    A+
Sbjct: 60  -AQSRHELDSKTIDPKVAF 77

>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 = 53.4 bits (128), Expect = 4e-10
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 8/75 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMG 320
           +++G L+ + TQ  L  +F   G      V         +GFGFV +   A     +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 321 NTTQSSYLFGKQMKV 335
                  L  K +  
Sbjct: 63  RHE----LDSKTIDP 73

>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 = 73.1 bits (179), Expect = 4e-17
 Identities = 27/79 (34%), Positives = 45/79 (56%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L  ++TD  L+A F      +  R+M D KTG S G+ FV F ++ D+Q AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 203 LTGKWLGSRQIRCNWATKG 221
           L G  + +++++ ++A  G
Sbjct: 64  LNGITVRNKRLKVSYARPG 82

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.9 bits (150), Expect = 4e-13
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILS 113
           ++ V  +   +T+  L  +F + GP+  C+++R  K+     Y F+ +     +  AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 114 LNGRHLFGQPIKVNWA 129
           LNG  +  + +KV++A
Sbjct: 64  LNGITVRNKRLKVSYA 79

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLG----AGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           T + V  L  ++T  +L+  F ++G      ++ + +     G+ FV +++  ++  AI+
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 319 MGNTTQSSYLFGKQMKV 335
           + N      +  K++KV
Sbjct: 63  VLNGIT---VRNKRLKV 76

>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 = 73.1 bits (179), Expect = 5e-17
 Identities = 24/90 (26%), Positives = 35/90 (38%), Gaps = 9/90 (10%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++ V  L  + T+  L   FS +      +V  D KTG S+GFGFV F   +     ++ 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSD 232
                +  R   C            KQS D
Sbjct: 70  R--HMIDGRWCDCKLP-------NSKQSQD 90

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 1e-09
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 9/77 (11%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQ 318
           + + V  L  + T+ DL  +F + G  ++ +V+         GFGFVR++ +      + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 319 MGNTTQSSYLFGKQMKV 335
             +      + G+    
Sbjct: 69  QRHM-----IDGRWCDC 80

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 13/84 (15%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
             + V  +  + TE  L+E FS+ G V   ++ +  K+     +GF+ + +  +    + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 113 SLNGRHLFGQPIKVNWAYASGQRE 136
             +   + G+        +   ++
Sbjct: 69  QRHM--IDGRWCDCKLPNSKQSQD 90

>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 = 71.9 bits (176), Expect = 1e-16
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V +L   +TD  L   F  Y S     ++ D+ TGR RG  FV +  +++AQ AI+ 
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 203 LTGKWL--GSRQIRCNWA 218
           L       GS+ +    A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 67.7 bits (165), Expect = 3e-15
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAIL 112
            ++YV N+   +T+  L  +F   G +    ++R   +       F+ Y  R  A  AI 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 113 SLNGRHLFG--QPIKVNWA 129
           +LN     G  QP+ V  A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 4/63 (6%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQ 318
           T +YV NL   +T   L   F   G+ V + +   +      G  FVRY+   EA  AI 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 319 MGN 321
             N
Sbjct: 67  ALN 69

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.7 bits (175), Expect = 2e-16
 Identities = 28/90 (31%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           A  Q+E   G  N+F+  L  E  D  L   F  + +   A+V  D++T  S+ FGFVS+
Sbjct: 9   AGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
            N   AQ+AI  + G  +G ++++      
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 97

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 3e-10
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSA 107
            P     +++ ++  +  +  L ++F   G V   K+    +      +GF+ Y +  SA
Sbjct: 15  GPEGAN-LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 73

Query: 108 AMAILSLNGRHLFGQPIKVNWAYASGQR 135
             AI S+NG  +  + +KV    +    
Sbjct: 74  QAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG----FGFVRYSTH 310
           + +  P+   +++ +L  E    DL + F   G  V  +V + +       FGFV Y   
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
             A  AIQ  N  Q   +  K++KV
Sbjct: 71  VSAQAAIQSMNGFQ---IGMKRLKV 92

>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 = 71.2 bits (174), Expect = 2e-16
 Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 2/95 (2%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG  E  S    + V ++     D  L   F  +    D  ++++++   S+GFGFV+F
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTF 58

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNN 225
            N  DA  A   L G  +  R+I  N AT     N
Sbjct: 59  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 63.2 bits (153), Expect = 2e-13
 Identities = 22/80 (27%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRSAAM 109
             ST + ++V NI  +  +P L+++F   G +   ++I  ++ S  +GF+ + +   A  
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 110 AILSLNGRHLFGQPIKVNWA 129
           A   L+G  + G+ I+VN A
Sbjct: 67  AREKLHGTVVEGRKIEVNNA 86

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 9e-07
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD--KGFGFVRYSTHAEA 313
            E+      ++V N+       DL + F   G  +  E+       KGFGFV +   A+A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
             A +  + T    + G++++V
Sbjct: 65  DRAREKLHGTV---VEGRKIEV 83

>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 = 71.2 bits (174), Expect = 2e-16
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
            P  C  VY G I + +T+ L+++ FS  G +   ++  +    Y F+ +    SAA AI
Sbjct: 15  SPKNCT-VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG--YSFVRFSTHESAAHAI 71

Query: 112 LSLNGRHLFGQPIKVNWA 129
           +S+NG  + G  +K  W 
Sbjct: 72  VSVNGTTIEGHVVKCYWG 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (168), Expect = 2e-15
 Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 130 YASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVS 189
           +     + +  +  ++ G ++  +TD  +   FS +    + RV  ++       + FV 
Sbjct: 7   FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVR 60

Query: 190 FRNQQDAQSAINDLTGKWLGSRQIRCNWA 218
           F   + A  AI  + G  +    ++C W 
Sbjct: 61  FSTHESAAHAIVSVNGTTIEGHVVKCYWG 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (150), Expect = 5e-13
 Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 5/79 (6%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
           +++P+  TVY G +A  +T   + + F   G   I E+RV  +KG+ FVR+STH  AA A
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ--IMEIRVFPEKGYSFVRFSTHESAAHA 70

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           I   N T    + G  +K 
Sbjct: 71  IVSVNGTT---IEGHVVKC 86

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.5 bits (172), Expect = 3e-16
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N++V  L   +T   L   FS Y     +R++ DQ TG SRG GF+ F  + +A+ AI  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 203 LTGKWLG--SRQIRCNWA 218
           L G+     +  I   +A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 5e-12
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
            ++YV  +   +T+  L+++FS  G +   +++    +      GFI +  R  A  AI 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 113 SLNGRHLFG--QPIKVNWA 129
            LNG+   G  +PI V +A
Sbjct: 67  GLNGQKPSGATEPITVKFA 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 = 46.6 bits (110), Expect = 1e-07
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQ 318
             +YV  L   +TQ +L + F   G  +   + V +     +G GF+R+    EA  AI+
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 319 MGNTTQSSYLFGKQMKV 335
             N  +     G    +
Sbjct: 67  GLNGQK---PSGATEPI 80

>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 = 70.5 bits (172), Expect = 5e-16
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 2/87 (2%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLI--RKDKSSYGFIHYFDRRSAAM 109
           D    R++YVGN+   VTE L+ ++FS  GP + CK+I        Y F+ +++ R AA 
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 110 AILSLNGRHLFGQPIKVNWAYASGQRE 136
           A+ ++NGR + G+ +KVNWA     ++
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 1e-14
 Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
           ED      ++VG+LS +VT+  +   FS    C   +++ +     +  + FV F   +D
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRD 60

Query: 196 AQSAINDLTGKWLGSRQIRCNWATK 220
           A +A+  + G+ +  ++++ NWAT 
Sbjct: 61  AAAALAAMNGRKILGKEVKVNWATT 85

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 9/83 (10%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG----FGFVRYSTHAE 312
           E++ Q  T+YVGNL+ +VT++ + + F  +G    +  ++  +      + FV +  H +
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGP--CKSCKMITEHTSNDPYCFVEFYEHRD 60

Query: 313 AALAIQMGNTTQSSYLFGKQMKV 335
           AA A+   N  +   + GK++KV
Sbjct: 61  AAAALAAMNGRK---ILGKEVKV 80

>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 = 69.8 bits (170), Expect = 7e-16
 Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVY-PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           IF+G+L PE+ +  L+  FS +       ++M D  TG S+G+ F++F +   + +AI  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 203 LTGKWLGSRQIRCNWATK 220
           + G++L +R I  ++A K
Sbjct: 61  MNGQYLCNRPITVSYAFK 78

>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 = 62.8 bits (152), Expect = 2e-13
 Identities = 22/82 (26%), Positives = 46/82 (56%), Gaps = 5/82 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-----YGFIHYFDRRSAAMAILS 113
           +++GN+  ++ E LL + FS+ G +     I +D  +     Y FI++    ++  AI +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 114 LNGRHLFGQPIKVNWAYASGQR 135
           +NG++L  +PI V++A+    +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 4e-08
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAG-----VIEEVRVQRDKGFGFVRYSTHAEAALAIQM 319
           +++GNL PE+ +  L+  F + G       ++ +      KG+ F+ +++   +  AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 320 GNTTQSSYLFGKQMKV 335
            N      L  + + V
Sbjct: 61  MNGQY---LCNRPITV 73

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.7 bits (170), Expect = 7e-16
 Identities = 30/82 (36%), Positives = 42/82 (51%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G R +   +  + V  LS   T+  L   FS Y   +D  +++DQ++ RSRGF FV F N
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 193 QQDAQSAINDLTGKWLGSRQIR 214
             DA+ A     G  L  R+IR
Sbjct: 61  VDDAKEAKERANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 5e-12
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYG----FIHYFDRRSA 107
           +P     + V  +    TE  L+EVFS  GP+    ++   +S       F+++ +   A
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

Query: 108 AMAILSLNGRHLFGQPIKV 126
             A    NG  L G+ I+V
Sbjct: 65  KEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 7e-09
 Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFG----FVRYSTHAE 312
            N      + V  L+   T+ DL   F   G      +   +         FV +    +
Sbjct: 4   ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 313 AALAIQMGNTTQSSYLFGKQMKV 335
           A  A +  N  +   L G++++V
Sbjct: 64  AKEAKERANGME---LDGRRIRV 83

>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 = 69.7 bits (170), Expect = 8e-16
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           SG  NIF+ +L   + +  L+  FS + +    +V+ D+    S+G+GFV F  Q+ A+ 
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 63

Query: 199 AINDLTGKWLGSRQIRCNWATK 220
           AI  + G  L  R++       
Sbjct: 64  AIEKMNGMLLNDRKVFVGRFKS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 3e-15
 Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS--YGFIHYFDRRS 106
           P    S   ++++ N+   +    L + FS+ G +  CK++  +  S  YGF+H+  + +
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 107 AAMAILSLNGRHLFGQPIKVNWAYASGQR 135
           A  AI  +NG  L  + + V    +  +R
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 7e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG--FGFVRYSTHAEAALAIQMG 320
             +++ NL   +    L+  F + G  +  +V    +    +GFV + T   A  AI+  
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 68

Query: 321 NTTQSSYLFGKQMKV 335
           N      L  +++ V
Sbjct: 69  NGML---LNDRKVFV 80

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.1 bits (171), Expect = 9e-16
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           ++ +      +F+G LS E T+ +L   +  +   +D  VM D  + RSRGFGFV+F + 
Sbjct: 13  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 72

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATK 220
            +  +A+       +  R +    A  
Sbjct: 73  AEVDAAMA-ARPHSIDGRVVEPKRAVA 98

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 17/102 (16%), Positives = 40/102 (39%), Gaps = 7/102 (6%)

Query: 38  QIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS-- 95
            +E +P        +    R +++G +  + TE  L+  +   G +  C ++R   S   
Sbjct: 4   TLETVPLERKKR--EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 61

Query: 96  --YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
             +GF+ +        A+ +     + G+ ++   A A  + 
Sbjct: 62  RGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAREES 102

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 2e-11
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 245 EDGKETTNTEAPENNP-QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----D 299
           E   ET   E  +    Q+  +++G L+ E T+  L  ++   G      V         
Sbjct: 2   EKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 61

Query: 300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           +GFGFV +S+ AE   A+     +    + G+ ++ 
Sbjct: 62  RGFGFVTFSSMAEVDAAMAARPHS----IDGRVVEP 93

>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 = 70.0 bits (171), Expect = 1e-15
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPV-EGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
           P   R +Y+ N+  ++T   + ++F   GP+ +       +     ++ Y D   A  A 
Sbjct: 4   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAC 63

Query: 112 LSLNGRHLFGQPIKVNWA 129
             L+G ++  + + V + 
Sbjct: 64  DHLSGFNVCNRYLVVLYY 81

>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 = 68.1 bits (166), Expect = 6e-15
 Identities = 15/96 (15%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++ +L  ++T   ++  F  Y        +    T  +RG  +V + +  DA++A + L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVEL 239
           +G  + +R +   +        +       + +  L
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 102

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGV-IEEVRVQRDKGFGFVRYSTHAEA 313
            PE N     +Y+ NL  ++T  +++  F   G    I        +G  +V Y    +A
Sbjct: 3   PPEVN---RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA 59

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
             A    +      +  + + V
Sbjct: 60  KNACDHLSGFN---VCNRYLVV 78

>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 = 69.0 bits (168), Expect = 1e-15
 Identities = 23/76 (30%), Positives = 42/76 (55%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           N+ V  L   +T     + F         +++ D+ TG+S G+GFV++ + +DA+ AIN 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 203 LTGKWLGSRQIRCNWA 218
           L G  L ++ I+ ++A
Sbjct: 64  LNGLRLQTKTIKVSYA 79

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 4e-12
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 4/77 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAIL 112
            ++ V  +   +T+   + +F S G +E CKL+R   +     YGF++Y D + A  AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 113 SLNGRHLFGQPIKVNWA 129
           +LNG  L  + IKV++A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG----FGFVRYSTHAEAALAIQ 318
           T + V  L   +TQ +    F S+G     ++   +  G    +GFV Y    +A  AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 319 MGNTTQSSYLFGKQMKV 335
             N  +   L  K +KV
Sbjct: 63  TLNGLR---LQTKTIKV 76

>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 = 69.1 bits (169), Expect = 1e-15
 Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 9/91 (9%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTD-ATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVS 189
           +SG+ +  S +  +F+G+L+  V   + + A FS Y       V         +GF FV 
Sbjct: 5   SSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQ 56

Query: 190 FRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           + N+++A++A+    G+ +  + +  N A +
Sbjct: 57  YVNERNARAAVAGEDGRMIAGQVLDINLAAE 87

>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 = 68.4 bits (167), Expect = 3e-15
 Identities = 27/99 (27%), Positives = 50/99 (50%), Gaps = 10/99 (10%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYF 102
           SG   P    S    V++GN++T  V +  ++ +FS  G + GC + +     + F+ Y 
Sbjct: 6   SGKTDPRSMNSR---VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK----GFAFVQYV 58

Query: 103 DRRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGH 141
           + R+A  A+   +GR + GQ + +N   A+  + + SG 
Sbjct: 59  NERNARAAVAGEDGRMIAGQVLDINL--AAEPKVNRSGP 95

>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 = 51.8 bits (124), Expect = 2e-09
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 256 PENNPQYTTVYVGNLAPEVT-QLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
            +     + V++GNL   V  + D+   F     G I    V +  GF FV+Y     A 
Sbjct: 9   TDPRSMNSRVFIGNLNTLVVKKSDVEAIFSK--YGKIVGCSVHK--GFAFVQYVNERNAR 64

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A+   +      + G+ + +
Sbjct: 65  AAVAGEDGRM---IAGQVLDI 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.5 bits (167), Expect = 2e-15
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS E TD +L + F  + + +D  VM D  T RSRGFGFV++   ++  +A+N  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-A 67

Query: 204 TGKWLGSRQIRCNWA 218
               +  R +    A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSA 107
           +P   R +++G +  + T+  L+  F   G +  C ++R   +     +GF+ Y      
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
             A+ +     + G+ ++   A
Sbjct: 62  DAAM-NARPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG----FGFVRYSTHAEAALA 316
           Q   +++G L+ E T   L  HF   G      V    +      FGFV Y+T  E   A
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           +          + G+ ++ 
Sbjct: 65  MNARPHK----VDGRVVEP 79

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.4 bits (167), Expect = 2e-15
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V +L   V+DA +   F+ + +   A V +D+ +GRS G   V F  + DA  A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 204 TGKWLGSRQIRCNWAT 219
            G  L  R +     T
Sbjct: 62  NGVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.8 bits (155), Expect = 6e-14
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLN 115
           + V N+   V++  +QE+F+  G ++   +             +H+  +  A  A+   N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 116 GRHLFGQPIKVNWA 129
           G  L G+P+ +   
Sbjct: 63  GVPLDGRPMNIQLV 76

>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 = 48.0 bits (114), Expect = 4e-08
 Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 6/74 (8%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGV---IEEVRVQRDKGFGFVRYSTHAEAALAIQMGN 321
           + V NL   V+  D+   F   G      +   R  R  G   V +   A+A  A++  N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 322 TTQSSYLFGKQMKV 335
                 L G+ M +
Sbjct: 63  GVP---LDGRPMNI 73

>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 = 68.1 bits (166), Expect = 2e-15
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG LSP+  +  +   F  +       +  D KT + RGF F++F+ ++  +  + + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 204 TGKWLGSRQIRCNWA 218
               +G  +     A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 1e-09
 Identities = 10/75 (13%), Positives = 28/75 (37%), Gaps = 8/75 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMG 320
           ++VG L+P+  +  +  +F   G     E+ +       +GF F+ +         ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 321 NTTQSSYLFGKQMKV 335
                  +   + ++
Sbjct: 62  YHN----VGLSKCEI 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 = 51.9 bits (124), Expect = 1e-09
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS----SYGFIHYFDRRSAAMAILSL 114
           ++VG +     E  ++E F   G VE  +L   +K+     + FI + +       +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 115 NGRHLFGQPIKVNWA 129
              ++     ++  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 69.0 bits (168), Expect = 2e-15
 Identities = 33/90 (36%), Positives = 49/90 (54%), Gaps = 2/90 (2%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G ++DT+    IFVG L    TDA+L   F  +    +A V+ D++TG+SRG+GFV+  +
Sbjct: 3   GSQKDTTFT-KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
           +  A+ A  D      G R+   N A  GA
Sbjct: 62  RAAAERACKDPNPIIDG-RKANVNLAYLGA 90

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTH 310
             + +  +T ++VG L    T   L ++F   G      V   R      G+GFV  +  
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
           A A  A +  N      + G++  V
Sbjct: 63  AAAERACKDPNPI----IDGRKANV 83

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAM 109
           +T   ++VG +    T+  L++ F   G +E   +I   ++     YGF+   DR +A  
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 110 AILSLNGRHLFGQPIKVNWAYASGQ-REDTSG 140
           A    N   + G+   VN AY   + R   +G
Sbjct: 68  ACKDPNP-IIDGRKANVNLAYLGAKPRSLQTG 98

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.1 bits (166), Expect = 2e-15
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ---KTGRSRGFGFVSFRNQQDAQSAI 200
           +F+ +L+   T+ TL   FS   +     +   +       S GFGFV ++  + AQ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 201 NDLTGKWLGSRQIRCNWATKG 221
             L G  +   ++    + + 
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.6 bits (149), Expect = 6e-13
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 60  YVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS-------SYGFIHYFDRRSAAMAIL 112
           ++ N++   TE  L+ VFS  G ++ C + +K           +GF+ Y     A  A+ 
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 113 SLNGRHLFGQPIKVNWA 129
            L G  + G  ++V  +
Sbjct: 62  QLQGHTVDGHKLEVRIS 78

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.3 bits (112), Expect = 6e-08
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 10/77 (12%)

Query: 266 YVGNLAPEVTQLDLHRHFHSLGA-------GVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           ++ NL    T+  L   F  +GA           +  V    GFGFV Y    +A  A++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 319 MGNTTQSSYLFGKQMKV 335
                    + G +++V
Sbjct: 62  QLQGHT---VDGHKLEV 75

>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 = 67.8 bits (165), Expect = 3e-15
 Identities = 18/86 (20%), Positives = 36/86 (41%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G      G   I V ++   V+   +   F  Y     +  +   + G   G   V+F +
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 193 QQDAQSAINDLTGKWLGSRQIRCNWA 218
           + +A +A+ DL  + +GSR+++    
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 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 = 53.5 bits (128), Expect = 4e-10
 Identities = 13/82 (15%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSA 107
            P     + V N+   V+   + + F     + G   ++ ++         + +  R  A
Sbjct: 6   KPGPTI-IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
             A++ LN R +  + +K+   
Sbjct: 65  TAAVIDLNDRPIGSRKVKLVLG 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 = 44.7 bits (105), Expect = 7e-07
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 7/85 (8%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTH 310
           A    P  T + V N+   V+  ++   F+              +     G   V + + 
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            EA  A+   N      +  +++K+
Sbjct: 62  DEATAAVIDLNDR---PIGSRKVKL 83

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.3 bits (164), Expect = 3e-15
 Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+G LS + T   L   FS +    D  +  D  TGRSRGFGFV F+  +     + D 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 204 TGKWLGSRQIRCNWA 218
               L  + I    A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAILSL 114
           +++G +    T+  L++ FS  G V  C L     +     +GF+ + +  S    +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 115 NGRHLFGQPIKVNWA 129
               L G+ I    A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 9e-09
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQMG 320
           +++G L+ + T+ DL  +F   G  V   +++       +GFGFV +         +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 321 NTTQSSYLFGKQMKV 335
                  L GK +  
Sbjct: 62  EHK----LNGKVIDP 72

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.4 bits (164), Expect = 6e-15
 Identities = 28/75 (37%), Positives = 42/75 (56%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           ++VG L+ EV D  L A F  +   +D ++  D +T + RGF FV F   +DA +AI+++
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 204 TGKWLGSRQIRCNWA 218
               L  R IR N A
Sbjct: 68  NESELFGRTIRVNLA 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 2e-14
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 4/87 (4%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAM 109
           +T R +YVG +  +V + +L   F   G +   ++    ++       F+ +     AA 
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 110 AILSLNGRHLFGQPIKVNWAYASGQRE 136
           AI ++N   LFG+ I+VN A     +E
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRIKE 89

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 2e-06
 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 11/78 (14%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKG------FGFVRYSTHAEAALAI 317
            +YVG LA EV    LH  F     G I ++++  D        F FV +    +AA AI
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIP--FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 318 QMGNTTQSSYLFGKQMKV 335
              N ++   LFG+ ++V
Sbjct: 65  DNMNESE---LFGRTIRV 79

>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 = 66.7 bits (162), Expect = 9e-15
 Identities = 35/81 (43%), Positives = 50/81 (61%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +FVG LS +  + +L   FS Y   S+  V+ D++T RSRGFGFV+F N  DA+ A+  +
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 204 TGKWLGSRQIRCNWATKGAGN 224
            GK +  RQIR + A K + N
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDN 88

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 8e-10
 Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAAMAIL 112
             ++VG +     E  L++VFS  G +    +++  ++     +GF+ + +   A  A++
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 113 SLNGRHLFGQPIKVNWA 129
           ++NG+ + G+ I+V+ A
Sbjct: 66  AMNGKSVDGRQIRVDQA 82

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAALAIQM 319
            ++VG L+ +  +  L + F   G      V   R     +GFGFV +    +A  A+  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 320 GNTTQSSYLFGKQMKV 335
            N      + G+Q++V
Sbjct: 67  MNGKS---VDGRQIRV 79

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 9e-15
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +R D +    I V +LS +  +  L   F  + S S   +  D+ TG+S+GF F+SF  +
Sbjct: 3   RRADDNA--TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWA 218
           +DA  AI  ++G       +   WA
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 4e-12
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAIL 112
            ++ V N+     E  LQE+F   G +    L +   +       FI +  R  AA AI 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 113 SLNGRHLFGQPIKVNWA 129
            ++G       + V WA
Sbjct: 69  GVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 4e-06
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQ 318
            T+ V NL+ +  + DL   F   G+     +   +      GF F+ +    +AA AI 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 319 MGNTTQSSYLFGKQMKV 335
             +           + V
Sbjct: 69  GVSGFG---YDHLILNV 82

>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 = 66.6 bits (162), Expect = 1e-14
 Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILS 113
           S+ + +YV N+    +E ++++ F++  P    ++ +     Y F+H+ +R  A  A+ +
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKA 63

Query: 114 LNGRHLFGQPIKVNWA 129
           LNG+ L G PI+V  A
Sbjct: 64  LNGKVLDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 3e-13
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
           +  S    ++V +L    ++  +   F+             ++  + R + FV F N++D
Sbjct: 3   DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNRED 56

Query: 196 AQSAINDLTGKWLGSRQIRCNWA 218
           A  A+  L GK L    I    A
Sbjct: 57  AVEAMKALNGKVLDGSPIEVTLA 79

>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 = 51.9 bits (124), Expect = 2e-09
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAAL 315
            +       +YV NL    ++  + + F++         RV++ + + FV +S   +A  
Sbjct: 2   EDTMSSVKILYVRNLMLSTSEEMIEKEFNN--IKPGAVERVKKIRDYAFVHFSNREDAVE 59

Query: 316 AIQMGNTTQSSYLFGKQMKV 335
           A++  N      L G  ++V
Sbjct: 60  AMKALNGKV---LDGSPIEV 76

>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 = 66.5 bits (162), Expect = 1e-14
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
           +  +    +FVG+L P++T+  +   F  Y    +  +  D+       FGF+    +  
Sbjct: 3   KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTL 56

Query: 196 AQSAINDLTGKWLGSRQIRCNWATKGAG 223
           A+ A  +L    L  +Q+R  +A   A 
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFACHSAS 84

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.3 bits (151), Expect = 3e-13
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILS 113
           +    ++VGN+   +TE  ++++F   G              +GFI    R  A +A + 
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV--FIHKDKGFGFIRLETRTLAEIAKVE 63

Query: 114 LNGRHLFGQPIKVNWA 129
           L+   L G+ ++V +A
Sbjct: 64  LDNMPLRGKQLRVRFA 79

>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 = 51.1 bits (122), Expect = 3e-09
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMG 320
           Q + ++VGNL P++T+ ++ + F   G      V + +DKGFGF+R  T   A +A    
Sbjct: 7   QRSRLFVGNLPPDITEEEMRKLFEKYGKAGE--VFIHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 321 NTTQSSYLFGKQMKV 335
           +      L GKQ++V
Sbjct: 65  DNMP---LRGKQLRV 76

>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 = 66.6 bits (162), Expect = 1e-14
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +   +LS  +T+  L   F               + G+S+G  ++ F+++ DA+  + +
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 203 LTGKWLGSRQIRCNWATKGAGN 224
             G  +  R +   +  +  G 
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGT 94

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 7/90 (7%)

Query: 52  DPST------CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRR 105
           DP T       R++   N+   +TE  L+EVF     +              +I +    
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGIAYIEFKSEA 64

Query: 106 SAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
            A   +    G  + G+ + + +    G  
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 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 = 43.5 bits (102), Expect = 2e-06
 Identities = 11/80 (13%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAAL 315
            +      T+   NL+  +T+ +L   F      +    +  + KG  ++ + + A+A  
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDAL-EIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 316 AIQMGNTTQSSYLFGKQMKV 335
            ++     +   + G+ + +
Sbjct: 69  NLEEKQGAE---IDGRSVSL 85

>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 = 66.7 bits (162), Expect = 1e-14
 Identities = 27/95 (28%), Positives = 50/95 (52%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++FVG++  E T+  L   FS        R+++D++TG+ +G+GF  +++Q+ A SA+ +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 203 LTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVV 237
           L G+    R +R + A       E K       V+
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.1 bits (150), Expect = 6e-13
 Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 5/99 (5%)

Query: 49  PGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDR 104
           P  D S  RSV+VGNI  + TE  L+++FS  GPV   +L+   ++      GF  Y D+
Sbjct: 2   PAVDRSL-RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 105 RSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSGHFN 143
            +A  A+ +LNGR   G+ ++V+ A +   +E+      
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 42.8 bits (100), Expect = 4e-06
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAG----VIEEVRVQRDKGFGFVRYSTHA 311
           P  +    +V+VGN+  E T+  L   F  +G      ++ +    + KG+GF  Y    
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
            A  A++  N  +     G+ ++V
Sbjct: 62  TALSAMRNLNGRE---FSGRALRV 82

>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 = 66.3 bits (161), Expect = 2e-14
 Identities = 25/94 (26%), Positives = 42/94 (44%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   +FV +LS   ++  L   FS Y   S+     D  T + +GF FV+F   + A 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 198 SAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSS 231
            A  ++ G+    R +    +T     ++   SS
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 57.0 bits (137), Expect = 4e-11
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS----YGFIHYFDRRSAA 108
            S    ++V N+    +E  L+++FS+ GP+          +     + F+ +     A 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 109 MAILSLNGRHLFGQPIKVNWA 129
            A   ++G+   G+ + V  +
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPS 85

>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 = 42.4 bits (99), Expect = 5e-06
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQ 318
             ++V NL+   ++ DL + F + G        +       KGF FV +     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 319 MGNTTQSSYLFGKQMKV 335
             +        G+ + V
Sbjct: 69  EVDGQV---FQGRMLHV 82

>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 = 65.9 bits (160), Expect = 2e-14
 Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 1/100 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG R   S  +  F+G+L  +VT+ ++   F      +           R +GFG+  F
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQS 230
            +     SA++ L  + LG+++IR + A +    +    S
Sbjct: 65  EDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 6/97 (6%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS--SYGFIH 100
            SG+  P   P T    ++GN+   VTE  ++E F                     GF +
Sbjct: 5   SSGSRLPKSPPYT---AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 101 Y-FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQRE 136
             F+   + ++ LSLN   L  + I+V+ A  +  ++
Sbjct: 62  AEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 17/100 (17%)

Query: 240 TNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD 299
           ++GSS        +  P++ P   T ++GNL  +VT+  +   F  L    +   R   +
Sbjct: 2   SSGSS-------GSRLPKSPP--YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSN 52

Query: 300 KG----FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
                 FG+  +        A+ +   +    L  K+++V
Sbjct: 53  PERLKGFGYAEFEDLDSLLSALSLNEES----LGNKRIRV 88

>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 = 65.5 bits (159), Expect = 2e-14
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 144 IFVGDLSPEVTDATL----FACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSA 199
           I++ +L+ ++    L     A FS +    D  V       + RG  FV F+    A +A
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSATNA 62

Query: 200 INDLTGKWLGSRQIRCNWATK 220
           +  + G     + +R  +A  
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKT 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 16/79 (20%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 56  CRSVYVGNIHTQVTEPLLQ----EVFSSTGPVEGCKLIRKDKSS-YGFIHYFDRRSAAMA 110
             ++Y+ N++ ++ +  L+     +FS  G +    + R  K     F+ + +  SA  A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 111 ILSLNGRHLFGQPIKVNWA 129
           + S+ G   + +P+++ +A
Sbjct: 63  LRSMQGFPFYDKPMRIQYA 81

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 13/78 (16%), Positives = 34/78 (43%), Gaps = 8/78 (10%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR-----VQRDKGFGFVRYSTHAEAALAI 317
            T+Y+ NL  ++ + +L +  H++ +   + +        + +G  FV +   + A  A+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 318 QMGNTTQSSYLFGKQMKV 335
           +          + K M++
Sbjct: 64  RSMQGFP---FYDKPMRI 78

>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 = 64.4 bits (156), Expect = 6e-14
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           + +FV  +  E  +  +   F  Y    +  +  D++TG S+G+  V +   + A +A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 202 DLTGKWLGSRQIRCNWA-TKG 221
            L G  +  + I+ +W   KG
Sbjct: 68  ALNGAEIMGQTIQVDWCFVKG 88

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 62.4 bits (151), Expect = 3e-13
 Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAIL 112
             ++V +IH +  E  +QE F   G ++   L           Y  + Y   + A  A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 113 SLNGRHLFGQPIKVNWAYASG 133
           +LNG  + GQ I+V+W +  G
Sbjct: 68  ALNGAEIMGQTIQVDWCFVKG 88

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHA 311
           P+ + +   ++V ++  E  + ++   F   G      + + R     KG+  V Y TH 
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
           +A  A +  N  +   + G+ ++V
Sbjct: 61  QALAAKEALNGAE---IMGQTIQV 81

>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 = 64.0 bits (155), Expect = 6e-14
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG LS   T   +   F  +    DA +M+D+ T R RGFGFV+F ++   +     +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 204 TGKWLGSRQIRCNWA 218
               + ++ + C  A
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.8 bits (139), Expect = 1e-11
 Identities = 9/74 (12%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHY---FDRRSAAMAILSLN 115
           ++VG +    T   ++  F   G V+   L+    ++         F+       +  ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 116 GRHLFGQPIKVNWA 129
              +  + ++   A
Sbjct: 62  FHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.6 bits (115), Expect = 2e-08
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 8/75 (10%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQMG 320
           ++VG L+   T  D+  +F   G      +   +      GFGFV + +        ++ 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 321 NTTQSSYLFGKQMKV 335
                  +  K ++ 
Sbjct: 62  FHE----INNKMVEC 72

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 20/79 (25%), Positives = 35/79 (44%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            S    + V N+   VT  +L ++FS  G V       K+      + Y D  SA  A L
Sbjct: 4   QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKL 63

Query: 113 SLNGRHLFGQPIKVNWAYA 131
           SL+G++++     +   ++
Sbjct: 64  SLDGQNIYNACCTLRIDFS 82

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 17/94 (18%), Positives = 34/94 (36%), Gaps = 8/94 (8%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            I V +L   VT   L   FS + +              ++    + + +   AQ A   
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLS 64

Query: 203 LTGKWL--GSRQIRCNWATKGAGN--NEDKQSSD 232
           L G+ +      +R +++   + N    + +S D
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRD 98

>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 = 50.8 bits (121), Expect = 6e-09
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
             + V NL   VT   LH+ F   G  +      + ++    ++Y+    A  A    + 
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDG 67

Query: 323 TQSSYLFGKQMKV 335
               Y     +++
Sbjct: 68  QN-IYNACCTLRI 79

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 64.5 bits (156), Expect = 2e-13
 Identities = 34/139 (24%), Positives = 56/139 (40%), Gaps = 10/139 (7%)

Query: 18  MQQALLQQQSLYHPGLLAAPQIEPIPSGNLPPGF---DPSTCRSVYVGNIHTQVTEPLLQ 74
           M Q  L  Q   +       Q++     ++PP     +P   R++ V  I T V E  L+
Sbjct: 1   MSQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLR 60

Query: 75  EVFS----STGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY 130
           ++F            C    +    YGF+ +    SA  AI  LNG ++  + +KV  A 
Sbjct: 61  QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

Query: 131 ASGQREDTSGHF---NIFV 146
           +  QR   +G     N ++
Sbjct: 121 SGHQRPGIAGAVGDGNGYL 139

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 58.8 bits (141), Expect = 2e-11
 Identities = 23/89 (25%), Positives = 42/89 (47%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
              +     N+ V  +   V +  L   F  Y      +++ D++T +SRG+GFV F++ 
Sbjct: 35  MNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSG 94

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATKGA 222
             AQ AI  L G  + +++++   A  G 
Sbjct: 95  SSAQQAIAGLNGFNILNKRLKVALAASGH 123

>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 = 35.7 bits (81), Expect = 0.002
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQR----DKGFGFVRYSTHAEAAL 315
                + V  +   V ++ L + F   G     ++   R     +G+GFV++ + + A  
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 316 AIQMGNTTQSSYLFGKQMKV 335
           AI   N      +  K++KV
Sbjct: 100 AIAGLNGFN---ILNKRLKV 116

>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 = 63.5 bits (154), Expect = 2e-13
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +F   L+  +    L   FS      D R++ D+ + RS+G  +V F   Q    AI  
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 78

Query: 203 LTGKWLGSRQIRCNWAT 219
           LTG+ L    I    + 
Sbjct: 79  LTGQRLLGVPIIVQASQ 95

>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 = 61.6 bits (149), Expect = 1e-12
 Identities = 23/96 (23%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHY- 101
           P  NL P  +    R+V+   +  ++    L++ FS+ G V   ++I    S        
Sbjct: 7   PVDNLSP--EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 102 --FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
             F    +    + L G+ L G PI V  + A   R
Sbjct: 65  VEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 13/94 (13%)

Query: 248 KETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KG 301
           +E  +  +PE      TV+   LA  +   DL   F +   G + +VR+  D      KG
Sbjct: 5   REPVDNLSPEERDA-RTVFCMQLAARIRPRDLEDFFSA--VGKVRDVRIISDRNSRRSKG 61

Query: 302 FGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
             +V +       LAI +        L G  + V
Sbjct: 62  IAYVEFCEIQSVPLAIGLTGQR----LLGVPIIV 91

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 3e-13
 Identities = 17/91 (18%), Positives = 29/91 (31%), Gaps = 4/91 (4%)

Query: 144 IFVGDLSPEVTDATLFACFSVY--PSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIN 201
           +F+G +        +    +                   ++RGF FV + + + A  A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 202 DLTGK--WLGSRQIRCNWATKGAGNNEDKQS 230
            L      L   QI  +WA      +ED   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVME 94

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 3e-10
 Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPV-EGCKLIRKDKSS-----YGFIHYFDRRSAAM 109
           CR +++G I        + E  +          +            + F+ Y   R+AAM
Sbjct: 2   CR-LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 110 AILSLNGR--HLFGQPIKVNWA 129
           A   L      L+G  I V+WA
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDWA 82

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTHAEAALA 316
             +++G +     + ++      +  GV++ +           +GF FV Y +H  AA+A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 317 IQMGNTTQSSYLFGKQMKV 335
            +     +   L+G Q+ V
Sbjct: 62  RRKLMPGRIQ-LWGHQIAV 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 7e-13
 Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           +Y+GN+   VT   L+++F         +++   KS Y F+ Y D+  A  AI +L+G+ 
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 119 -LFGQPIKVNWAYASGQR 135
            L G+ ++V+++ +   R
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 4e-10
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++G+LSP VT   L   F         ++    +     G+ FV + +Q  A  AI  L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 204 TGKW-LGSRQIRCNWAT 219
           +GK  L  + +  +++ 
Sbjct: 58  SGKVELHGKIMEVDYSV 74

>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 = 47.0 bits (111), Expect = 7e-08
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT 323
            +Y+GNL+P VT  DL + F      +    +V    G+ FV Y     A  AI+  +  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGD--RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS-- 58

Query: 324 QSSYLFGKQMKV 335
               L GK M+V
Sbjct: 59  GKVELHGKIMEV 70

>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 = 60.9 bits (147), Expect = 1e-12
 Identities = 10/80 (12%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARV-----MWDQKTGRSRGFGFVSFRNQQDAQS 198
           ++VG++   +T+  +   F+               +   +  + + F F+ FR+  +   
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 199 AINDLTGKWLGSRQIRCNWA 218
           A+    G     + ++    
Sbjct: 64  AMA-FDGIIFQGQSLKIRRP 82

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 4e-11
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---------KSSYGFIHYFDRRSA 107
           R +YVGNI   +TE  + + F++   + G      +           ++ F+ +      
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 108 AMAILSLNGRHLFGQPIKVNWA 129
             A+ + +G    GQ +K+   
Sbjct: 62  TQAM-AFDGIIFQGQSLKIRRP 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 = 47.1 bits (111), Expect = 1e-07
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGA---------GVIEEVRVQRDKGFGFVRYSTHAEAA 314
            +YVGN+   +T+  +   F++              +  V++ +DK F F+ + +  E  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A+            G+ +K+
Sbjct: 63  QAMAFDGII----FQGQSLKI 79

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.6 bits (146), Expect = 2e-12
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 8/93 (8%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVY--------PSCSDARVMWDQKTGRSRGFGF 187
           ++ S +  I+V  L+  VT   L   F                  +  D++TG+ +G   
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 188 VSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK 220
           VS+ +   A++A+    GK     +++ + A K
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.8 bits (144), Expect = 4e-12
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 12/90 (13%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR-------KDKSS-----YGFI 99
           + S   ++YV  ++  VT   L + F   G V+  K           DK +        +
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            Y D  +A  A+   +G+   G  +KV+ A
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 93

>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 = 46.7 bits (110), Expect = 2e-07
 Identities = 19/92 (20%), Positives = 30/92 (32%), Gaps = 15/92 (16%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLG------AGVIEEVRVQRDKG------FG 303
           P+ +   + +YV  L   VT  DL   F   G            + +  DK         
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 304 FVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            V Y     A  A++  +        G ++KV
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKD---FQGSKLKV 90

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 48  PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRS 106
           P G   + CR +YVGN+   +    +++VF   G +    L  +     + F+ + D R 
Sbjct: 9   PAG--NNDCR-IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRD 65

Query: 107 AAMAILSLNGRHLFGQPIKVNWA 129
           A  A+   +G    G  ++V + 
Sbjct: 66  AEDAVYGRDGYDYDGYRLRVEFP 88

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           I+VG+L P++    +   F  Y +  D  +   +       F FV F + +DA+ A+   
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAVYGR 73

Query: 204 TGKWLGSRQIRCNWATKGAGN 224
            G      ++R  +   G G 
Sbjct: 74  DGYDYDGYRLRVEFPRSGRGT 94

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGV-IEEVRVQRDKGFGFVRYSTHAEA 313
            P  N     +YVGNL P++   D+   F+  GA   I+    +    F FV +    +A
Sbjct: 8   GPAGNND-CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 66

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
             A+   +        G +++V
Sbjct: 67  EDAVYGRDGYD---YDGYRLRV 85

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 3e-12
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 7/83 (8%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   +FVG  + ++T+  L   FS Y    D  +         R F FV+F + Q AQ
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQ 56

Query: 198 SAINDLTGKWLGSRQIRCNWATK 220
           S   +     +    +  + A  
Sbjct: 57  SLCGE--DLIIKGISVHISNAEP 77

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            S    V+VG     +TE  L+E FS  G V     I K   ++ F+ + D + A     
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF-IPKPFRAFAFVTFADDQIAQSLC- 59

Query: 113 SLNGRHLFGQPIKVNWA 129
                 + G  + ++ A
Sbjct: 60  -GEDLIIKGISVHISNA 75

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 12/77 (15%), Positives = 28/77 (36%), Gaps = 6/77 (7%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
           +   + V+VG    ++T+ +L   F   G  + +    +  + F FV ++    A     
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVM-DVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 319 MGNTTQSSYLFGKQMKV 335
                    + G  + +
Sbjct: 61  EDLI-----IKGISVHI 72

>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 = 59.3 bits (143), Expect = 3e-12
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           IFVG +  +  +  L   F  Y       +M D+ +G+ RGF FV+F +  D+   I   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 63

Query: 204 TGKWLGSRQIRCNWA 218
               +         A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 55  TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHY----FDRRSAAMA 110
           T + ++VG I     E  L++ F   G +E  + I  D+ S     +    FD   +   
Sbjct: 1   TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE-IMTDRGSGKKRGFAFVTFDDHDSVDK 59

Query: 111 ILSLNGRHLFGQPIKVNWA 129
           I+      + G   +V  A
Sbjct: 60  IVIQKYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 8/76 (10%)

Query: 264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQM 319
            ++VG +  +  +  L  +F   G   + E+   R      GF FV +  H      +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 320 GNTTQSSYLFGKQMKV 335
              T    + G   +V
Sbjct: 64  KYHT----VNGHNCEV 75

>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 = 57.9 bits (139), Expect = 1e-11
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
            D +    +F+ +LS +  +  L      +      RV+    T  S+G  F  F  Q+ 
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 196 AQSAINDL------TGKWLGSRQIRCNWATK 220
           AQ  +          G  L  RQ++ + A  
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.9 bits (113), Expect = 5e-08
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 12/93 (12%)

Query: 47  LPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYF 102
           LP   D +  ++V++ N+     E  L EV    G ++  +++            F  + 
Sbjct: 1   LPS--DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFM 58

Query: 103 DRRSAAMAILSLN------GRHLFGQPIKVNWA 129
            + +A   + + +      G  L G+ +KV+ A
Sbjct: 59  TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 91

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (106), Expect = 5e-07
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 11/89 (12%)

Query: 256 PENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK------GFGFVRYST 309
           P +  +  TV++ NL+ +  +  L         G ++ VRV          G  F ++ T
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQ--FGDLKYVRVVLHPDTEHSKGCAFAQFMT 59

Query: 310 HAEAALAIQMGNTTQSS---YLFGKQMKV 335
              A   +   +         L G+Q+KV
Sbjct: 60  QEAAQKCLAAASLEAEGGGLKLDGRQLKV 88

>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 = 57.1 bits (137), Expect = 2e-11
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 3/85 (3%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACF--SVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQD 195
           T     I + +LS E+ D  L                    ++   +    F+ F N+  
Sbjct: 1   TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 196 AQSAINDLTGKWLGSRQIRCNWATK 220
           A+ A+  +    LG+R+I  + A K
Sbjct: 61  AERAL-QMNRSLLGNREISVSLADK 84

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.3 bits (122), Expect = 3e-09
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 57  RSVYVGNIHTQVT-EPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHY----FDRRSAAMAI 111
           R + + N+ T++  E LL+E F   G +E   +    K            F+ + +A   
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 112 LSLNGRHLFGQPIKVNWA 129
           L +N   L  + I V+ A
Sbjct: 65  LQMNRSLLGNREISVSLA 82

>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 = 41.7 bits (97), Expect = 6e-06
 Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 10/81 (12%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHF------HSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
           +   + + NL+ E+   +L R                 +     +    F+ +     A 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A+QM  +     L  +++ V
Sbjct: 63  RALQMNRSL----LGNREISV 79

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 4e-11
 Identities = 19/77 (24%), Positives = 39/77 (50%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            +++ +LSP VT+  L + F+ +       + +   TGR RG  F++F N++ A  A++ 
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 203 LTGKWLGSRQIRCNWAT 219
           + G  L  + +   +  
Sbjct: 80  VNGYKLYGKILVIEFGK 96

>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 = 55.2 bits (132), Expect = 1e-10
 Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 8/103 (7%)

Query: 38  QIEPIP-SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY 96
           +I  IP   +  PG +P+  + +Y+ N+  +VTE  L  +F+     +G  +  +  +  
Sbjct: 2   EIRKIPMFSSYNPG-EPN--KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR 58

Query: 97  G----FIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
                FI + ++  A  A+  +NG  L+G+ + + +     QR
Sbjct: 59  MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 101

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.004
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSL----GAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
             +Y+ NL+P VT+ DL   F       G  +   +   R +G  F+ +     A  A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 319 MGNTTQSSYLFGKQMKV 335
           + N  +   L+GK + +
Sbjct: 79  LVNGYK---LYGKILVI 92

>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 = 56.3 bits (135), Expect = 4e-11
 Identities = 9/75 (12%), Positives = 28/75 (37%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++ +  P  T   +          + +  +   +   SR F ++   +++DA+  +  L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 204 TGKWLGSRQIRCNWA 218
            G  +    +    +
Sbjct: 64  NGLKIEGYTLVTKVS 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 = 52.5 bits (125), Expect = 9e-10
 Identities = 9/77 (11%), Positives = 26/77 (33%), Gaps = 4/77 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAIL 112
            ++++ N     T+  ++++      V     +          + +I    +  A   + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 113 SLNGRHLFGQPIKVNWA 129
            LNG  + G  +    +
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.7 bits (97), Expect = 6e-06
 Identities = 10/77 (12%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGV----IEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
            T+++ N  P  TQ ++      +        +  +R    + F ++  ++  +A   ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 319 MGNTTQSSYLFGKQMKV 335
             N  +   + G  +  
Sbjct: 62  KLNGLK---IEGYTLVT 75

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 6e-11
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 47  LPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRS 106
            PP        ++++ NI   V+E  L+ +FSS G V       +       I       
Sbjct: 7   FPP------SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE 60

Query: 107 AAMAILSLNGRHLF-GQPIKVNWA 129
           A  A++ L+   L     ++V+++
Sbjct: 61  AVQALIDLHNHDLGENHHLRVSFS 84

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 4e-07
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
            P   T+++ N+ P V++ DL   F S G  V      Q+D+    ++  +  EA  A+ 
Sbjct: 7   FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 319 MGNTTQSSYLFGKQMKV 335
             +           ++V
Sbjct: 67  DLHNHD--LGENHHLRV 81

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 8e-11
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 53  PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
           P    ++YV      +T  LL+  FS  G +    L      +  F+ Y    SA  A+ 
Sbjct: 2   PRKGNTLYVYGED--MTPTLLRGAFSPFGNI--IDLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 113 SLNGRHLFGQPIKVNWA 129
            LNG  +    +KVN A
Sbjct: 58  ELNGTQVESVQLKVNIA 74

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 8/78 (10%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            ++V      +T   L   FS + +  D  +   +         FV++   + A  A+ +
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAE 58

Query: 203 LTGKWLGSRQIRCNWATK 220
           L G  + S Q++ N A K
Sbjct: 59  LNGTQVESVQLKVNIARK 76

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 2e-06
 Identities = 21/81 (25%), Positives = 31/81 (38%), Gaps = 10/81 (12%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
           AP       T+YV     ++T   L   F     G I ++ +   +   FV Y     A 
Sbjct: 1   APRKG---NTLYVYGE--DMTPTLLRGAFSP--FGNIIDLSMDPPRNCAFVTYEKMESAD 53

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A+   N TQ   +   Q+KV
Sbjct: 54  QAVAELNGTQ---VESVQLKV 71

>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 = 55.9 bits (134), Expect = 8e-11
 Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 5/85 (5%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
             +    V  G +   V+   L  V           L+      Y F  Y     +  A 
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEK--CGLVDALLMPPNKPYSFARYRTTEESKRAY 73

Query: 112 LSLNGRHLF---GQPIKVNWAYASG 133
           ++LNG+ +    GQ I +   +   
Sbjct: 74  VTLNGKEVVDDLGQKITLYLNFVEK 98

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 11/82 (13%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +  G L   V+   L              +  ++       + F  +R  ++++ A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 204 TGKWLGSRQ-----IRCNWATK 220
            GK +         +  N+  K
Sbjct: 77  NGKEVVDDLGQKITLYLNFVEK 98

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEA 313
           E      Q   V  G L   V++  L         G+++ + +  +K + F RY T  E+
Sbjct: 12  ETVSYATQSLVVANGGLGNGVSRNQLLPVLEK--CGLVDALLMPPNKPYSFARYRTTEES 69

Query: 314 ALAIQMGN 321
             A    N
Sbjct: 70  KRAYVTLN 77

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.5 bits (133), Expect = 1e-10
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 9/94 (9%)

Query: 50  GFDPST-CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAA 108
           G+  +     ++VG +    +   L   F   G +           S+ +I Y    +A 
Sbjct: 10  GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI--DHVKGDSFAYIQYESLDAAQ 67

Query: 109 MAILSLNGRHLFGQ--PIKVNWAYASGQREDTSG 140
            A   + G  L G    ++V++A    +   +SG
Sbjct: 68  AACAKMRGFPLGGPDRRLRVDFA----KSGPSSG 97

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            ++VG L P  + A L   F  + S      +          F ++ + +   AQ+A   
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACAK 72

Query: 203 LTGKWLG--SRQIRCNWATKG 221
           + G  LG   R++R ++A  G
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSG 93

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.0 bits (98), Expect = 6e-06
 Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 5/77 (6%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ 318
               T ++VG L P  +   L R F     G I  +   +   F +++Y +   A  A  
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDR--FGSIRTIDHVKGDSFAYIQYESLDAAQAACA 71

Query: 319 MGNTTQSSYLFGKQMKV 335
                    L G   ++
Sbjct: 72  KMRGFP---LGGPDRRL 85

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 2e-10
 Identities = 17/71 (23%), Positives = 32/71 (45%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +++  L P  TD  L      Y      + + D+ T + +G+GFV F +   AQ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 204 TGKWLGSRQIR 214
               + ++  +
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 2e-07
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 4/71 (5%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSY----GFIHYFDRRSAAMAILSL 114
           +Y+  +    T+  L ++    G +   K I    ++     GF+ +    +A  A+ +L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 115 NGRHLFGQPIK 125
               +  Q  K
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 5e-04
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDK----GFGFVRYSTHAEAALAIQMG 320
           +Y+  L P  T  DL +     G  V  +  + +      G+GFV + + + A  A+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 321 NTTQSSYLFGKQMK 334
             +    +  +  K
Sbjct: 61  KASG---VQAQMAK 71

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (132), Expect = 2e-10
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 3/86 (3%)

Query: 52  DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAA-MA 110
           +   C   + G++  Q     L  +FS+ G ++    +R  K   G I + ++   A   
Sbjct: 7   EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK--EGIILFKEKAKEALGK 64

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQRE 136
               N  +L  +  +V W    G+ E
Sbjct: 65  AKDANNGNLQLRNKEVTWEVLEGEVE 90

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (128), Expect = 7e-10
 Identities = 18/91 (19%), Positives = 26/91 (28%), Gaps = 7/91 (7%)

Query: 133 GQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRN 192
           G  E+  G    F GDL  +     L   FS +        +      R    G + F+ 
Sbjct: 3   GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV------RGAKEGIILFKE 56

Query: 193 -QQDAQSAINDLTGKWLGSRQIRCNWATKGA 222
             ++A     D     L  R     W     
Sbjct: 57  KAKEALGKAKDANNGNLQLRNKEVTWEVLEG 87

>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 = 39.8 bits (92), Expect = 6e-05
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
           + E        + G+L  +  + DLH  F +   G I+ +   R    G + +   A+ A
Sbjct: 4   SLEEKIGCLLKFSGDLDDQTCREDLHILFSN--HGEIKWIDFVRGAKEGIILFKEKAKEA 61

Query: 315 L-AIQMGNTTQSSYLFGKQMKV 335
           L   +  N      L  +  +V
Sbjct: 62  LGKAKDANNGN---LQLRNKEV 80

>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 = 54.6 bits (131), Expect = 2e-10
 Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 7/84 (8%)

Query: 143 NIF-----VGDLSPEVTDATLFACFSVYPSCSDARVM--WDQKTGRSRGFGFVSFRNQQD 195
           N+      + D   E     +    S Y       +    D       G  FV F +  D
Sbjct: 11  NMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFD 70

Query: 196 AQSAINDLTGKWLGSRQIRCNWAT 219
            Q A+  LTG+   +R +   +  
Sbjct: 71  CQKAMQGLTGRKFANRVVVTKYCD 94

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 4e-06
 Identities = 12/93 (12%), Positives = 29/93 (31%), Gaps = 18/93 (19%)

Query: 53  PSTCRSVYVGNIHT----------QVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGF 98
           P+    + + N+            +     +++  S  G V+  ++ R     +    G 
Sbjct: 3   PTEV--LCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60

Query: 99  IH--YFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
           I   +        A+  L GR    + +   + 
Sbjct: 61  IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.5 bits (130), Expect = 3e-10
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           S      + ++   +T   +       P   +A  +     G+  G   V F+N+ DA+ 
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 199 AINDLTGKWLGSRQIRCNWATK 220
           +   L  K L  R+   +  T 
Sbjct: 66  SE-RLHRKKLNGREAFVHVVTL 86

>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 = 47.9 bits (113), Expect = 7e-08
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 3/86 (3%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKS--SYGFIH-YFDRRSAAMA 110
           S     ++ NI   +T+  + +        E    +  D +    G     F     A  
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 111 ILSLNGRHLFGQPIKVNWAYASGQRE 136
              L+ + L G+   V+       RE
Sbjct: 66  SERLHRKKLNGREAFVHVVTLEDMRE 91

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 4e-04
 Identities = 12/85 (14%), Positives = 29/85 (34%), Gaps = 12/85 (14%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD------KGFGFVRYSTH 310
           + N      ++ N+   +T++D+ +        V E              G   V++   
Sbjct: 3   DVNSAKVCAHITNIPFSITKMDVLQFLEG--IPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            +A  + ++        L G++  V
Sbjct: 61  DDARKSERLHRK----KLNGREAFV 81

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 5/101 (4%)

Query: 117 RHLFGQPIKVNWAYASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWD 176
            +++  P + +   A G R   S   ++ + +   E  +         Y    +  V  +
Sbjct: 7   LNIYRNP-QNSSQSADGLRSAVS---DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN 62

Query: 177 QKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
                  G  +V FR ++DA+ A+ DL  +W   + I    
Sbjct: 63  -LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 18/95 (18%), Positives = 30/95 (31%), Gaps = 8/95 (8%)

Query: 37  PQIEPIPSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSS- 95
           PQ     +  L           V +   + +  E +  E+    G VE   +        
Sbjct: 13  PQNSSQSADGLRSAVSD-----VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHL 67

Query: 96  --YGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW 128
               ++ +     A  A++ LN R   GQPI    
Sbjct: 68  VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 38.9 bits (90), Expect = 8e-05
 Identities = 16/92 (17%), Positives = 34/92 (36%), Gaps = 18/92 (19%)

Query: 259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLG----------AGVIEEVRVQRD-----KGFG 303
           NPQ ++     L   V+ +++  H+               G +EE+ V  +      G  
Sbjct: 12  NPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV 71

Query: 304 FVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           +V++    +A  A+   N     +  G+ +  
Sbjct: 72  YVKFRREEDAEKAVIDLNNR---WFNGQPIHA 100

>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 = 53.7 bits (128), Expect = 4e-10
 Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 143 NIFVGDLSPEVTDATL---FACFSVYPSCSDARVMWDQKTGRS---RGFGFVSFRNQQDA 196
            +FV  LS  + D  +      F  +       +        S       +V++   +DA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 197 QSAINDLTGKWLGSRQIRC 215
             AI  +    +  R ++ 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 57  RSVYVGNIHTQVTEPLL---QEVFSSTGPVEGCKLIR-------KDKSSYGFIHYFDRRS 106
             V+V  +  ++ +P +    E F   G +    +         +  S+  ++ Y     
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 107 AAMAILSLNGRHLFGQPIKV 126
           A  AI  +N   + G+ +K 
Sbjct: 69  ALRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.3 bits (101), Expect = 2e-06
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 13/85 (15%)

Query: 261 QYTTVYVGNLAPEVTQLDLHRHFHSLGA-GVIEEVRVQRDK---------GFGFVRYSTH 310
           Q   V+V  L+  +   ++ +     G  G I +V +                +V Y   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            +A  AIQ  N   +  + G+ +K 
Sbjct: 67  EDALRAIQCVN---NVVVDGRTLKA 88

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.3 bits (127), Expect = 8e-10
 Identities = 10/81 (12%), Positives = 24/81 (29%), Gaps = 1/81 (1%)

Query: 138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQ 197
           +SG   +     + +V   +                    +  +S     ++F N   A 
Sbjct: 2   SSGSSGLIACVANDDVFSESET-RAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAA 60

Query: 198 SAINDLTGKWLGSRQIRCNWA 218
            A   L       ++++  +A
Sbjct: 61  DARLRLHKTEFLGKEMKLYFA 81

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.9 bits (126), Expect = 1e-09
 Identities = 12/77 (15%), Positives = 26/77 (33%), Gaps = 7/77 (9%)

Query: 58  SVYVGNIHTQVTEP-----LLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL 112
            +     +  V          + +F +       +           I++ +  SAA A L
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY--FKSFKRVRINFSNPLSAADARL 64

Query: 113 SLNGRHLFGQPIKVNWA 129
            L+     G+ +K+ +A
Sbjct: 65  RLHKTEFLGKEMKLYFA 81

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 12/81 (14%), Positives = 24/81 (29%), Gaps = 10/81 (12%)

Query: 260 PQYTTVYVGNLAPEV-----TQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
              + +       +V     T+      F +         +  +      + +S    AA
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRT--YDKDTTFQYFKSFKRVRINFSNPLSAA 60

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A    + T      GK+MK+
Sbjct: 61  DARLRLHKT---EFLGKEMKL 78

>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 = 53.0 bits (126), Expect = 8e-10
 Identities = 14/86 (16%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 46  NLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFD 103
           ++  G + +T  ++++GN++   +   L+   S         ++      +       F+
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 62

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWA 129
                   L L G  +FG  IK+   
Sbjct: 63  SAEDLEKALELTGLKVFGNEIKLEKP 88

>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 = 51.5 bits (122), Expect = 3e-09
 Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 134 QREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQ 193
           +  +++  FN+F+G+L+P  + A L    S   + +D  V+   +TG +R FG+V F + 
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESA 64

Query: 194 QDAQSAINDLTGKWLGSRQIRCNWATK 220
           +D + A+  LTG  +   +I+      
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKG 90

>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 = 35.7 bits (81), Expect = 0.001
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 8/85 (9%)

Query: 254 EAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGA---GVIEEVRVQRDKGFGFVRYSTH 310
           E  E+   +  +++GNL P  +  +L      L A     + +VR   ++ FG+V + + 
Sbjct: 6   EGSESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 311 AEAALAIQMGNTTQSSYLFGKQMKV 335
            +   A+++        +FG ++K+
Sbjct: 65  EDLEKALELTGLK----VFGNEIKL 85

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.2 bits (125), Expect = 9e-10
 Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 3/61 (4%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           T V V           L   F     G I +  +     +  +RY +  +A  A+     
Sbjct: 5   TWVTVFGFPQASASYIL-LQFAQ--YGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGR 61

Query: 323 T 323
            
Sbjct: 62  I 62

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 8/70 (11%), Positives = 24/70 (34%), Gaps = 8/70 (11%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V           L   F+ Y +     +        +  +  + ++++  A+ A++  
Sbjct: 7   VTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-K 58

Query: 204 TGKWLGSRQI 213
            G+  G   +
Sbjct: 59  DGRIFGESIM 68

>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 = 52.9 bits (126), Expect = 1e-09
 Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 8/91 (8%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG     S    + V  L   V +A L      + +     +M  ++         V F
Sbjct: 5   SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEF 58

Query: 191 RNQQDAQSAINDLTGK--WLGSRQIRCNWAT 219
            N   A+  +        ++  +Q   N++T
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 18/104 (17%), Positives = 36/104 (34%), Gaps = 9/104 (8%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFD 103
           SG+       S    V+V  +   V E  L E     G +    ++   +     + + +
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR--QALVEFEN 60

Query: 104 RRSAAMAI--LSLNGRHLFGQPIKVNWAYAS-----GQREDTSG 140
             SA   +   +    ++ GQ    N++ +      G    +SG
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 3e-06
 Identities = 15/79 (18%), Positives = 22/79 (27%), Gaps = 3/79 (3%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
                   V+V  L   V + DL         G I  V +   K    V +     A   
Sbjct: 10  HKVSVSPVVHVRGLCESVVEADLVEALEK--FGTICYVMMMPFKRQALVEFENIDSAKEC 67

Query: 317 IQMGNTTQSSYLFGKQMKV 335
           +         Y+ G+Q   
Sbjct: 68  VTFAADVP-VYIAGQQAFF 85

>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 = 52.1 bits (124), Expect = 2e-09
 Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           A   ++      N+++ +L   + +  L      +        +    +G SRG GF   
Sbjct: 8   AQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARM 66

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
            + +  ++ I    GK++ +        
Sbjct: 67  ESTEKCEAVIGHFNGKFIKTPPGVSAPT 94

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 3/76 (3%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILS 113
            ++Y+ N+   + E  L+ +    G V   +++R         GF            I  
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 114 LNGRHLFGQPIKVNWA 129
            NG+ +   P      
Sbjct: 79  FNGKFIKTPPGVSAPT 94

>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 = 37.5 bits (86), Expect = 3e-04
 Identities = 13/84 (15%), Positives = 25/84 (29%), Gaps = 6/84 (7%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFH---SLGAGVIEEVRVQRDKGFGFVRYSTHA 311
           A +     T +Y+ NL   + + +L         + +  I        +G GF R  +  
Sbjct: 11  AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTE 70

Query: 312 EAALAIQMGNTTQSSYLFGKQMKV 335
           +    I   N      +       
Sbjct: 71  KCEAVIGHFNGKF---IKTPPGVS 91

>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 = 50.9 bits (121), Expect = 4e-09
 Identities = 12/78 (15%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 53  PSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAI 111
             T R V++ +          L ++    G +    ++ K   ++  +   +   AA+  
Sbjct: 5   VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDY 64

Query: 112 LSLNGRHLFGQPIKVNWA 129
            +     +FG+P++V+ +
Sbjct: 65  YTTTPALVFGKPVRVHLS 82

>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 = 51.4 bits (122), Expect = 4e-09
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
           R      F +++  L  E  +  +   F       D+  +     G++ G GFV FRN+ 
Sbjct: 12  RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 71

Query: 195 DAQSAINDLTGKWLGSRQIRCNWATK 220
           D ++A+     +++G+R I+ +  TK
Sbjct: 72  DYKAAL-CRHKQYMGNRFIQVHPITK 96

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 6e-09
 Identities = 9/76 (11%), Positives = 19/76 (25%), Gaps = 3/76 (3%)

Query: 54  STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILS 113
           S    + V N+        + ++                     F+   +   A  AI  
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCY---VDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 114 LNGRHLFGQPIKVNWA 129
            +     G+ + V   
Sbjct: 60  FHQYSFRGKDLIVQLQ 75

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 7/84 (8%)

Query: 139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           SG   I V +L  +     +      Y        +      R++   FV+  N + AQ+
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQN 55

Query: 199 AINDLTGKWLGSRQIRCNWATKGA 222
           AI          + +        A
Sbjct: 56  AIQMFHQYSFRGKDLIVQLQPTDA 79

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNT 322
           + + V NL  +    ++H          ++   V R+K   FV      +A  AIQM + 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD---LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQ 62

Query: 323 TQSSYLFGKQMKV 335
                  GK + V
Sbjct: 63  YS---FRGKDLIV 72

>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 = 50.3 bits (120), Expect = 7e-09
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 4/61 (6%)

Query: 158 LFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW 217
           L    S +       +          G   VSFR+ ++A   I  L G+W G RQI    
Sbjct: 36  LRVECSKFGQIRKLLLF----DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

Query: 218 A 218
            
Sbjct: 92  W 92

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 11/84 (13%)

Query: 57  RSVYVGNIHTQV-----------TEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRR 105
           R V + N+   +               L+   S  G +    L  +       + + D  
Sbjct: 9   RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPE 68

Query: 106 SAAMAILSLNGRHLFGQPIKVNWA 129
            A   I +L+GR   G+ I     
Sbjct: 69  EADYCIQTLDGRWFGGRQITAQAW 92

>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 = 35.7 bits (82), Expect = 0.001
 Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 5/47 (10%)

Query: 291 IEEVRVQRD--KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
           I ++ +      G   V +    EA   IQ  +     +  G+Q+  
Sbjct: 46  IRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR---WFGGRQITA 89

>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 = 50.5 bits (120), Expect = 7e-09
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 57  RSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN 115
             + V N++ + VT   L  +F   G V+  K I  +K     +   D   A +A+  LN
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVK-ILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 116 GRHLFGQPIKVNWAYASGQREDTSGH 141
           G  L G+PI++  +     +    G 
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQ 87

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 6/105 (5%)

Query: 140 GHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQS 198
           G+  + V +L+PE VT  +LF  F VY      ++++++K         V   +   AQ 
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 199 AINDLTGKWLGSRQIRCNWATKGAGNNEDKQSSDAKSVVELTNGS 243
           A++ L G  L  + IR   +         +   D     +  N  
Sbjct: 56  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 100

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 263 TTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN 321
           + + V NL PE VT   L   F   G     ++   + +    V+ +   +A LA+   N
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-NALVQMADGNQAQLAMSHLN 61

Query: 322 TTQSSYLFGKQMKV 335
             +   L GK +++
Sbjct: 62  GHK---LHGKPIRI 72

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 8/76 (10%), Positives = 23/76 (30%), Gaps = 2/76 (2%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
           ++++     + T   +           +   M        +G  FV F + + A+  +  
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFVE- 65

Query: 203 LTGKWLGSRQIRCNWA 218
             G+      +   + 
Sbjct: 66  TPGQKYKETDLLILFK 81

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 4e-07
 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRH---FHSLGAGVIEEVRVQRDKGFGFVRYSTHAEA 313
           +N+ +  +VY+     + T  D+         +    +     +  KG  FV + +   A
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 314 ALAIQMGNTTQSSYLFGKQMKV 335
              ++              + +
Sbjct: 61  KKFVETPGQK----YKETDLLI 78

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 4/76 (5%)

Query: 57  RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL---IRKDKSSYGFIHYFDRRSAAMAILS 113
           RSVY+    T  T   ++E     G V   ++   + K      F+ +    SA   +  
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 114 LNGRHLFGQPIKVNWA 129
             G+      + + + 
Sbjct: 66  TPGQKYKETDLLILFK 81

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 17/94 (18%), Positives = 36/94 (38%), Gaps = 1/94 (1%)

Query: 43  PSGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIH-Y 101
            SG+    F  +T   V++  +  + TE  +   FS   P+     I  D    G     
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVE 61

Query: 102 FDRRSAAMAILSLNGRHLFGQPIKVNWAYASGQR 135
           F     A+A ++ +  ++  + +++     +G  
Sbjct: 62  FATHEDAVAAMAKDKANMQHRYVELFLNSTAGTS 95

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 19/100 (19%), Positives = 34/100 (34%), Gaps = 4/100 (4%)

Query: 132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFR 191
           SG    ++    + +  L    T+  ++  FS          +     GR  G   V F 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFA 63

Query: 192 NQQDAQSAINDLTGKWLGSRQIRCNWATKGAGNNEDKQSS 231
             +DA +A+       +  R +     +  AG +    SS
Sbjct: 64  THEDAVAAMA-KDKANMQHRYVELFLNST-AGTSGSGPSS 101

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 16/96 (16%), Positives = 33/96 (34%), Gaps = 12/96 (12%)

Query: 242 GSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVR--VQRD 299
           GSS     +        +     V++  L    T+ D++  F  L    +        R 
Sbjct: 1   GSSGSSGSSFQ------STTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRV 54

Query: 300 KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV 335
            G   V ++TH +A  A+          +  + +++
Sbjct: 55  TGEADVEFATHEDAVAAMAKDKA----NMQHRYVEL 86

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 16/97 (16%), Positives = 28/97 (28%), Gaps = 7/97 (7%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFD 103
           S   PP     +   V V  +    +   L++     G           K   G + Y  
Sbjct: 5   SSGGPPT--RRSDFRVLVSGLPPSGSWQDLKDHMREAGD---VCYADVQKDGMGMVEYLR 59

Query: 104 RRSAAMAILSLNGRHLFGQPIKVNWAYASGQREDTSG 140
           +     A+  L+         + +  Y     E +SG
Sbjct: 60  KEDMEYALRKLDDTKFRSHEGETS--YIRVYPERSSG 94

>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 = 47.8 bits (113), Expect = 5e-08
 Identities = 16/88 (18%), Positives = 27/88 (30%), Gaps = 7/88 (7%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
           +SG        F + V  L P  +   L            A V  D         G V +
Sbjct: 5   SSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEY 57

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWA 218
             ++D + A+  L      S +   ++ 
Sbjct: 58  LRKEDMEYALRKLDDTKFRSHEGETSYI 85

>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 = 37.1 bits (85), Expect = 4e-04
 Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 6/81 (7%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
            P        V V  L P  +  DL  H    G          +  G G V Y    +  
Sbjct: 8   GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCY---ADVQKDGMGMVEYLRKEDME 64

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A++  + T+       + + 
Sbjct: 65  YALRKLDDTK---FRSHEGET 82

>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 = 48.8 bits (115), Expect = 4e-08
 Identities = 21/116 (18%), Positives = 32/116 (27%), Gaps = 12/116 (10%)

Query: 131 ASGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSF 190
            S  R  T     I   +L      A +   FS + S     +              V F
Sbjct: 4   GSSGRSKT----VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEF 53

Query: 191 RNQQDAQSAINDLTGKWLGSRQIRCNWATKG--AGNNEDKQSSDAKSVVELTNGSS 244
               +A+ A   L         +   WA  G      + K S   +   +  +G S
Sbjct: 54  LEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPS 109

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.2 bits (103), Expect = 2e-06
 Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 5/83 (6%)

Query: 50  GFDPSTCRS---VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRS 106
           G   S+ RS   +   N+        +QE FS  G +        +      + + +   
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL--LPEGGITAIVEFLEPLE 58

Query: 107 AAMAILSLNGRHLFGQPIKVNWA 129
           A  A   L        P+ + WA
Sbjct: 59  ARKAFRHLAYSKFHHVPLYLEWA 81

>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 = 47.2 bits (111), Expect = 8e-08
 Identities = 10/75 (13%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 56  CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLN 115
            + +++ N+  +  E +L  +F+     +  + +  ++    F+ +     +  A  +L 
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVR-LVPNRHDIAFVEFTTELQSNAAKEALQ 66

Query: 116 GRHLF-GQPIKVNWA 129
           G  +     +K+ +A
Sbjct: 67  GFKITPTHAMKITFA 81

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.5 bits (99), Expect = 3e-06
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           +F+ +L  E  +  L   F+ +P          +         FV F  +  + +A   L
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPG-----FKEVRLVPNRHDIAFVEFTTELQSNAAKEAL 65

Query: 204 TGKWL-GSRQIRCNWATK 220
            G  +  +  ++  +A K
Sbjct: 66  QGFKITPTHAMKITFAKK 83

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.8 bits (92), Expect = 3e-05
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 3/81 (3%)

Query: 255 APENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAA 314
           A    P    +++ NL  E  ++ L   F+    G  E   V       FV ++T  ++ 
Sbjct: 1   AQTEQPPNQILFLTNLPEETNEMMLSMLFNQ-FPGFKEVRLVPNRHDIAFVEFTTELQSN 59

Query: 315 LAIQMGNTTQSSYLFGKQMKV 335
            A +     +        MK+
Sbjct: 60  AAKEALQGFK--ITPTHAMKI 78

>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 = 45.8 bits (107), Expect = 3e-07
 Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 3/90 (3%)

Query: 43  PSGNLPPGFD--PSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFI 99
           P G     FD      R +++ N+     ++  + ++    G ++   L+R    ++  +
Sbjct: 3   PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEM 62

Query: 100 HYFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
              +   A +           G+ +KV+ +
Sbjct: 63  ETREDAMAMVDHCLKKALWFQGRCVKVDLS 92

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.8 bits (105), Expect = 5e-07
 Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 3/74 (4%)

Query: 58  SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSLN 115
           +V V N+     +  + + F   GP+    +    K    +  I +     A    ++  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALA-AITKT 60

Query: 116 GRHLFGQPIKVNWA 129
            + +    I V+  
Sbjct: 61  HKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.7 bits (102), Expect = 1e-06
 Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 3/77 (3%)

Query: 143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAIND 202
            + V +L        ++  F          V    K  ++  F  + F     A +AI  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITK 59

Query: 203 LTGKWLGSRQIRCNWAT 219
            T K +G  +I  +  T
Sbjct: 60  -THKVVGQNEIIVSHLT 75

>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 = 38.3 bits (88), Expect = 7e-05
 Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 10/77 (12%)

Query: 263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD----KGFGFVRYSTHAEAALAIQ 318
           TTV V NL     Q  ++++F     G I  V V         F  + ++ +        
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKH--CGPIIHVDVADSLKKNFRFARIEFARYDG----AL 54

Query: 319 MGNTTQSSYLFGKQMKV 335
              T     +   ++ V
Sbjct: 55  AAITKTHKVVGQNEIIV 71

>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 = 44.5 bits (104), Expect = 7e-07
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 4/81 (4%)

Query: 51  FDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMA 110
            D +  R +++  +  +VTE  +  +    G V     +     +  F+      +A   
Sbjct: 3   MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNI--LMLKGKNQAFLELATEEAAITM 60

Query: 111 I--LSLNGRHLFGQPIKVNWA 129
           +   S    HL  QPI + ++
Sbjct: 61  VNYYSAVTPHLRNQPIYIQYS 81

>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 = 41.0 bits (95), Expect = 1e-05
 Identities = 11/88 (12%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 135 REDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQ 194
           + D +    + +  L  EVT         V         + +    + +   F+    ++
Sbjct: 2   KMDGAPSRVLHIRKLPGEVT------ETEVIALGLPFGKVTNILMLKGKNQAFLELATEE 55

Query: 195 DAQSAINDLTGK--WLGSRQIRCNWATK 220
            A + +N  +     L ++ I   ++  
Sbjct: 56  AAITMVNYYSAVTPHLRNQPIYIQYSNH 83

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 5e-05
 Identities = 9/79 (11%), Positives = 26/79 (32%), Gaps = 3/79 (3%)

Query: 257 ENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALA 316
            +      +++  L  EVT+ ++       G      +   +++ F  +     A   + 
Sbjct: 3   MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVN 62

Query: 317 IQMGNTTQSSYLFGKQMKV 335
                T    +L  + + +
Sbjct: 63  YYSAVTP---HLRNQPIYI 78

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (98), Expect = 5e-06
 Identities = 15/92 (16%), Positives = 24/92 (26%), Gaps = 7/92 (7%)

Query: 144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL 203
           + V  L P  +   L            A V  D         G V F  ++D   A+  L
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRKL 55

Query: 204 TGKWLGSRQIRCNWATKGAGNNEDKQSSDAKS 235
                 S +    +               ++S
Sbjct: 56  DNTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 87

>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 = 38.7 bits (89), Expect = 8e-05
 Identities = 7/83 (8%), Positives = 21/83 (25%), Gaps = 3/83 (3%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           V V  +    +   L++     G           +   G + +  +     A+  L+   
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGD---VCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTK 59

Query: 119 LFGQPIKVNWAYASGQREDTSGH 141
                 +  +         +  +
Sbjct: 60  FRSHEGETAYIRVKVDGPRSPSY 82

>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 = 42.5 bits (99), Expect = 5e-06
 Identities = 12/89 (13%), Positives = 28/89 (31%), Gaps = 3/89 (3%)

Query: 44  SGNLPPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIH--- 100
           SG+     D +    V +  +    ++  + + FS    V     +  D           
Sbjct: 3   SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 101 YFDRRSAAMAILSLNGRHLFGQPIKVNWA 129
            F  +  A   L  +   +  + I++  +
Sbjct: 63  QFASQEIAEKALKKHKERIGHRYIEIFKS 91

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (86), Expect = 2e-04
 Identities = 10/71 (14%), Positives = 22/71 (30%), Gaps = 3/71 (4%)

Query: 59  VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRH 118
           + +  +   VT   + ++ S     E             F+   +   A  AI + +   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLS---DYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSR 57

Query: 119 LFGQPIKVNWA 129
           L  + + V   
Sbjct: 58  LRERELSVQLQ 68

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	335
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.8
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.79
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.79
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.79
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.78
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.78
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.77
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	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
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.77
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.76
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.75
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.75
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.74
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.74
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.74
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.74
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.74
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.73
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.73
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.72
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.72
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.72
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.71
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.71
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.7
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.69
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.69
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.69
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.69
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.67
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.65
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.65
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.61
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.57
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.56
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	99.53
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.52
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.51
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	99.49
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.47
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.43
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.38
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.8
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.65
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.64
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.59
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.56
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.53
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.3
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.89

>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=99.97  E-value=1.3e-30  Score=206.66  Aligned_cols=167  Identities=19%  Similarity=0.363  Sum_probs=146.3

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      |...++|||+|||+++|+++|+++|++||.|.+++++.+.    ++|||||+|.+.++|.+|+. +.+..+.++.+.+.+
T Consensus         3 p~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   81 (183)
T ss_dssp             CHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhh
Confidence            4456899999999999999999999999999999998764    35899999999999999986 456777888888877


Q ss_pred             eccCCCc---cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 019811          129 AYASGQR---EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTG  205 (335)
Q Consensus       129 ~~~~~~~---~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  205 (335)
                      .......   ......++|||+|||..+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|+. +++
T Consensus        82 ~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~  160 (183)
T d1u1qa_          82 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKY  160 (183)
T ss_dssp             CCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSC
T ss_pred             hhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCC
Confidence            6544432   234556799999999999999999999999999999999998889999999999999999999997 788


Q ss_pred             ceeCCeeeEEEEccCC
Q 019811          206 KWLGSRQIRCNWATKG  221 (335)
Q Consensus       206 ~~~~g~~l~v~~~~~~  221 (335)
                      ..+.|+.|+|.++.++
T Consensus       161 ~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         161 HTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEETTEEEEEEECCCH
T ss_pred             CeECCEEEEEEecCCc
Confidence            8999999999998653

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=4e-28  Score=192.20  Aligned_cols=159  Identities=26%  Similarity=0.467  Sum_probs=134.4

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||+++|+++|+++|+.||.|.++.++++..++.++|+|||+|.+.++|.+|+. +.+..+.++.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3789999999999999999999999999999999998899999999999999999999997 567778888888877644


Q ss_pred             CCCCCCCCCCcccccchhccCCCCcCCcCCCCCCCCCCCCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecc-
Q 019811          221 GAGNNEDKQSSDAKSVVELTNGSSEDGKETTNTEAPENNPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRD-  299 (335)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~-  299 (335)
                      ......                             .......++|||+|||..+++++|+++|+.||  .+..+.+..+ 
T Consensus        85 ~~~~~~-----------------------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G--~v~~~~i~~~~  133 (183)
T d1u1qa_          85 REDSQR-----------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDR  133 (183)
T ss_dssp             TTGGGS-----------------------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGS--CEEEEEEEECT
T ss_pred             cccccc-----------------------------cccccccceeEEccCCCcCCHHHHhhhhccCC--ceeeeeeeccc
Confidence            321110                             11222347899999999999999999999999  4777776543 


Q ss_pred             -----cceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          300 -----KGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       300 -----~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                           +|+|||+|.+.++|.+|++ +++.   .++|++|+|
T Consensus       134 ~~~~~~g~~fV~f~~~e~A~~Al~-~~~~---~~~G~~i~V  170 (183)
T d1u1qa_         134 GSGKKRGFAFVTFDDHDSVDKIVI-QKYH---TVNGHNCEV  170 (183)
T ss_dssp             TTCCEEEEEEEEESCHHHHHHHHT-SSCE---EETTEEEEE
T ss_pred             ccCccceeEEEEECCHHHHHHHHH-hCCC---eECCEEEEE
Confidence                 6799999999999999996 6888   899999875

>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=99.83  E-value=1.3e-20  Score=128.87  Aligned_cols=84  Identities=20%  Similarity=0.408  Sum_probs=78.8

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ...+++|||+|||.++++++|.++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..|+|..+.|+.|+|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      +..+
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            8764

>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=1e-20  Score=128.03  Aligned_cols=80  Identities=33%  Similarity=0.542  Sum_probs=76.9

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      +++|||+|||+++++++|+++|++||.|.++.+.+++.+|.++|||||+|.+.++|.+|++.|++..+.|+.|+|.|+.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999875

>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=3e-20  Score=128.45  Aligned_cols=85  Identities=27%  Similarity=0.409  Sum_probs=79.9

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||..+++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..|++..++|+.|+|.|
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            34457999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +..+.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97754

>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=99.82  E-value=4.2e-20  Score=127.03  Aligned_cols=81  Identities=38%  Similarity=0.822  Sum_probs=74.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..+.++|||+|||.++|+++|+++|+.||+|.+|++..++  .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.|+.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            4556789999999999999999999999999999998765  36899999999999999999999999999999999997


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            554

>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=99.82  E-value=3.9e-20  Score=127.20  Aligned_cols=84  Identities=29%  Similarity=0.457  Sum_probs=79.2

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+..+|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|++..++|+.|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34557899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      +.++
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9764

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.7e-20  Score=124.75  Aligned_cols=79  Identities=29%  Similarity=0.512  Sum_probs=76.2

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      ++|||+|||.++++++|+++|+.||.|.++.++++..++.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.|+++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999988999999999999999999999999999999999999999865

>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=2.7e-20  Score=127.69  Aligned_cols=83  Identities=34%  Similarity=0.492  Sum_probs=78.5

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..|++..++|+.|+|.|+.
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            34689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      +..
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.82  E-value=3.4e-20  Score=125.37  Aligned_cols=76  Identities=25%  Similarity=0.486  Sum_probs=70.9

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      .++|||+|||.++|+++|+++|++||.|.++++.+++.    +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+.+
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            46799999999999999999999999999999988653    58999999999999999999999999999999999864

>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=5e-20  Score=127.28  Aligned_cols=81  Identities=35%  Similarity=0.630  Sum_probs=74.0

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ....++|||+|||.++|+++|+++|++||.|.+++++.++    ++|||||+|.+.++|.+|++.|||..+.|+.|+|.|
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            4456789999999999999999999999999999998764    468999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97654

>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=99.82  E-value=3.6e-20  Score=124.34  Aligned_cols=78  Identities=32%  Similarity=0.589  Sum_probs=75.3

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      +|||+|||+.+|+++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|..|++.|+|..+.|+.|+|.|+..
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            599999999999999999999999999999999999999999999999999999999999999999999999999853

>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=99.81  E-value=1.2e-19  Score=125.41  Aligned_cols=82  Identities=27%  Similarity=0.386  Sum_probs=74.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .....++|||+|||.++++++|+++|+.||+|.+|++..++  ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            34556789999999999999999999999999999998765  4689999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            7654

>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=99.81  E-value=3.8e-20  Score=126.96  Aligned_cols=80  Identities=28%  Similarity=0.451  Sum_probs=73.2

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999998754    4689999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .+..
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.81  E-value=1.2e-19  Score=125.42  Aligned_cols=82  Identities=26%  Similarity=0.427  Sum_probs=78.0

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+++|||+|||.++|+++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|..|++.|++..++|+.|+|.|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CC
Q 019811          220 KG  221 (335)
Q Consensus       220 ~~  221 (335)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=1.5e-19  Score=127.14  Aligned_cols=80  Identities=21%  Similarity=0.338  Sum_probs=73.1

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ++++|||+|||.++++++|+++|+.||.|.+++++.++.    +|||||+|.+.++|..|++.|||..|.|+.|+|.|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            456799999999999999999999999999999988653    5799999999999999999999999999999999997


Q ss_pred             cCCC
Q 019811          131 ASGQ  134 (335)
Q Consensus       131 ~~~~  134 (335)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            6653

>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=99.81  E-value=9.8e-20  Score=123.26  Aligned_cols=80  Identities=35%  Similarity=0.473  Sum_probs=75.3

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ..+.++++|||+|||..+|+++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|+..|++..++|+.|+|
T Consensus         4 ~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           4 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34456789999999999999999999999999999999999888999999999999999999999999999999999986

>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=1.2e-19  Score=127.65  Aligned_cols=85  Identities=28%  Similarity=0.470  Sum_probs=79.9

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .++++|||+|||+++++++|+++|+.||.+.++.++.++.+|.++|||||+|.+.++|..|++.|++..++|+.|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 019811          219 TKGAG  223 (335)
Q Consensus       219 ~~~~~  223 (335)
                      .++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            77643

>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=99.81  E-value=1.4e-19  Score=126.73  Aligned_cols=85  Identities=27%  Similarity=0.347  Sum_probs=79.8

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .+.++|||+|||+++++++|+++|..||.|.++.+++++.++.++|||||+|.+.++|.+|+..|++..++|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 019811          219 TKGAG  223 (335)
Q Consensus       219 ~~~~~  223 (335)
                      ..+..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87543

>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=99.81  E-value=1.7e-19  Score=126.30  Aligned_cols=82  Identities=18%  Similarity=0.295  Sum_probs=74.5

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..+++|||+|||.++++++|+++|++||.|.++++..++    ++|||||+|.+.++|.+|++.||+..|.|++|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            446779999999999999999999999999999998764    3689999999999999999999999999999999999


Q ss_pred             ccCCCc
Q 019811          130 YASGQR  135 (335)
Q Consensus       130 ~~~~~~  135 (335)
                      ..+...
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            876543

>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=99.81  E-value=1.6e-19  Score=124.65  Aligned_cols=79  Identities=25%  Similarity=0.457  Sum_probs=72.8

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|.+..++.    +|||||+|.+.++|..|++.|||..+.|++|+|.|+
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            3568999999999999999999999999999999988754    479999999999999999999999999999999998


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=6.3e-20  Score=124.52  Aligned_cols=81  Identities=23%  Similarity=0.435  Sum_probs=77.5

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKG  221 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~  221 (335)
                      ..|||+|||..+|+++|+++|+.||.|.++.+++|+.+|.++|||||+|.+.++|..|+..|++..++|+.|.|.|+...
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            47999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             C
Q 019811          222 A  222 (335)
Q Consensus       222 ~  222 (335)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.80  E-value=1.4e-19  Score=122.36  Aligned_cols=75  Identities=35%  Similarity=0.619  Sum_probs=69.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ++|||+|||.++++++|+++|++||.|.++++.++..    +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+.|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5699999999999999999999999999999987643    47999999999999999999999999999999999864

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.80  E-value=1.5e-19  Score=123.61  Aligned_cols=79  Identities=27%  Similarity=0.510  Sum_probs=72.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+.++|||+|||.++|+++|+++|+.||.|.+|++..++.    +|||||+|.+.++|.+|+..|||..+.|++|+|.|+
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            3467899999999999999999999999999999988653    589999999999999999999999999999999999


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            764

>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=1e-19  Score=125.06  Aligned_cols=80  Identities=26%  Similarity=0.400  Sum_probs=73.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+.++|||+|||.++++++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|++.|+|..+.|+.|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999998653    57999999999999999999999999999999999


Q ss_pred             eccC
Q 019811          129 AYAS  132 (335)
Q Consensus       129 ~~~~  132 (335)
                      +.++
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9764

>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=99.80  E-value=1.3e-19  Score=125.81  Aligned_cols=76  Identities=30%  Similarity=0.564  Sum_probs=71.0

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      .++|||+|||.++++++|+++|++||.|.+|++.++  +|||||+|.+.++|..|+..|||..+.|+.|+|.|+.+++
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~--kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec--ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            468999999999999999999999999999999876  5799999999999999999999999999999999986543

>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=99.80  E-value=1.8e-19  Score=123.40  Aligned_cols=77  Identities=21%  Similarity=0.267  Sum_probs=71.5

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccc-cCceeEEeeecc
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHL-FGQPIKVNWAYA  131 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~-~g~~l~v~~~~~  131 (335)
                      ++++|||+|||.++++++|+++|+.||.|.++.+..++++|||||+|.+.++|.+|+..|+|..+ .|+.|+|.|+++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            46789999999999999999999999999988888888889999999999999999999999988 589999999864

>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=99.80  E-value=9.4e-20  Score=124.96  Aligned_cols=78  Identities=23%  Similarity=0.464  Sum_probs=72.3

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC--CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD--KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~--~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ..+|||+|||.++++++|+++|+.||.|.++++..++  ++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            4579999999999999999999999999999998875  36899999999999999999999999999999999997654

>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=99.80  E-value=2.1e-19  Score=123.70  Aligned_cols=81  Identities=25%  Similarity=0.473  Sum_probs=73.5

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ++.++|||+|||.++++++|+++|+.||.|..+.+..+.    .+|||||+|.+.++|.+|++.|+|..+.|+.|+|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456789999999999999999999999999999887753    4689999999999999999999999999999999998


Q ss_pred             ccCCC
Q 019811          130 YASGQ  134 (335)
Q Consensus       130 ~~~~~  134 (335)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.80  E-value=2.3e-19  Score=121.93  Aligned_cols=80  Identities=29%  Similarity=0.461  Sum_probs=75.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eeeEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS--RQIRCN  216 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~  216 (335)
                      ..+++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++.|++..+.|  ++|.|+
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            345689999999999999999999999999999999999999999999999999999999999999999876  889999


Q ss_pred             Ec
Q 019811          217 WA  218 (335)
Q Consensus       217 ~~  218 (335)
                      |+
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2.4e-19  Score=121.35  Aligned_cols=75  Identities=27%  Similarity=0.381  Sum_probs=69.0

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEE
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKV  126 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v  126 (335)
                      +|.++++|||+|||.++|+++|+++|++||.|.+|++..++.    +|||||+|.+.++|.+|+..|||..|.|+.|+|
T Consensus         5 ~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           5 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345678899999999999999999999999999999988653    579999999999999999999999999999987

>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=99.79  E-value=2.4e-19  Score=129.20  Aligned_cols=104  Identities=17%  Similarity=0.240  Sum_probs=85.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +..+++|||+|||.++++++|+++|+.||.|.+|++..+. ++|||||+|.+.++|..|++.|||..|.|+.|+|.++..
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4457899999999999999999999999999999998764 479999999999999999999999999999999999854


Q ss_pred             CCCccCCCCcceEEECCCCccccHHHHHHHhccCCC
Q 019811          132 SGQREDTSGHFNIFVGDLSPEVTDATLFACFSVYPS  167 (335)
Q Consensus       132 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~  167 (335)
                      ....           ........++.+..+...+|.
T Consensus        84 ~~~~-----------~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          84 NRAF-----------QKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHHT-----------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             Cchh-----------hhhHHHHHHHHHHHHHHHhCC
Confidence            3211           122333456777777777663

>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=99.79  E-value=1.9e-19  Score=120.81  Aligned_cols=73  Identities=30%  Similarity=0.615  Sum_probs=69.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      +|||+|||+.+|+++|+++|++||+|.+|++.+++.    +|||||+|.+.++|..|++.|+|..+.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            599999999999999999999999999999998754    4899999999999999999999999999999999985

>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=99.79  E-value=3.1e-19  Score=123.53  Aligned_cols=84  Identities=29%  Similarity=0.455  Sum_probs=77.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeeeEEE
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQK-TGRSRGFGFVSFRNQQDAQSAINDL-TGKWLGSRQIRCN  216 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~g~~l~v~  216 (335)
                      ..+++|||+|||.++++++|+++|+.||.|.++.++++.. +|.++|||||+|.+.++|.+|++.| ++..+.|+.|.|.
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            3457899999999999999999999999999999988754 6889999999999999999999998 8999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      |++...
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997754

>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=99.79  E-value=6.2e-19  Score=122.36  Aligned_cols=80  Identities=20%  Similarity=0.408  Sum_probs=72.5

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ..+.++|||+|||.++|+++|+++|+.||.|..+.+..+. .++||||+|.+.++|..|++.|||..|.|++|+|.|+..
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            4556789999999999999999999999999999887653 568999999999999999999999999999999999864


Q ss_pred             C
Q 019811          132 S  132 (335)
Q Consensus       132 ~  132 (335)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.79  E-value=3.7e-19  Score=123.11  Aligned_cols=80  Identities=26%  Similarity=0.525  Sum_probs=72.4

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHh-CCccccCceeEEe
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSL-NGRHLFGQPIKVN  127 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l-~~~~~~g~~l~v~  127 (335)
                      ..+++|||+|||.++++++|+++|+.||.|.+|++..+.     ++|||||+|.+.++|.+|+..| ||..+.|++|+|.
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            345679999999999999999999999999999997653     4689999999999999999998 8999999999999


Q ss_pred             eeccCC
Q 019811          128 WAYASG  133 (335)
Q Consensus       128 ~~~~~~  133 (335)
                      |+....
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997654

>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=99.79  E-value=3.9e-19  Score=120.12  Aligned_cols=76  Identities=14%  Similarity=0.298  Sum_probs=69.3

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc-CceeEEeeec
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF-GQPIKVNWAY  130 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~-g~~l~v~~~~  130 (335)
                      .++++|||+|||.++++++|.++|+.||.|.++++.+++ +|||||+|.+.++|..|++.|+|..+. |+.|+|.|++
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            346889999999999999999999999999999997654 589999999999999999999998885 6899999985

>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=99.79  E-value=2.6e-19  Score=121.48  Aligned_cols=78  Identities=33%  Similarity=0.526  Sum_probs=73.6

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eeeEEEEc
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGS--RQIRCNWA  218 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g--~~l~v~~~  218 (335)
                      +++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.|+
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4689999999999999999999999999999999998889999999999999999999999999999987  55999885

>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=99.79  E-value=3e-19  Score=119.09  Aligned_cols=73  Identities=21%  Similarity=0.331  Sum_probs=68.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      +|||+|||+++++++|+++|++||.|.++++..++   ++|||||+|.+.++|.+|++.|||..+.|++|+|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999999999998765   36899999999999999999999999999999999874

>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=99.79  E-value=1.3e-18  Score=129.97  Aligned_cols=82  Identities=33%  Similarity=0.548  Sum_probs=74.7

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +...++|||+|||.++|+++|+++|+.||.|.+|++++++.    +|||||+|.+.++|.+|++.|||..|.|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44567899999999999999999999999999999998754    58999999999999999999999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.....
T Consensus       119 a~~~~~  124 (139)
T d1u6fa1         119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             cCCCCC
Confidence            876544

>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=99.79  E-value=5e-19  Score=132.21  Aligned_cols=85  Identities=27%  Similarity=0.450  Sum_probs=79.5

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++.|++..|+|+.|+|.|+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 019811          219 TKGAG  223 (335)
Q Consensus       219 ~~~~~  223 (335)
                      ..+..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76543

>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=2.1e-19  Score=121.87  Aligned_cols=77  Identities=23%  Similarity=0.475  Sum_probs=71.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      .+|||+|||..+|+++|+++|++||+|.++++.+++    ++|||||+|.+.++|..|++.|||..+.|+.|.|.++...
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            369999999999999999999999999999998864    4699999999999999999999999999999999999754


Q ss_pred             C
Q 019811          133 G  133 (335)
Q Consensus       133 ~  133 (335)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.79  E-value=2e-19  Score=121.14  Aligned_cols=79  Identities=11%  Similarity=0.214  Sum_probs=69.1

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      ++|||+|||+++|+++|+++|+.||.|..+.++.+...|.++|||||+|.+.++|.+|++.|++..+.|+.|+|+++++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5899999999999999999999999999888888878889999999999999999999999999999999999999865

>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=99.79  E-value=4.9e-19  Score=121.08  Aligned_cols=82  Identities=24%  Similarity=0.368  Sum_probs=75.6

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..+++|||+|||+++|+++|+++|+.||.|..+.+++|+.+|.++|||||+|.+.++|.+|++.  ...++|+.|.|.++
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            4457899999999999999999999999999999999999999999999999999999999984  45899999999998


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7754

>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=2.8e-19  Score=120.43  Aligned_cols=75  Identities=12%  Similarity=0.221  Sum_probs=67.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec----CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~----~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ++|||+|||.++|+++|+++|+.||.|..+.++.+    +++|||||+|.+.++|.+|++.|||..+.|++|+|.++.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            68999999999999999999999999988877654    3468999999999999999999999999999999999864

>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=99.78  E-value=5.7e-19  Score=119.35  Aligned_cols=80  Identities=33%  Similarity=0.499  Sum_probs=75.0

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ...++|||+|||.++++++|+++|+.||.|..+.+++|+.+|.++|||||+|.+.++|.+|++ +++..+.|+.|+|..+
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            344689999999999999999999999999999999999999999999999999999999997 6999999999999887


Q ss_pred             c
Q 019811          219 T  219 (335)
Q Consensus       219 ~  219 (335)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=4.1e-19  Score=120.23  Aligned_cols=79  Identities=32%  Similarity=0.680  Sum_probs=73.9

Q ss_pred             EEECCCCccccHHHHHHHhccCCCceee-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccCCC
Q 019811          144 IFVGDLSPEVTDATLFACFSVYPSCSDA-RVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATKGA  222 (335)
Q Consensus       144 l~v~nlp~~~t~~~l~~~f~~~g~v~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~~~  222 (335)
                      |||+|||+++++++|+++|+.||.|.++ .+++++.+|.++|||||+|.+.++|.+|++.+++..++|+.|+|.|+.++.
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            7999999999999999999999998764 788888889999999999999999999999999999999999999987654

>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=6.8e-19  Score=120.85  Aligned_cols=83  Identities=24%  Similarity=0.547  Sum_probs=75.5

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.||.|.++.+++++.+  .+|||||+|.+.++|.+|+..+++..+.|+.|+|.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344579999999999999999999999999999999988654  478999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +.++.
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            97654

>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=99.78  E-value=8.4e-19  Score=123.48  Aligned_cols=82  Identities=27%  Similarity=0.430  Sum_probs=72.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +.+.++|||+|||..+++++|+++|+.||.|.+|++..++    ++|||||+|.+.++|.+|++.+++ .+.|++|+|.+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            3455779999999999999999999999999999998864    468999999999999999998876 79999999999


Q ss_pred             eccCCCc
Q 019811          129 AYASGQR  135 (335)
Q Consensus       129 ~~~~~~~  135 (335)
                      +.....+
T Consensus        86 a~~~~~p   92 (103)
T d2cqda1          86 AYLGAKP   92 (103)
T ss_dssp             STTTCCC
T ss_pred             cCCCCCC
Confidence            8765543

>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=99.78  E-value=3.7e-19  Score=122.41  Aligned_cols=83  Identities=41%  Similarity=0.606  Sum_probs=78.1

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ...+|||+|||+++++++|.++|+.||.|..+.++++..++.++|||||+|.+.++|.+|+..|++..++|+.|+|+++.
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            44679999999999999999999999999999999888889999999999999999999999999999999999999987


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      ++.
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=99.78  E-value=1.1e-18  Score=122.93  Aligned_cols=82  Identities=35%  Similarity=0.527  Sum_probs=76.0

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ..++|||+|||..+++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+++ .+.|+.|.|.++.
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            346799999999999999999999999999999999998999999999999999999999998775 7999999999987


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      .+.
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>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=5.8e-19  Score=117.66  Aligned_cols=76  Identities=29%  Similarity=0.431  Sum_probs=72.7

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .|||+|||+++++++|+++|+.||.|.++.+.+++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|+|++++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999999999999885 78899999999999999999999999999999999999975

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.1e-18  Score=118.41  Aligned_cols=75  Identities=29%  Similarity=0.491  Sum_probs=67.9

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNW  128 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~  128 (335)
                      ..++|||+|||.++|+++|+++|++||.|.+++++.++.    +|||||+|.+.++|.+|++.|||..+.|  ++|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            346799999999999999999999999999999998653    5799999999999999999999999998  4588887


Q ss_pred             e
Q 019811          129 A  129 (335)
Q Consensus       129 ~  129 (335)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=5.5e-19  Score=119.98  Aligned_cols=77  Identities=25%  Similarity=0.447  Sum_probs=71.0

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ..++|||+|||.++++++|+++|++||.|.+|++.++  +|||||+|.+.++|.+|++.|||..|.|+.|+|.|+....
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~--k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD--KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT--TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc--cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3467999999999999999999999999999999765  4799999999999999999999999999999999997654

>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=99.77  E-value=1.2e-18  Score=118.28  Aligned_cols=76  Identities=28%  Similarity=0.424  Sum_probs=69.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEe
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVN  127 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~  127 (335)
                      ...++|||+|||.++++++|+++|++||.|.++++++++.    +|||||+|.+.++|.+|++.|||..+.|  ++|+|.
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            3456799999999999999999999999999999998653    4799999999999999999999999976  889998


Q ss_pred             ee
Q 019811          128 WA  129 (335)
Q Consensus       128 ~~  129 (335)
                      |+
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            85

>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=99.77  E-value=5.4e-19  Score=125.02  Aligned_cols=81  Identities=30%  Similarity=0.566  Sum_probs=77.1

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||.++++++|.++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|++..+.|+.|+|.|+..
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            35899999999999999999999999999999999998999999999999999999999999999999999999999865


Q ss_pred             C
Q 019811          221 G  221 (335)
Q Consensus       221 ~  221 (335)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.1e-19  Score=122.11  Aligned_cols=76  Identities=28%  Similarity=0.576  Sum_probs=68.2

Q ss_pred             CCcceEEEeCCC-CCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           54 STCRSVYVGNIH-TQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        54 ~~~~~v~v~nlp-~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ...++|||+||| ..+++++|+++|++||.|.++++    .+|||||+|.+.++|.+|++.|||..+.|++|+|.|+.+.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i----~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV----HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE----ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE----eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            345679999997 56888999999999999999988    3589999999999999999999999999999999999754


Q ss_pred             C
Q 019811          133 G  133 (335)
Q Consensus       133 ~  133 (335)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.77  E-value=5.3e-19  Score=125.82  Aligned_cols=81  Identities=25%  Similarity=0.347  Sum_probs=74.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccc--cCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHL--FGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~--~g~~l~v~~~~  130 (335)
                      +++..+|||+|||.++|+++|+++|++||.|.++++..++++|||||+|.+.++|.+|+..|||..+  .|+.|+|.++.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            5667889999999999999999999999999999999998889999999999999999999999988  47888998886


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            544

>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=99.77  E-value=3.6e-18  Score=117.87  Aligned_cols=84  Identities=29%  Similarity=0.469  Sum_probs=76.2

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|.++.+++++.  .++|||||+|.+.++|.+|+..|++..++|+.|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            344557899999999999999999999999999999998853  468999999999999999999999999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      |+.++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998754

>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=2.7e-19  Score=118.64  Aligned_cols=76  Identities=33%  Similarity=0.476  Sum_probs=72.4

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ++|||+|||.++|+++|+++|+.||.|.++.+++|+.+|.++|||||+|.+.++|.+|++ +++..++|+.|.|+.+
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            469999999999999999999999999999999999999999999999999999999997 6999999999999875

>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=1.1e-18  Score=118.60  Aligned_cols=78  Identities=23%  Similarity=0.436  Sum_probs=72.1

Q ss_pred             EEECCCCccccHHHHHHHhccCCCceeeEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTG---RSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       144 l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      |||+|||.++|+++|+++|+.||.|.++.+++++.++   .++|||||+|.+.++|.+|++.+++..++|+.|.|.|+..
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            7999999999999999999999999999999886654   3689999999999999999999999999999999999864


Q ss_pred             C
Q 019811          221 G  221 (335)
Q Consensus       221 ~  221 (335)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.77  E-value=7.5e-19  Score=126.12  Aligned_cols=79  Identities=16%  Similarity=0.225  Sum_probs=71.4

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      ....++|||+|||+++++++|+++|+.||.|.+|.+.  +.+|||||.|.+.++|.+|++.|||..|.|++|.|.|+...
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~--~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP--EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC--SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee--ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            3456789999999999999999999999999998874  45689999999999999999999999999999999998654


Q ss_pred             C
Q 019811          133 G  133 (335)
Q Consensus       133 ~  133 (335)
                      .
T Consensus        85 ~   85 (111)
T d1whxa_          85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.77  E-value=1.4e-18  Score=124.25  Aligned_cols=76  Identities=25%  Similarity=0.419  Sum_probs=70.0

Q ss_pred             cceEEEeCCCC-CCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           56 CRSVYVGNIHT-QVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        56 ~~~v~v~nlp~-~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      +++|||+|||+ .+|+++|+++|+.||.|.+|++++++ +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47899999965 59999999999999999999998875 589999999999999999999999999999999998643

>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=99.77  E-value=1.2e-18  Score=116.35  Aligned_cols=77  Identities=27%  Similarity=0.349  Sum_probs=69.8

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccC
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYAS  132 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~  132 (335)
                      |..+++|||+|+|  +|+++|+++|++||.|.++++.++  +|||||+|.+.++|..|++.|||..+.|++|+|.|+.++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~--~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP--RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT--TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC--CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            4567899999996  899999999999999999998654  579999999999999999999999999999999999754


Q ss_pred             C
Q 019811          133 G  133 (335)
Q Consensus       133 ~  133 (335)
                      +
T Consensus        78 P   78 (79)
T d2bz2a1          78 P   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=5.8e-19  Score=123.50  Aligned_cols=76  Identities=25%  Similarity=0.487  Sum_probs=70.0

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++++++|+++|+.||.|.+|.+++++    ++|||||+|.+.++|.+|+. |||..|.|+.|+|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999864    46899999999999999994 99999999999999875


Q ss_pred             c
Q 019811          131 A  131 (335)
Q Consensus       131 ~  131 (335)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.7e-18  Score=117.73  Aligned_cols=74  Identities=26%  Similarity=0.535  Sum_probs=68.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      |||+|||.++|+++|+++|++||.|.++++.+++.       +|||||+|.+.++|.+|++.|||..+.|+.|+|.++..
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            79999999999999999999999999999987542       47999999999999999999999999999999999854


Q ss_pred             C
Q 019811          132 S  132 (335)
Q Consensus       132 ~  132 (335)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.76  E-value=1.8e-18  Score=117.71  Aligned_cols=77  Identities=27%  Similarity=0.495  Sum_probs=69.7

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..  ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.+..
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~--~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK--IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE--CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc--ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            357899999999999999999999999998777644  56899999999999999999999999999999999987543

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2e-18  Score=116.60  Aligned_cols=77  Identities=19%  Similarity=0.436  Sum_probs=69.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      |...++|||+|||.++|+++|+++|+.||.|.++++..++.    +|||||+|.+.++|.+|++ +++..|.|+.|+|..
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            45668999999999999999999999999999999988653    5899999999999999996 689999999999987


Q ss_pred             ec
Q 019811          129 AY  130 (335)
Q Consensus       129 ~~  130 (335)
                      +.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            63

>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=99.76  E-value=4e-19  Score=121.97  Aligned_cols=79  Identities=16%  Similarity=0.324  Sum_probs=70.7

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec---CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK---DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~---~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+...++|||+|||.++|+++|+++|+.||.|.+++++.+   +++|||||+|.+.++|.+|++ |||..+.|+.|+|.+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            4556778999999999999999999999999888877553   467999999999999999995 999999999999999


Q ss_pred             ecc
Q 019811          129 AYA  131 (335)
Q Consensus       129 ~~~  131 (335)
                      +..
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.76  E-value=5.4e-19  Score=117.17  Aligned_cols=72  Identities=22%  Similarity=0.445  Sum_probs=66.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      |+|||+|||.++|+++|+++|++||.|.++++..++    ++|||||+|.+.++|.+|++ +++..+.|+.|.|..+
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            579999999999999999999999999999998765    46899999999999999996 7999999999999875

>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=99.76  E-value=1.4e-18  Score=117.57  Aligned_cols=75  Identities=29%  Similarity=0.615  Sum_probs=67.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeE-EEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGC-KLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v-~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      |||+|||.++|+++|+++|++||.|.++ ++.+++    ++|||||+|.+.++|.+|++.|+|..+.|++|+|.|+.++.
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            7999999999999999999999998664 676654    36899999999999999999999999999999999987654

>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=8.5e-19  Score=115.82  Aligned_cols=75  Identities=32%  Similarity=0.512  Sum_probs=70.8

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .|||+|||+++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++ +++..+.|+.|.|..+
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            48999999999999999999999999999999999999999999999999999999997 7889999999998653

>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=99.76  E-value=2e-18  Score=121.02  Aligned_cols=82  Identities=28%  Similarity=0.449  Sum_probs=76.6

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.++.+
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            3689999999999999999999999999999999998889999999999999999999996 799999999999999887


Q ss_pred             CCC
Q 019811          221 GAG  223 (335)
Q Consensus       221 ~~~  223 (335)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            543

>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=99.75  E-value=1.6e-18  Score=122.48  Aligned_cols=78  Identities=38%  Similarity=0.664  Sum_probs=72.0

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++++++|+++|++||.|.+|++..++.    +|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            457899999999999999999999999999999988754    4799999999999999999999999999999999986


Q ss_pred             cC
Q 019811          131 AS  132 (335)
Q Consensus       131 ~~  132 (335)
                      +.
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.75  E-value=1e-18  Score=118.79  Aligned_cols=77  Identities=25%  Similarity=0.338  Sum_probs=68.4

Q ss_pred             CcceEEEeCCCCCCC-HHHHHHHHhccCCceeEEEeec-----CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           55 TCRSVYVGNIHTQVT-EPLLQEVFSSTGPVEGCKLIRK-----DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t-~~~l~~~f~~~G~v~~v~~~~~-----~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +.++|||+|||.+++ +++|+++|++||.|.+|++..+     +++|||||+|.+.++|.+|++ |||..+.|+.|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            568999999999976 5679999999999999998653     246899999999999999995 999999999999999


Q ss_pred             eccC
Q 019811          129 AYAS  132 (335)
Q Consensus       129 ~~~~  132 (335)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>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=99.75  E-value=1.2e-18  Score=121.90  Aligned_cols=79  Identities=27%  Similarity=0.357  Sum_probs=75.1

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||.++++++|+++|+.||.|.++.++++..+|.++|||||+|.+.++|.+|++ |++..+.|+.|.|.++..
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            4689999999999999999999999999999999999899999999999999999999995 999999999999999754

>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=99.75  E-value=1.4e-18  Score=118.98  Aligned_cols=80  Identities=28%  Similarity=0.521  Sum_probs=73.9

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      ..+|||+|||.++++++|+++|+.||.|..+.++.+.  +.++|||||+|.+.++|.+|++.|+|..++|+.|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999999885  34789999999999999999999999999999999999976


Q ss_pred             CC
Q 019811          221 GA  222 (335)
Q Consensus       221 ~~  222 (335)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.75  E-value=4.8e-18  Score=118.12  Aligned_cols=78  Identities=12%  Similarity=0.173  Sum_probs=70.5

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ....+|||+|||.++++++|+++|+.||.|.++++.+   +|||||+|.+.++|.+|++.|||..|.|+.|+|.+.....
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~---~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK---DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET---TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc---cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            3456799999999999999999999999999998864   4799999999999999999999999999999999986544


Q ss_pred             C
Q 019811          134 Q  134 (335)
Q Consensus       134 ~  134 (335)
                      .
T Consensus        90 ~   90 (98)
T d1wg4a_          90 E   90 (98)
T ss_dssp             C
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=99.75  E-value=4.6e-18  Score=119.68  Aligned_cols=86  Identities=23%  Similarity=0.328  Sum_probs=77.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCce--------eeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCS--------DARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      +....++|||+|||..+++++|+++|+.||.|.        .+.+.+++.++.++|||||+|.+.++|.+|++.|++..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            344567999999999999999999999999874        456667777889999999999999999999999999999


Q ss_pred             CCeeeEEEEccCCC
Q 019811          209 GSRQIRCNWATKGA  222 (335)
Q Consensus       209 ~g~~l~v~~~~~~~  222 (335)
                      .|+.|+|.++..+.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999997754

>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=99.75  E-value=4.1e-18  Score=119.27  Aligned_cols=81  Identities=19%  Similarity=0.352  Sum_probs=71.9

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhC------CccccCc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLN------GRHLFGQ  122 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~------~~~~~g~  122 (335)
                      ..+.++|||+|||.++|+++|+++|++||.|.++.+..++    ++|||||+|.+.++|.+|++.++      |..+.|+
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            3456789999999999999999999999999999988754    46899999999999999999886      6778899


Q ss_pred             eeEEeeeccCC
Q 019811          123 PIKVNWAYASG  133 (335)
Q Consensus       123 ~l~v~~~~~~~  133 (335)
                      .|+|.++.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987654

>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=99.75  E-value=1.4e-18  Score=116.37  Aligned_cols=76  Identities=28%  Similarity=0.488  Sum_probs=68.6

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCc-cccCceeEEeeeccCCC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGR-HLFGQPIKVNWAYASGQ  134 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~-~~~g~~l~v~~~~~~~~  134 (335)
                      .+|||+|||.++|+++|+++|++||.|.++++..+  +|||||+|.+.++|.+|++.|||. .+.|++|+|.|+.++..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~--rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK--SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE--TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc--cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            36999999999999999999999999988777665  479999999999999999999996 59999999999987653

>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=99.75  E-value=5.9e-18  Score=115.63  Aligned_cols=78  Identities=17%  Similarity=0.222  Sum_probs=69.3

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ...++|||+|||+++|+++|+++|+.||.|.+|++..++.    +|||||.|.+.++|.+|++.  +..+.|+.|.|.++
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            3456799999999999999999999999999999998653    58999999999999999974  45889999999998


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7654

>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=99.75  E-value=2.6e-18  Score=113.42  Aligned_cols=71  Identities=23%  Similarity=0.397  Sum_probs=65.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +|||+|||+++|+++|+++|++||.|.++.+..++    ++|||||+|.+.++|++|++ +++..+.|+.|.|..+
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            49999999999999999999999999999998865    46899999999999999996 7999999999998643

>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=2.8e-18  Score=120.28  Aligned_cols=78  Identities=18%  Similarity=0.397  Sum_probs=70.9

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||+++++++|+++|++||.|.++.|.+++    ++|||||+|.+.++|.+|+. +++..|.|+.|.|.++.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            45789999999999999999999999999999998764    46999999999999999985 79999999999999987


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      ++.
T Consensus        98 ~ke  100 (103)
T d1x4ba1          98 ARE  100 (103)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            654

>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=99.75  E-value=5.3e-18  Score=118.73  Aligned_cols=85  Identities=22%  Similarity=0.344  Sum_probs=77.4

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCCe
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLT------GKWLGSR  211 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~------~~~~~g~  211 (335)
                      ...+++|||+|||.++|+++|+++|+.||.+..+.+..+..++.++|||||+|.+.++|.+|++.++      +..+.|+
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            3445789999999999999999999999999999999998888999999999999999999999886      5678999


Q ss_pred             eeEEEEccCCC
Q 019811          212 QIRCNWATKGA  222 (335)
Q Consensus       212 ~l~v~~~~~~~  222 (335)
                      .|+|.|+.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987653

>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=99.75  E-value=1.6e-18  Score=120.56  Aligned_cols=82  Identities=16%  Similarity=0.266  Sum_probs=72.3

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      ...+.++|||+|||.++|+++|+++|+.||.|..++. ..+++|||||+|.+.++|.+|++.|||..+.|+.|+|.|+.+
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3456789999999999999999999999999877653 334568999999999999999999999999999999999987


Q ss_pred             CCC
Q 019811          132 SGQ  134 (335)
Q Consensus       132 ~~~  134 (335)
                      +..
T Consensus        91 k~~   93 (96)
T d1fjca_          91 KGG   93 (96)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>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=99.74  E-value=6.7e-18  Score=113.00  Aligned_cols=76  Identities=22%  Similarity=0.395  Sum_probs=72.4

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ++|||+|||+++|+++|+++|+.||.+..+.+..++.++.++|||||+|.+.+++.+|+. +++..++|+.|.|+.+
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999995 8999999999999875

>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=99.74  E-value=4.1e-18  Score=119.49  Aligned_cols=77  Identities=17%  Similarity=0.269  Sum_probs=69.8

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ...++|||+|||.++++++|+++|+.||.|..+.+..+..   +|||||+|.+.++|.+|++.|||..|.|+++.|.++.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            3457899999999999999999999999999998887643   5899999999999999999999999999999987764

>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=99.74  E-value=7e-18  Score=112.93  Aligned_cols=73  Identities=19%  Similarity=0.365  Sum_probs=66.8

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC----CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK----SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~----~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .++|||+|||.++|+++|+++|++||.|..+++..++.    +|||||+|.+.++|.+|+ .++|..|.|+.|+|..+
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            57899999999999999999999999999999988653    489999999999999998 48999999999999865

>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=99.74  E-value=2.9e-18  Score=117.94  Aligned_cols=79  Identities=19%  Similarity=0.437  Sum_probs=70.4

Q ss_pred             CcceEEEeCCCCCCCHHHHHH----HHhccCCceeEEEeec-CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           55 TCRSVYVGNIHTQVTEPLLQE----VFSSTGPVEGCKLIRK-DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~----~f~~~G~v~~v~~~~~-~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ++++|||+|||..+++++|++    +|++||.|.+|++..+ +++|||||+|.+.++|.+|+..+||..+.|+.|+|.|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            468899999999999998864    6899999999988664 35789999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      ..++
T Consensus        82 k~~~   85 (91)
T d1nu4a_          82 KTDS   85 (91)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            7654

>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=1.1e-17  Score=118.26  Aligned_cols=79  Identities=27%  Similarity=0.391  Sum_probs=67.7

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .+.++|||+|||.++|+++|+++|+.|| +.+++++.+.     .+|||||+|.+.++|++|+ .||+..|.|+.|+|.+
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            3458899999999999999999999999 5677776543     3589999999999998666 6999999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876544

>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=99.74  E-value=1.7e-18  Score=122.07  Aligned_cols=80  Identities=20%  Similarity=0.326  Sum_probs=72.3

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec----CCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK----DKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~----~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .++++|||+|||.++++++|+++|+.||.|..+.+..+    +.+|||||+|.+.++|.+|++.|||..|.|+.|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            34678999999999999999999999999988877653    45799999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      .++.
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            7654

>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=99.74  E-value=1.6e-18  Score=118.16  Aligned_cols=71  Identities=13%  Similarity=0.195  Sum_probs=66.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeecc
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYA  131 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~  131 (335)
                      +|||+|||+++++++|+++|++||.|.++++.++   |||||+|.+.++|.+|++.|||..|.|+.|+|.++..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc---ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            5999999999999999999999999999998654   7999999999999999999999999999999887643

>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=99.74  E-value=1.3e-18  Score=122.68  Aligned_cols=85  Identities=22%  Similarity=0.372  Sum_probs=79.2

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .++++|||+|||.++++++|.++|..||.|..+.+..+..+|.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45679999999999999999999999999999999888778899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 019811          219 TKGAG  223 (335)
Q Consensus       219 ~~~~~  223 (335)
                      +.+..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87543

>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=99.74  E-value=2.1e-17  Score=114.90  Aligned_cols=78  Identities=19%  Similarity=0.365  Sum_probs=70.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC--ceeEEeeecc
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG--QPIKVNWAYA  131 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~~~  131 (335)
                      .++++|||+|||.++++++|+++|++||.|..+++.++  ++||||+|.+.++|.+|++.||+..|.|  ++|+|.|+.+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~--~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG--DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc--ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCC
Confidence            45688999999999999999999999999999998765  4699999999999999999999999986  5799999875


Q ss_pred             CC
Q 019811          132 SG  133 (335)
Q Consensus       132 ~~  133 (335)
                      .+
T Consensus        93 ~~   94 (97)
T d1whya_          93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=2.8e-18  Score=116.58  Aligned_cols=81  Identities=22%  Similarity=0.338  Sum_probs=70.3

Q ss_pred             CcceEEECCCCcccc-HHHHHHHhccCCCceeeEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          140 GHFNIFVGDLSPEVT-DATLFACFSVYPSCSDARVMWD-QKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t-~~~l~~~f~~~g~v~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..++|||+|||.+++ +++|+++|+.||.|.++.+..+ ..++.++|||||+|.+.++|.+|++ +++..++|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            357999999999986 5679999999999999998764 4678899999999999999999996 999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>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=99.73  E-value=5.5e-18  Score=111.71  Aligned_cols=72  Identities=18%  Similarity=0.196  Sum_probs=66.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC--CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK--SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~--~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+|||+|||+++++++|+++|+.||.|.+|++..++.  ++||||+|.+.++|.+|+ .+++..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            3799999999999999999999999999999987653  579999999999999998 58999999999999864

>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=99.73  E-value=2.8e-17  Score=115.84  Aligned_cols=80  Identities=16%  Similarity=0.115  Sum_probs=70.9

Q ss_pred             CCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh--CCccccCceeEEeee
Q 019811           52 DPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL--NGRHLFGQPIKVNWA  129 (335)
Q Consensus        52 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l--~~~~~~g~~l~v~~~  129 (335)
                      ...++++|||+|||.++|+++|+++|++||.|.++++.++  +++|||+|.+.++|..|+..+  ++..+.|++|+|.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~--k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF--KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec--ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            3456789999999999999999999999999999998754  479999999999999999877  567788999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T d1wexa_          89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             CCCc
Confidence            7644

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1e-17  Score=120.54  Aligned_cols=79  Identities=19%  Similarity=0.311  Sum_probs=72.9

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..+++|||+|||.++++++|.++|+.||.|.++.+..+   +.++|||||+|.+.++|..|+..|+|..++|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44679999999999999999999999999999988754   567899999999999999999999999999999999997


Q ss_pred             cC
Q 019811          219 TK  220 (335)
Q Consensus       219 ~~  220 (335)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            54

>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=99.73  E-value=3.9e-18  Score=113.03  Aligned_cols=75  Identities=31%  Similarity=0.545  Sum_probs=71.5

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .|||+|||+++|+++|+++|+.||.+..+.+..++.++.+++||||+|.+.++|.+|++ +++..++|+.|+|+++
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            48999999999999999999999999999999998889999999999999999999996 9999999999999875

>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=99.73  E-value=1e-17  Score=117.93  Aligned_cols=82  Identities=22%  Similarity=0.292  Sum_probs=70.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCce--------eEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVE--------GCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~--------~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      ....++|||+|||..+|+++|+++|+.||.|.        .+.+..++    .+|||||+|.+.++|.+|++.|||..|.
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            44567899999999999999999999999885        34444432    3589999999999999999999999999


Q ss_pred             CceeEEeeeccCCC
Q 019811          121 GQPIKVNWAYASGQ  134 (335)
Q Consensus       121 g~~l~v~~~~~~~~  134 (335)
                      |+.|+|.++.++.+
T Consensus        85 gr~i~V~~a~~~~p   98 (101)
T d2cpea1          85 GSKLKVSLARKKPP   98 (101)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CEEEEEEEcCCCCC
Confidence            99999999976654

>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=99.73  E-value=8.1e-18  Score=114.64  Aligned_cols=76  Identities=12%  Similarity=0.196  Sum_probs=66.3

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      .+++|||+|||.++++++|+++|++||. ..+.+  .+.+|||||+|.+.++|.+|++.||+..+.|+.|+|.++..+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~--~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV--DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE--EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee--eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4567999999999999999999999993 33343  3456899999999999999999999999999999999996554

>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=99.73  E-value=1.1e-17  Score=114.21  Aligned_cols=79  Identities=16%  Similarity=0.217  Sum_probs=70.7

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh--CCccccCceeEEeeec
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL--NGRHLFGQPIKVNWAY  130 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l--~~~~~~g~~l~v~~~~  130 (335)
                      ..++++|||+|||.++++++|+++|++||.|.++++.+++  +||||+|.+.++|.+|+..+  ++..+.|++|+|.|+.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~--~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK--NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT--TEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc--eEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            4577899999999999999999999999999999987654  69999999999999999864  6789999999999996


Q ss_pred             cCC
Q 019811          131 ASG  133 (335)
Q Consensus       131 ~~~  133 (335)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.6e-18  Score=114.00  Aligned_cols=75  Identities=24%  Similarity=0.462  Sum_probs=70.2

Q ss_pred             eEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          143 NIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       143 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .|||+|||+++|+++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++ .++..++|+.|.|+.+
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            48999999999999999999999999999999999999999999999999999999997 4778899999998764

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=6.9e-18  Score=116.92  Aligned_cols=70  Identities=40%  Similarity=0.581  Sum_probs=66.5

Q ss_pred             CCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       261 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..++|||+|||.++++++|+++|+.||  .|.++++.+++|+|||+|.+.++|.+|+..|+|.   .|+|++|+|
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG--~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~---~i~g~~l~v   86 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFG--QIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT---TIEGHVVKC   86 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHS--CEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTC---EETTEECEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhC--CceEEEEEecceEEEEEECCHHHHHHHHHHhCCC---EECCEEEEE
Confidence            347899999999999999999999999  5999999999999999999999999999999999   999999876

>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=99.73  E-value=3.5e-18  Score=116.64  Aligned_cols=78  Identities=22%  Similarity=0.278  Sum_probs=69.0

Q ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           54 STCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      ..+++|||+|||.++|+++|+++|++||.|.+|++..+ ++|||||+|.+.++|++|+.  ++..|.|++|+|.++.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            35678999999999999999999999999999987543 56899999999999999984  7889999999999997655


Q ss_pred             C
Q 019811          134 Q  134 (335)
Q Consensus       134 ~  134 (335)
                      .
T Consensus        80 ~   80 (88)
T d1wf0a_          80 N   80 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.72  E-value=1.1e-17  Score=116.31  Aligned_cols=80  Identities=23%  Similarity=0.334  Sum_probs=69.5

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCC-ceeEEEeecC-----CCCeEEEEEcCHHHHHHHHHHhCC--ccccCceeEEe
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGP-VEGCKLIRKD-----KSSYGFIHYFDRRSAAMAILSLNG--RHLFGQPIKVN  127 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~-v~~v~~~~~~-----~~g~afv~f~~~~~A~~a~~~l~~--~~~~g~~l~v~  127 (335)
                      .|+|||+|||.++++++|+++|+.||+ |.++.+.++.     ++|||||+|.+.++|..|++.|++  ..+.|+.|+|.
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            368999999999999999999999996 8899987653     468999999999999999998864  45579999999


Q ss_pred             eeccCCCc
Q 019811          128 WAYASGQR  135 (335)
Q Consensus       128 ~~~~~~~~  135 (335)
                      |+.++..+
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99876544

>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=99.72  E-value=1.7e-17  Score=118.41  Aligned_cols=77  Identities=25%  Similarity=0.468  Sum_probs=70.2

Q ss_pred             cceEEECCCCc-cccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          141 HFNIFVGDLSP-EVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       141 ~~~l~v~nlp~-~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      +++|||+|||+ .+++++|+++|+.||.|.++.+++++     +|+|||+|.+.++|.+|++.|++..+.|+.|+|.|++
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            56899999965 59999999999999999999998663     6899999999999999999999999999999999987


Q ss_pred             CCC
Q 019811          220 KGA  222 (335)
Q Consensus       220 ~~~  222 (335)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>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=99.72  E-value=1.9e-17  Score=109.06  Aligned_cols=72  Identities=14%  Similarity=0.260  Sum_probs=64.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeeccCC
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAYASG  133 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~  133 (335)
                      |||+|||+++++++|+++|++|| +..+++  ++++|||||.|.+.++|.+|+..|||..+.|++|+|.++....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~--~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV--DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE--ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee--cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444444  5567899999999999999999999999999999999996543

>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=99.72  E-value=1.3e-17  Score=117.11  Aligned_cols=85  Identities=13%  Similarity=0.177  Sum_probs=72.2

Q ss_pred             CCCCCCCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCcee
Q 019811           48 PPGFDPSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPI  124 (335)
Q Consensus        48 ~~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l  124 (335)
                      .....+....+|||+|||+++|+++|+++|..||.+ .|.+..+..   +|||||+|.+.++|.+|++ +|+..|.|+.|
T Consensus         7 ~~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I   84 (102)
T d1weza_           7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYV   84 (102)
T ss_dssp             CSSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCC
T ss_pred             CCCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEE
Confidence            334456667889999999999999999999999865 667766543   5899999999999999985 89999999999


Q ss_pred             EEeeeccCCC
Q 019811          125 KVNWAYASGQ  134 (335)
Q Consensus       125 ~v~~~~~~~~  134 (335)
                      +|.++.....
T Consensus        85 ~V~~s~~~~~   94 (102)
T d1weza_          85 ELFLNSTAGT   94 (102)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEcCCCCC
Confidence            9999876654

>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=99.72  E-value=2.4e-17  Score=114.17  Aligned_cols=81  Identities=22%  Similarity=0.418  Sum_probs=72.9

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..++++|||+|||+++++++|+++|+.||.|..+.+.++   +.+++||||+|.+.++|..|++.|++..+.|+.|+|+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345568999999999999999999999999999887644   45789999999999999999999999999999999999


Q ss_pred             ccCC
Q 019811          218 ATKG  221 (335)
Q Consensus       218 ~~~~  221 (335)
                      ++..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8654

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.6e-17  Score=112.37  Aligned_cols=75  Identities=19%  Similarity=0.179  Sum_probs=68.6

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC---CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK---SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~---~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ..++|||+|||.++|+++|+++|+.||+|.+|++..+.+   +|||||+|.+.++|.+|++ ++|..+.|+.|.|.|..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999999987653   5899999999999999995 79999999999999864

>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=99.72  E-value=5.7e-18  Score=118.76  Aligned_cols=81  Identities=17%  Similarity=0.379  Sum_probs=73.4

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..+.|+++.|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            344578999999999999999999999999999988887 4678999999999999999999999999999999988766


Q ss_pred             cc
Q 019811          218 AT  219 (335)
Q Consensus       218 ~~  219 (335)
                      +.
T Consensus        94 ~~   95 (101)
T d1x5oa1          94 TE   95 (101)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.72  E-value=3.2e-18  Score=116.92  Aligned_cols=72  Identities=19%  Similarity=0.339  Sum_probs=65.6

Q ss_pred             cceEEEeCCCCCCCHHHH---HHHHhccCCceeEEEeecCC-------CCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           56 CRSVYVGNIHTQVTEPLL---QEVFSSTGPVEGCKLIRKDK-------SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l---~~~f~~~G~v~~v~~~~~~~-------~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      .++|||+|||+++++++|   +++|++||.|.+|.+.+++.       +|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            456999999999999999   67899999999999987642       37999999999999999999999999999999


Q ss_pred             Ee
Q 019811          126 VN  127 (335)
Q Consensus       126 v~  127 (335)
                      +.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            74

>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=99.72  E-value=8.7e-18  Score=111.34  Aligned_cols=71  Identities=14%  Similarity=0.291  Sum_probs=65.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +|||+|||+++|+++|+++|+.||.|..+.+..++    .+|||||+|.+.++|.+|++ +||..+.|+.|+|.++
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            49999999999999999999999999998887754    35899999999999999996 9999999999999864

>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=99.72  E-value=7.7e-18  Score=114.22  Aligned_cols=69  Identities=36%  Similarity=0.631  Sum_probs=65.7

Q ss_pred             CCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          262 YTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       262 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      .++|||+|||.++++++|+++|+.||  .|.++++.+++++|||+|.+.++|.+|+..|||.   .|+|++|+|
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G--~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~---~i~g~~l~V   76 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM---PLRGKQLRV   76 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTC--CCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTC---CBTTBCCEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhC--CceEeeeecccceEEEEECCHHHHHHHHHHhCCC---EECCEEEEE
Confidence            36799999999999999999999999  5999999999999999999999999999999999   999999976

>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=99.72  E-value=4.9e-18  Score=111.70  Aligned_cols=71  Identities=17%  Similarity=0.300  Sum_probs=64.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           58 SVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        58 ~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      +|||+|||+++|+++|+++|++||.|.+|++..++    ++|||||+|.+.++|.+|++ .++..+.|+.|.|..+
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            49999999999999999999999999999998865    46899999999999999996 5778899999988753

>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=118.75  Aligned_cols=82  Identities=29%  Similarity=0.467  Sum_probs=74.3

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .+...++|||+|||+++++++|+++|+.||.|..+.++.+ .+|.++|||||+|.+.++|.+|++ +++..++|+.|+|.
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3445679999999999999999999999999998888654 678999999999999999999996 99999999999999


Q ss_pred             EccC
Q 019811          217 WATK  220 (335)
Q Consensus       217 ~~~~  220 (335)
                      +++.
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9875

>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=99.71  E-value=3e-17  Score=111.67  Aligned_cols=79  Identities=22%  Similarity=0.320  Sum_probs=70.9

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..++|||+|||.++++++|+++|+.||.+....++.+..++.++|+|||+|.+.++|.+|+..|++..+.|+.|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4468999999999999999999999999876544445578899999999999999999999999999999999999874

>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=99.71  E-value=2.7e-17  Score=114.61  Aligned_cols=79  Identities=16%  Similarity=0.201  Sum_probs=70.1

Q ss_pred             CCCcceEEEeCCCCC-CCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHH--HhCCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAIL--SLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~--~l~~~~~~g~~l~v~~~  129 (335)
                      +..+++|||+|||.+ +|+++|.++|+.||.|.++.+.+++  |+|||+|.+.++|.+|++  .+++..+.|+.|+|.++
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k--~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK--SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT--TEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC--CcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            456688999999985 8999999999999999999997654  799999999999999997  57889999999999999


Q ss_pred             ccCC
Q 019811          130 YASG  133 (335)
Q Consensus       130 ~~~~  133 (335)
                      ..+.
T Consensus        93 ~~~~   96 (99)
T d1x4fa1          93 EKYK   96 (99)
T ss_dssp             CSCS
T ss_pred             CCcc
Confidence            6543

>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=99.71  E-value=4.3e-17  Score=110.22  Aligned_cols=77  Identities=9%  Similarity=0.119  Sum_probs=71.8

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .++|||+|||.++|+++|+++|+.||.|..+.+.++ .+|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.|..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999877 478899999999999999999996 79999999999999864

>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=99.71  E-value=7.5e-17  Score=113.68  Aligned_cols=81  Identities=10%  Similarity=0.039  Sum_probs=68.6

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeec-C---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRK-D---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~-~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      ..+...|||+|||+++|+++|+++|..+|.+..+.++.+ .   .+|||||+|.+.++|.+|++ +|+..|.|+.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            445557999999999999999999999998876444443 2   36899999999999999985 899999999999999


Q ss_pred             eccCCC
Q 019811          129 AYASGQ  134 (335)
Q Consensus       129 ~~~~~~  134 (335)
                      +.....
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            876543

>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=99.70  E-value=1.3e-17  Score=111.43  Aligned_cols=76  Identities=26%  Similarity=0.406  Sum_probs=68.6

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeeeEEEEccC
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK-WLGSRQIRCNWATK  220 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~-~~~g~~l~v~~~~~  220 (335)
                      ++|||+|||.++++++|+++|++||.+..+.+..      .+|||||+|.+.++|.+|++.|+|. .+.|+.|+|+|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4699999999999999999999999998877764      4689999999999999999999986 69999999999987


Q ss_pred             CCC
Q 019811          221 GAG  223 (335)
Q Consensus       221 ~~~  223 (335)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            653

>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=99.70  E-value=3.7e-17  Score=111.65  Aligned_cols=77  Identities=16%  Similarity=0.321  Sum_probs=69.2

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCeeeEEEEc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL-GSRQIRCNWA  218 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~-~g~~l~v~~~  218 (335)
                      ++++|||+|||.++++++|+++|+.||.+..+.+...    ..+|+|||+|.+.++|.+|+..|+|..+ +|+.|+|+|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            4679999999999999999999999999988766533    4578999999999999999999999988 5899999998


Q ss_pred             cC
Q 019811          219 TK  220 (335)
Q Consensus       219 ~~  220 (335)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>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=99.70  E-value=1.6e-17  Score=113.40  Aligned_cols=77  Identities=16%  Similarity=0.226  Sum_probs=69.5

Q ss_pred             CcceEEECCCCccccHHHH---HHHhccCCCceeeEEeecCCCCC---cceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          140 GHFNIFVGDLSPEVTDATL---FACFSVYPSCSDARVMWDQKTGR---SRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l---~~~f~~~g~v~~~~~~~~~~~~~---~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      ..+.|||+|||+++++++|   .++|++||.|..+.+.+++.++.   .+|||||+|.+.++|.+|++.|||..++|+.|
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            3468999999999999999   67899999999999998876554   45899999999999999999999999999999


Q ss_pred             EEE
Q 019811          214 RCN  216 (335)
Q Consensus       214 ~v~  216 (335)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.70  E-value=4.8e-17  Score=108.49  Aligned_cols=75  Identities=24%  Similarity=0.333  Sum_probs=68.3

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..+++|||+|++  +|+++|+++|++||.|.++.+.      ..+++|||+|.+.++|..|+..|++..++|+.|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~------~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeec------cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345799999996  8999999999999999999887      34679999999999999999999999999999999999


Q ss_pred             cCC
Q 019811          219 TKG  221 (335)
Q Consensus       219 ~~~  221 (335)
                      +++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            764

>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=5e-17  Score=109.55  Aligned_cols=77  Identities=18%  Similarity=0.369  Sum_probs=69.4

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCeeeEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL-GSRQIRCN  216 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~-~g~~l~v~  216 (335)
                      ..++++|||+|||.++++++|.++|+.||.|..+.+.++     .+|+|||+|.+.++|..|+..|+|..+ +|+.|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            345679999999999999999999999999999998743     367999999999999999999999888 57899999


Q ss_pred             Ecc
Q 019811          217 WAT  219 (335)
Q Consensus       217 ~~~  219 (335)
                      |++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.70  E-value=6.6e-18  Score=110.84  Aligned_cols=71  Identities=24%  Similarity=0.493  Sum_probs=68.0

Q ss_pred             EEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeE
Q 019811          144 IFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIR  214 (335)
Q Consensus       144 l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~  214 (335)
                      |||+|||.++|+++|+++|+.||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.|||..+.|+.++
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            79999999999999999999999999999999988999999999999999999999999999999998764

>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=99.70  E-value=6.6e-18  Score=110.84  Aligned_cols=67  Identities=21%  Similarity=0.337  Sum_probs=62.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC----CCCeEEEEEcCHHHHHHHHHHhCCccccCceeE
Q 019811           59 VYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD----KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIK  125 (335)
Q Consensus        59 v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~----~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~  125 (335)
                      |||+|||.++|+++|+++|+.||.|.++++..++    .+|||||+|.+.++|.+|++.|||..|.|+.++
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            7999999999999999999999999999988764    468999999999999999999999999998874

>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=99.69  E-value=3.8e-17  Score=111.35  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=69.8

Q ss_pred             CCCcceEEEeCCCCC-CCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh--CCccccCceeEEeee
Q 019811           53 PSTCRSVYVGNIHTQ-VTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL--NGRHLFGQPIKVNWA  129 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~-~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l--~~~~~~g~~l~v~~~  129 (335)
                      ..++++|||+|||.. +|++||+++|++||.|.++++..++  ++|||+|.+.++|..|+..+  ++..+.|++|+|.|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k--~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s   82 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   82 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS--SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc--eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEEC
Confidence            456789999999986 7899999999999999999997765  59999999999999999865  678899999999999


Q ss_pred             ccC
Q 019811          130 YAS  132 (335)
Q Consensus       130 ~~~  132 (335)
                      ...
T Consensus        83 ~~~   85 (89)
T d1x4da1          83 QKY   85 (89)
T ss_dssp             CCC
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=99.69  E-value=1.1e-16  Score=113.05  Aligned_cols=83  Identities=27%  Similarity=0.477  Sum_probs=72.1

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQ-KTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ..+.++|||+|||.++++++|+++|+.|| +..+.++.+. .++.++|||||+|.+.++|.+|+ .|++..|.|+.|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            34568999999999999999999999998 7777776654 46788999999999999998777 599999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++..+.
T Consensus        90 ~a~~~~   95 (104)
T d1wi8a_          90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            987654

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=8.1e-17  Score=109.41  Aligned_cols=76  Identities=25%  Similarity=0.337  Sum_probs=69.4

Q ss_pred             cceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEccC
Q 019811          141 HFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWATK  220 (335)
Q Consensus       141 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~~  220 (335)
                      .++|||+|||.++++++|+++|+.||.+..+.+.      .++|||||+|.+.++|..|+..|++..++|+.|.|.|+.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4689999999999999999999999998877764      4578999999999999999999999999999999999876


Q ss_pred             CC
Q 019811          221 GA  222 (335)
Q Consensus       221 ~~  222 (335)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpda1          82 VD   83 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.69  E-value=2.4e-17  Score=118.08  Aligned_cols=68  Identities=15%  Similarity=0.174  Sum_probs=65.3

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ++|||+|||+++++++|+++|+.||  .|..|.+.+.+|+|||+|.+.++|.+|++.|||.   .|.|++|.|
T Consensus        11 ~~l~V~nLp~~~t~~~L~~~F~~fG--~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~---~~~gr~l~v   78 (111)
T d1whxa_          11 TVILAKNLPAGTLAAEIQETFSRFG--SLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS---KFHHVPLYL   78 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTS--CEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTC---BSSSSBCEE
T ss_pred             CEEEEECCCCCCCHHHHHhhhhccC--CccEEEeeccCceEEEEEcCHHHHHHHHHHHcCC---ccCCCeEEE
Confidence            7899999999999999999999999  6999999999999999999999999999999999   999999975

>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=99.69  E-value=9.6e-17  Score=109.23  Aligned_cols=77  Identities=21%  Similarity=0.260  Sum_probs=66.8

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      .++++|||+|||.++++++|+++|+.|| +..+.+      +..++||||+|.+.++|.+|++.|++..+.|+.|+|+|+
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3457899999999999999999999999 333333      256889999999999999999999999999999999998


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      ....
T Consensus        76 ~~~~   79 (88)
T d1wg1a_          76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3.7e-17  Score=113.52  Aligned_cols=82  Identities=21%  Similarity=0.329  Sum_probs=72.5

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCC-ceeeEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeeeEEEE
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPS-CSDARVMWDQ-KTGRSRGFGFVSFRNQQDAQSAINDLTG--KWLGSRQIRCNW  217 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~-v~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~g~~l~v~~  217 (335)
                      +.|||+|||.++++++|+++|+.||. |..+.++++. .++.++|||||+|.+.++|..|++.|++  ..++|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999995 8999998875 3578999999999999999999999865  456899999999


Q ss_pred             ccCCCC
Q 019811          218 ATKGAG  223 (335)
Q Consensus       218 ~~~~~~  223 (335)
                      ++++..
T Consensus        82 A~p~~~   87 (96)
T d2disa1          82 AEPEID   87 (96)
T ss_dssp             SCSSCS
T ss_pred             cCCCCC
Confidence            977543

>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=99.69  E-value=6.2e-17  Score=110.05  Aligned_cols=74  Identities=18%  Similarity=0.233  Sum_probs=65.1

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCcee-EEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEG-CKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~-v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..+|||+|||.++++++|+++|+.||.+.. +.+..+.   ++|+|||+|.+.++|.+|++.||+..+.|++|+|.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            456999999999999999999999998865 4555443   3589999999999999999999999999999999864

>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=5e-17  Score=112.82  Aligned_cols=82  Identities=17%  Similarity=0.359  Sum_probs=72.8

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||.++++++|+++|+.||.|..+.     .++.+++||||+|.+.++|.+|+..|++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345568999999999999999999999999876553     256889999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 019811          217 WATKGAG  223 (335)
Q Consensus       217 ~~~~~~~  223 (335)
                      |+.++..
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9987653

>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=99.69  E-value=1.1e-16  Score=111.11  Aligned_cols=76  Identities=26%  Similarity=0.459  Sum_probs=68.2

Q ss_pred             CCcceEEECCCC-ccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          139 SGHFNIFVGDLS-PEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       139 ~~~~~l~v~nlp-~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ..+.+|||+||| ..+++++|+++|++||.|.++.+.        +|||||+|.+.++|.+|+..|++..+.|+.|+|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445679999997 567889999999999999999873        68999999999999999999999999999999999


Q ss_pred             ccCCC
Q 019811          218 ATKGA  222 (335)
Q Consensus       218 ~~~~~  222 (335)
                      +..+.
T Consensus        85 a~~~~   89 (98)
T d1wf2a_          85 AAEPK   89 (98)
T ss_dssp             TTSCC
T ss_pred             CCCCC
Confidence            87643

>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=99.69  E-value=3.9e-17  Score=107.53  Aligned_cols=65  Identities=22%  Similarity=0.305  Sum_probs=62.2

Q ss_pred             EEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          265 VYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       265 l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      |||+|||+++++++|+++|++||   +..+.+.+.+|+|||+|.+.++|.+|+..|||.   .++|++|+|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g---~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~---~~~g~~l~V   65 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE---LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQS---RLRERELSV   65 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC---EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTE---ESSSCEEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc---ccceeecccceeEEEEECCHHHHHHHHHHhCCc---cCCCCEEEE
Confidence            79999999999999999999999   778888999999999999999999999999999   999999976

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.8e-16  Score=111.63  Aligned_cols=85  Identities=21%  Similarity=0.232  Sum_probs=75.9

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      ......+|||+|||+++|+++|+++|..+|.+....++.+..++.++|+|||+|.+.++|.+|++ +++..|+||.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34455689999999999999999999999998887677777788999999999999999999996 89999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            997754

>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=99.68  E-value=5.1e-17  Score=110.50  Aligned_cols=66  Identities=23%  Similarity=0.314  Sum_probs=61.8

Q ss_pred             eEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          264 TVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       264 ~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      +|||+|||+++++++|+++|+.||  .|.++.+.+ +|+|||+|.+.++|.+|+..|+|.   .|+|+.|+|
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G--~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~l~g~---~~~g~~i~v   67 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAG--DVCYADVYR-DGTGVVEFVRKEDMTYAVRKLDNT---KFRSHEGET   67 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGS--CEEEEEECT-TSEEEEEESSHHHHHHHHHHHTTC---BCCCTTSCC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhc--ccccccccc-cceeeEEeCCHHHHHHHHHHhCCC---EECCcEeEE
Confidence            599999999999999999999999  588888876 499999999999999999999999   999999875

>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=99.67  E-value=3.5e-17  Score=112.41  Aligned_cols=80  Identities=21%  Similarity=0.355  Sum_probs=71.1

Q ss_pred             CcceEEECCCCccccHHHHHH----HhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEE
Q 019811          140 GHFNIFVGDLSPEVTDATLFA----CFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRC  215 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~----~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v  215 (335)
                      ++++|||+|||..+++++|++    +|+.||.|.++.+.+   ++.++|||||+|.+.++|.+|++.+++..+.|+.|+|
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            457999999999999998864    589999999988763   3567899999999999999999999999999999999


Q ss_pred             EEccCCC
Q 019811          216 NWATKGA  222 (335)
Q Consensus       216 ~~~~~~~  222 (335)
                      .|++.+.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9997653

>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=99.67  E-value=3e-16  Score=107.01  Aligned_cols=80  Identities=14%  Similarity=0.204  Sum_probs=71.1

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeeeE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL--TGKWLGSRQIR  214 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~g~~l~  214 (335)
                      +..++++|||+|||.++++++|+++|+.||.|.++.+.+      .+++|||+|.+.++|.+|++.+  ++..+.|+.|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~------~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc------cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            456778999999999999999999999999999998873      3579999999999999999865  67789999999


Q ss_pred             EEEccCCC
Q 019811          215 CNWATKGA  222 (335)
Q Consensus       215 v~~~~~~~  222 (335)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997653

>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=2e-16  Score=110.93  Aligned_cols=83  Identities=16%  Similarity=0.200  Sum_probs=73.0

Q ss_pred             CCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEE
Q 019811          137 DTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCN  216 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~  216 (335)
                      .....++|||+|||+++|+++|+++|..|| +..+.++++ .++..+|||||+|.+.++|.+|++ +++..|+||.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            344557999999999999999999999997 456777777 457899999999999999999986 89999999999999


Q ss_pred             EccCCC
Q 019811          217 WATKGA  222 (335)
Q Consensus       217 ~~~~~~  222 (335)
                      ++....
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            988754

>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=99.67  E-value=1.5e-16  Score=104.72  Aligned_cols=74  Identities=19%  Similarity=0.231  Sum_probs=67.7

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ++|||+|||+++++++|+++|+.||.|..+.+.+++.  ..+++|||+|.+.++|.+|+. +++..++|+.|.|...
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999998854  346799999999999999995 8999999999999865

>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=99.67  E-value=3.3e-16  Score=108.75  Aligned_cols=71  Identities=24%  Similarity=0.415  Sum_probs=64.8

Q ss_pred             CCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCc--cccC
Q 019811          260 PQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGK--QMKV  335 (335)
Q Consensus       260 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~--~l~v  335 (335)
                      +++++|||+|||+++++++|+++|+.||  .|..+++.+++++|||+|.+.++|.+|++.|+|.   .|+|+  +|+|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~---~i~g~~~~l~v   87 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFG--SIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF---PLGGPDRRLRV   87 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTS--CEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTC---BCSSSSCBCEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhc--ccceEeeeccccEEEeccCCHHHHHHHHHHhCCC---EeCCCceEEEE
Confidence            4568999999999999999999999999  5899999999999999999999999999999999   88775  5543

>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=99.66  E-value=2.4e-16  Score=111.84  Aligned_cols=82  Identities=18%  Similarity=0.177  Sum_probs=73.0

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeeeEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWL--GSRQIRC  215 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~--~g~~l~v  215 (335)
                      ..+...|||+|||..+|+++|+++|++||.|..+.+.++    +.+|+|||+|.+.++|..|+..|++..+  .++.|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~----~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee----CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            345578999999999999999999999999999999876    3579999999999999999999999988  5789999


Q ss_pred             EEccCCCC
Q 019811          216 NWATKGAG  223 (335)
Q Consensus       216 ~~~~~~~~  223 (335)
                      .|+.....
T Consensus        80 ~~s~~~~~   87 (108)
T d2adba1          80 DFSKLTSL   87 (108)
T ss_dssp             EECSSCSC
T ss_pred             EecCCccc
Confidence            99876543

>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=99.65  E-value=2.8e-16  Score=109.03  Aligned_cols=69  Identities=23%  Similarity=0.320  Sum_probs=63.6

Q ss_pred             CCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccccC
Q 019811          261 QYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       261 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ...+|||+|||+++++++|+++|+.||  .|..+.+.+ +|+|||+|.+.++|.+|++.|||.   .|+|+.|+|
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G--~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~lng~---~~~g~~i~v   82 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAG--DVCYADVQK-DGMGMVEYLRKEDMEYALRKLDDT---KFRSHEGET   82 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSS--CEEEEEEET-TTEEEEEESSHHHHHHHHHHHSSE---EEECTTSCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhc--ccccccccc-cceEEEEECCHHHHHHHHHHhCCC---EeCCeEEEE
Confidence            447899999999999999999999999  588888765 699999999999999999999999   999999875

>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=99.65  E-value=1.1e-15  Score=107.59  Aligned_cols=82  Identities=17%  Similarity=0.172  Sum_probs=71.7

Q ss_pred             cCCCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeee
Q 019811          136 EDTSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL--TGKWLGSRQI  213 (335)
Q Consensus       136 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~g~~l  213 (335)
                      ....++.+|||+|||..+++++|.++|+.||.|..+.+.+      .+++|||+|.+.++|..|+..+  ++..++|+.|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            3445678999999999999999999999999999998873      4679999999999999999977  5567899999


Q ss_pred             EEEEccCCCC
Q 019811          214 RCNWATKGAG  223 (335)
Q Consensus       214 ~v~~~~~~~~  223 (335)
                      +|.|++.+..
T Consensus        84 ~v~~s~~~~~   93 (104)
T d1wexa_          84 FFNYSTSKRI   93 (104)
T ss_dssp             EEEECSSSSC
T ss_pred             EEEEcCCCcc
Confidence            9999977543

>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=99.65  E-value=1.6e-16  Score=108.28  Aligned_cols=77  Identities=27%  Similarity=0.340  Sum_probs=68.3

Q ss_pred             CCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          139 SGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..+++|||+|||.++|+++|+++|++||.|.++.+.     +.+++||||+|.+.++|.+|+.  ++..+.|+.|+|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            356799999999999999999999999999998765     3467899999999999999985  788999999999998


Q ss_pred             cCCC
Q 019811          219 TKGA  222 (335)
Q Consensus       219 ~~~~  222 (335)
                      .++.
T Consensus        76 ~~k~   79 (88)
T d1wf0a_          76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.65  E-value=2.7e-16  Score=110.71  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=71.6

Q ss_pred             CcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          140 GHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       140 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      ...+|||+|||+++++++|+++|..||.+....++.+..+|.++|+|||+|.+.++|.+|++ +++..|.|+.|.|.++.
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            44689999999999999999999999998876555555788999999999999999999996 89999999999999874


Q ss_pred             C
Q 019811          220 K  220 (335)
Q Consensus       220 ~  220 (335)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
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=99.62  E-value=5.4e-16  Score=107.88  Aligned_cols=71  Identities=17%  Similarity=0.256  Sum_probs=64.3

Q ss_pred             CCCCeEEEcCCCcc-cCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHH--hhcCCCcccccCccccC
Q 019811          260 PQYTTVYVGNLAPE-VTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQ--MGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       260 ~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~--~l~g~~~~~~~g~~l~v  335 (335)
                      ..+++|||+|||.+ +|+++|.++|+.||  .|..+.+.+++|+|||+|.+.++|.+|++  .+++.   .|+|++|+|
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 ELGRVIHLSNLPHSGYSDSAVLKLAEPYG--KIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL---WFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTS--CCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCC---CSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhcccc--ceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCc---eECCEEEEE
Confidence            34589999999985 89999999999999  69999999999999999999999999997  46787   899999976

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.7e-16  Score=109.43  Aligned_cols=76  Identities=12%  Similarity=0.103  Sum_probs=65.7

Q ss_pred             CcceEEEeCCCCCCCHHHHHHHHhccCCcee-EEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           55 TCRSVYVGNIHTQVTEPLLQEVFSSTGPVEG-CKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        55 ~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~-v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ...+|||+|||+++|+++|+++|..||.|.. +.+..+.   .+|+|||+|.+.++|.+|+. +|+..|.|+.|.|.++.
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            3466999999999999999999999998876 4444432   47999999999999999995 99999999999998874


Q ss_pred             c
Q 019811          131 A  131 (335)
Q Consensus       131 ~  131 (335)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=1.2e-15  Score=103.72  Aligned_cols=79  Identities=14%  Similarity=0.154  Sum_probs=69.6

Q ss_pred             CCCCcceEEECCCCcc-ccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeee
Q 019811          137 DTSGHFNIFVGDLSPE-VTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDL--TGKWLGSRQI  213 (335)
Q Consensus       137 ~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~g~~l  213 (335)
                      ....+++|||+|||.. +|++||.++|++||.|..+.+.++      +++|||+|++.++|..|++.+  ++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            3456789999999986 889999999999999999999844      468999999999999999966  6778999999


Q ss_pred             EEEEccCC
Q 019811          214 RCNWATKG  221 (335)
Q Consensus       214 ~v~~~~~~  221 (335)
                      +|.|++..
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99999754

>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=99.61  E-value=5.4e-16  Score=110.60  Aligned_cols=77  Identities=13%  Similarity=0.129  Sum_probs=65.2

Q ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhccCCceeEEE-eecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           53 PSTCRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKL-IRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        53 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~-~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      .....+|||+|||+++|+++|+++|+.||.+..+.+ ..+.   .+|+|||+|.+.++|.+|+. +||..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            445668999999999999999999999998865433 3332   35899999999999999985 999999999999987


Q ss_pred             ec
Q 019811          129 AY  130 (335)
Q Consensus       129 ~~  130 (335)
                      +.
T Consensus        94 ~~   95 (112)
T d1wela1          94 IT   95 (112)
T ss_dssp             EC
T ss_pred             cC
Confidence            64

>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=99.61  E-value=4.2e-16  Score=109.13  Aligned_cols=78  Identities=18%  Similarity=0.195  Sum_probs=68.4

Q ss_pred             CCcceEEEeCCCCCC-CH----HHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEee
Q 019811           54 STCRSVYVGNIHTQV-TE----PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNW  128 (335)
Q Consensus        54 ~~~~~v~v~nlp~~~-t~----~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~  128 (335)
                      +.+.+|||+||+.++ ++    ++|+++|+.||.|.++++.+  +++||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k--~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   80 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK--SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET--TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec--CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEee
Confidence            345679999999886 33    56999999999999999875  457999999999999999999999999999999999


Q ss_pred             eccCC
Q 019811          129 AYASG  133 (335)
Q Consensus       129 ~~~~~  133 (335)
                      +....
T Consensus        81 a~~~~   85 (104)
T d1weya_          81 AQTLH   85 (104)
T ss_dssp             CCCSS
T ss_pred             cccCC
Confidence            96554

>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=99.61  E-value=6.3e-16  Score=110.25  Aligned_cols=82  Identities=24%  Similarity=0.398  Sum_probs=73.3

Q ss_pred             CCCcceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEE
Q 019811          138 TSGHFNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNW  217 (335)
Q Consensus       138 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~  217 (335)
                      ....++|||+|||+++|+++|.++|+.||.+..+.++.+..+|.++|+|||+|.+.++|.+|+. +++..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3456799999999999999999999999998776666666789999999999999999999996 899999999999988


Q ss_pred             ccC
Q 019811          218 ATK  220 (335)
Q Consensus       218 ~~~  220 (335)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            754

>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=99.60  E-value=3.8e-17  Score=112.09  Aligned_cols=74  Identities=22%  Similarity=0.423  Sum_probs=64.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEee---------cCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEe
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIR---------KDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVN  127 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~---------~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~  127 (335)
                      |+|||+|||.++|+++|+++|+.||.+.++.+..         .+++|||||+|.+.++|.+|+ .|||..+.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            7899999999999999999999999887665532         235799999999999999998 599999999999998


Q ss_pred             eecc
Q 019811          128 WAYA  131 (335)
Q Consensus       128 ~~~~  131 (335)
                      .+..
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.57  E-value=3.6e-15  Score=104.31  Aligned_cols=79  Identities=16%  Similarity=0.100  Sum_probs=69.4

Q ss_pred             CCcceEEECCCCcccc-----HHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeee
Q 019811          139 SGHFNIFVGDLSPEVT-----DATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQI  213 (335)
Q Consensus       139 ~~~~~l~v~nlp~~~t-----~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l  213 (335)
                      .++++|||+||+.++.     +++|+++|+.||.|.++.+.      +++++|||+|.+.++|.+|+..|+|..+.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~------k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE------TTTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe------cCCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            3557899999999863     36799999999999999888      456799999999999999999999999999999


Q ss_pred             EEEEccCCCC
Q 019811          214 RCNWATKGAG  223 (335)
Q Consensus       214 ~v~~~~~~~~  223 (335)
                      +|.|+.....
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999976543

>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=99.56  E-value=8.3e-15  Score=101.60  Aligned_cols=80  Identities=19%  Similarity=0.204  Sum_probs=71.3

Q ss_pred             CCCcceEEEeCC--CCCCC---------HHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           53 PSTCRSVYVGNI--HTQVT---------EPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        53 ~~~~~~v~v~nl--p~~~t---------~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      ...+++|+|+|+  |.++.         +++|++.|++||.|..|++..+..+|+|||+|.+.++|.+|+..|||..|.|
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            466789999999  65432         3689999999999999999888888999999999999999999999999999


Q ss_pred             ceeEEeeeccC
Q 019811          122 QPIKVNWAYAS  132 (335)
Q Consensus       122 ~~l~v~~~~~~  132 (335)
                      ++|+|.++.++
T Consensus        85 r~i~v~~~~g~   95 (99)
T d2dita1          85 RQITAQAWDGT   95 (99)
T ss_dssp             EECEEEECCSC
T ss_pred             EEEEEEEeCCc
Confidence            99999998654

>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=99.53  E-value=1e-15  Score=107.15  Aligned_cols=76  Identities=18%  Similarity=0.307  Sum_probs=70.7

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEc
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWA  218 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~  218 (335)
                      ..++|.+++.++++++|+++|++||.|.++.|+++ .++.++|+|||+|.+.++|.+|+..|+|++++|+.|+|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35778888889999999999999999999999877 57899999999999999999999999999999999999986

>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=99.52  E-value=1.6e-14  Score=100.39  Aligned_cols=65  Identities=23%  Similarity=0.373  Sum_probs=57.5

Q ss_pred             CCcceEEEeC--CCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCcccc
Q 019811           54 STCRSVYVGN--IHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLF  120 (335)
Q Consensus        54 ~~~~~v~v~n--lp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~  120 (335)
                      .++++|+|+|  ||.++|+++|+++|++||.|.+|.+.++  ++||||+|.+.++|.+|+..|||..+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~--k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN--KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT--CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC--ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            3456788855  9999999999999999999999888765  469999999999999999999998773

>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=99.51  E-value=2.1e-14  Score=99.79  Aligned_cols=61  Identities=23%  Similarity=0.331  Sum_probs=57.0

Q ss_pred             CCCeEEEcC--CCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCC
Q 019811          261 QYTTVYVGN--LAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTT  323 (335)
Q Consensus       261 ~~~~l~v~n--lp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~  323 (335)
                      +.++|+|.|  ||.++|+++|+++|++||  .+..+.+.+++++|||+|.+.++|.+|+..|||+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G--~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCG--LVDALLMPPNKPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHS--CEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhC--cccEEeeccCccEEEEEECCHHHHHHHHHHhCCC
Confidence            347888855  999999999999999999  5999999999999999999999999999999999

>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=99.49  E-value=1.6e-15  Score=106.19  Aligned_cols=73  Identities=21%  Similarity=0.283  Sum_probs=67.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecC---CCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKD---KSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~---~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      ..++|++++.++++++|+++|++||.|.+|+|.++.   .+|+|||+|.+.++|.+|+..|||..+.|++|+|.++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            458899999999999999999999999999998754   4699999999999999999999999999999999986

>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=99.48  E-value=3.5e-15  Score=102.10  Aligned_cols=69  Identities=22%  Similarity=0.393  Sum_probs=58.5

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCee---------eEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGV---------IEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~---------i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      ++|||+|||.++++++|+++|+.||.+.         +......+++|+|||+|.+.++|.+|+ .|||.   .+.|++|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~---~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGI---IFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSC---CSSSSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCc---EECCEEE
Confidence            6899999999999999999999988311         222333456899999999999999998 59999   9999999


Q ss_pred             cC
Q 019811          334 KV  335 (335)
Q Consensus       334 ~v  335 (335)
                      +|
T Consensus        78 ~V   79 (90)
T d1u2fa_          78 KI   79 (90)
T ss_dssp             CC
T ss_pred             EE
Confidence            87

>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=99.48  E-value=3.9e-14  Score=100.80  Aligned_cols=73  Identities=21%  Similarity=0.359  Sum_probs=64.7

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCH-HHHHHHHHHhCCccccCceeEEeeec
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDR-RSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~-~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      ...+||+|||..+|+++|+++|++||+|.+|.++++  +|||||.|.+. ++|..|+..+++..+.++.+.|.+..
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            455699999999999999999999999999999865  57999999996 68889999999999988887777664

>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=99.47  E-value=5.6e-14  Score=100.01  Aligned_cols=68  Identities=22%  Similarity=0.254  Sum_probs=60.8

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCH-HHHHHHHHhhcCCCcccccCccccC
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTH-AEAALAIQMGNTTQSSYLFGKQMKV  335 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~-~~a~~A~~~l~g~~~~~~~g~~l~v  335 (335)
                      ..+||+|||+.+|+++|+++|++||  .|.+|.+.+++|+|||+|.+. ++|..|+..|++.   .+.++.++|
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG--~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~---~l~~~~~~v   80 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHG--EIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNG---NLQLRNKEV   80 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSC--CEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTS---CBCTTSSSE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcC--ChheEEEecCCceEEEEecCcHHHHHHHHHHhcCC---ceecCceEE
Confidence            4569999999999999999999999  699999999999999999985 7899999999999   777766543

>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=99.43  E-value=1.7e-13  Score=90.59  Aligned_cols=72  Identities=18%  Similarity=0.107  Sum_probs=60.5

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCce-eEEeeecc
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQP-IKVNWAYA  131 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~-l~v~~~~~  131 (335)
                      .+.|+|+|+|++++++.| +.|++||.|.++++.+  .+|||||+|.+.++|.+|++ +||..+.|+. |.|.+..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~--~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN--TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS--SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC--CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            467999999999986555 6799999999998754  45799999999999999995 9999999985 56876643

>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=99.41  E-value=7.3e-13  Score=91.59  Aligned_cols=80  Identities=20%  Similarity=0.309  Sum_probs=68.2

Q ss_pred             CCCcceEEECCC--Cccc---------cHHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 019811          138 TSGHFNIFVGDL--SPEV---------TDATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGK  206 (335)
Q Consensus       138 ~~~~~~l~v~nl--p~~~---------t~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  206 (335)
                      ...+++|+|.|+  |.++         .+++|++.|++||.|..+.+..+    ..+|+|||+|.+.++|.+|+..|+|.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            345679999999  5432         24789999999999999988744    56799999999999999999999999


Q ss_pred             eeCCeeeEEEEccCC
Q 019811          207 WLGSRQIRCNWATKG  221 (335)
Q Consensus       207 ~~~g~~l~v~~~~~~  221 (335)
                      .++|+.|.|.|...+
T Consensus        81 ~~~gr~i~v~~~~g~   95 (99)
T d2dita1          81 WFGGRQITAQAWDGT   95 (99)
T ss_dssp             EETTEECEEEECCSC
T ss_pred             EECCEEEEEEEeCCc
Confidence            999999999998654

>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=99.39  E-value=2.5e-13  Score=94.98  Aligned_cols=77  Identities=13%  Similarity=0.169  Sum_probs=66.3

Q ss_pred             CCcceEEEeCC--CCCCC--------HHHHHHHHhccCCceeEEEeecC------CCCeEEEEEcCHHHHHHHHHHhCCc
Q 019811           54 STCRSVYVGNI--HTQVT--------EPLLQEVFSSTGPVEGCKLIRKD------KSSYGFIHYFDRRSAAMAILSLNGR  117 (335)
Q Consensus        54 ~~~~~v~v~nl--p~~~t--------~~~l~~~f~~~G~v~~v~~~~~~------~~g~afv~f~~~~~A~~a~~~l~~~  117 (335)
                      .+++.|.|+|+  |.++.        .++|++.|++||.|.+|+|.++.      ..|++||+|.+.++|.+|+..|||.
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            35788999999  55543        46789999999999999987643      2489999999999999999999999


Q ss_pred             cccCceeEEeeec
Q 019811          118 HLFGQPIKVNWAY  130 (335)
Q Consensus       118 ~~~g~~l~v~~~~  130 (335)
                      .+.||.|.+.++.
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999875

>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=99.38  E-value=5.7e-13  Score=88.06  Aligned_cols=64  Identities=19%  Similarity=0.168  Sum_probs=57.4

Q ss_pred             CeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccCccc
Q 019811          263 TTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFGKQM  333 (335)
Q Consensus       263 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g~~l  333 (335)
                      +.|+|.++|++.+++.| ..|+.||  .|.++++.+++++|||+|.+.++|.+|++ +||.   .|+|+.+
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G--~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~---~~~g~~~   68 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYG--NILKHVMSNTGNWMHIRYQSKLQARKALS-KDGR---IFGESIM   68 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTS--CEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTC---EETTTEE
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhh--hhheEEecCCCCEEEEEEcccHHHHHHHh-cCCC---eECCcEE
Confidence            67999999999886555 5799999  69999999999999999999999999995 8999   9999854

>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=99.34  E-value=1.3e-12  Score=91.28  Aligned_cols=81  Identities=17%  Similarity=0.150  Sum_probs=68.3

Q ss_pred             CcceEEECCC--Ccc--------ccHHHHHHHhccCCCceeeEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCce
Q 019811          140 GHFNIFVGDL--SPE--------VTDATLFACFSVYPSCSDARVMWDQKTG--RSRGFGFVSFRNQQDAQSAINDLTGKW  207 (335)
Q Consensus       140 ~~~~l~v~nl--p~~--------~t~~~l~~~f~~~g~v~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~  207 (335)
                      ++++|.|.|+  |..        ...++|++.|++||.|.++.|+++..+.  ...|++||+|.+.++|.+|+..|+|+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678999999  332        2356899999999999999998765432  346899999999999999999999999


Q ss_pred             eCCeeeEEEEccC
Q 019811          208 LGSRQIRCNWATK  220 (335)
Q Consensus       208 ~~g~~l~v~~~~~  220 (335)
                      ++||.|.+.|...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999753

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.80  E-value=4e-05  Score=50.04  Aligned_cols=65  Identities=12%  Similarity=0.215  Sum_probs=55.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCC------CCeEEEEEcCHHHHHHHHHHhCCccccC
Q 019811           57 RSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDK------SSYGFIHYFDRRSAAMAILSLNGRHLFG  121 (335)
Q Consensus        57 ~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~------~g~afv~f~~~~~A~~a~~~l~~~~~~g  121 (335)
                      ..|.||.||+.+|++++.+.++..|.+........+.      -.-|||.|.+.++.....+..+|..|.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            4689999999999999999999999887766655442      1479999999999999999999988864

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.65  E-value=3.8e-05  Score=49.17  Aligned_cols=68  Identities=22%  Similarity=0.301  Sum_probs=52.0

Q ss_pred             CCCCeEEEcCCCcccC---------HHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhcCCCcccccC
Q 019811          260 PQYTTVYVGNLAPEVT---------QLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGNTTQSSYLFG  330 (335)
Q Consensus       260 ~~~~~l~v~nlp~~~t---------~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~g  330 (335)
                      |+.-||.|.-...+..         -.+|.+.|..||  ++.-+++..+  ..+|+|.+-.+|.+|+ .++|.   .+.|
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~G--eViLvRFv~d--~mwVTF~dG~SAL~al-~l~g~---~v~G   84 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYG--TIVLVRINQG--QMLVTFADSHSALSVL-DVDGM---KVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHS--CCSEEEEETT--EEEEECSCSHHHHHHH-HGGGS---EETT
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCC--eEEEEEEeCC--eEEEEECCcHHHHHHh-ccCCe---EEcc
Confidence            3446677744432222         246788899999  5888888865  9999999999999998 67999   9999


Q ss_pred             ccccC
Q 019811          331 KQMKV  335 (335)
Q Consensus       331 ~~l~v  335 (335)
                      +.|+|
T Consensus        85 ~~l~I   89 (95)
T d1ufwa_          85 RAVKI   89 (95)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            99875

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.64  E-value=0.00012  Score=44.34  Aligned_cols=62  Identities=24%  Similarity=0.209  Sum_probs=51.8

Q ss_pred             HHHHHHHhccCCCceeeEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeeeEEEEcc
Q 019811          155 DATLFACFSVYPSCSDARVMWDQKTGRSRGFGFVSFRNQQDAQSAINDLTGKWLGSRQIRCNWAT  219 (335)
Q Consensus       155 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~g~~l~v~~~~  219 (335)
                      .+-|.+.|.++|.|.++.+... .  ...-.|-|...+..+|..|+..|+...+++++|.|.++.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~-~--dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPH-T--DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSC-C--STTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHhheeEEEEEEEec-c--CCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3456678899999999988633 2  234469999999999999999999999999999999975

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.59  E-value=0.00013  Score=47.52  Aligned_cols=67  Identities=15%  Similarity=0.220  Sum_probs=56.0

Q ss_pred             ceEEECCCCccccHHHHHHHhccCCCceeeEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCcee
Q 019811          142 FNIFVGDLSPEVTDATLFACFSVYPSCSDARVMWDQKTGR--SRGFGFVSFRNQQDAQSAINDLTGKWL  208 (335)
Q Consensus       142 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~a~~~l~~~~~  208 (335)
                      ++|.|+.||+++|++++.+.+...|.+........+.+..  ....|||.|.+.++.....+..+|..+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            4789999999999999999999999888877765443322  235699999999999999999999877

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.56  E-value=0.00028  Score=42.72  Aligned_cols=60  Identities=25%  Similarity=0.257  Sum_probs=51.7

Q ss_pred             HHHHHHHhccCCceeEEEeecCC-CCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeeec
Q 019811           71 PLLQEVFSSTGPVEGCKLIRKDK-SSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWAY  130 (335)
Q Consensus        71 ~~l~~~f~~~G~v~~v~~~~~~~-~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~  130 (335)
                      +.|.+.|.++|.|.++.+..... .-.|-|...+..+|.-|+..|+-..|++++|.|.+++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            44566789999999999876432 3589999999999999999999999999999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=4.4e-05  Score=48.87  Aligned_cols=54  Identities=17%  Similarity=0.293  Sum_probs=46.9

Q ss_pred             HHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHhCCccccCceeEEeee
Q 019811           71 PLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSLNGRHLFGQPIKVNWA  129 (335)
Q Consensus        71 ~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~  129 (335)
                      .+|.+.|..||.|.-|++..+    ..+|.|.+-++|.+|+ .++|..+.|+.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d----~mwVTF~dG~SAL~al-~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG----QMLVTFADSHSALSVL-DVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT----EEEEECSCSHHHHHHH-HGGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC----eEEEEECCcHHHHHHh-ccCCeEEcceEEEEecC
Confidence            568888999999988887665    4999999999999998 58999999999999754

>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=97.30  E-value=0.00075  Score=43.88  Aligned_cols=55  Identities=15%  Similarity=0.177  Sum_probs=45.3

Q ss_pred             cceEEEeCCCCCCCHHHHHHHHhccCCceeEEEeecCCCCeEEEEEcCHHHHHHHHHHh
Q 019811           56 CRSVYVGNIHTQVTEPLLQEVFSSTGPVEGCKLIRKDKSSYGFIHYFDRRSAAMAILSL  114 (335)
Q Consensus        56 ~~~v~v~nlp~~~t~~~l~~~f~~~G~v~~v~~~~~~~~g~afv~f~~~~~A~~a~~~l  114 (335)
                      ...||.-..|..+...||.++|+.||.|. |..+.+.   .|||...+.++|..++..+
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT---Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT---SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT---EEEEECSCHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc---eEEEEecCHHHHHHHHHHh
Confidence            34599999999999999999999999984 3333444   5999999999998888654

>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=96.89  E-value=0.0032  Score=40.85  Aligned_cols=59  Identities=22%  Similarity=0.287  Sum_probs=48.3

Q ss_pred             CCCCCeEEEcCCCcccCHHHHHHHhhhcCCeeeEEEEEecccceEEEEeCCHHHHHHHHHhhc
Q 019811          259 NPQYTTVYVGNLAPEVTQLDLHRHFHSLGAGVIEEVRVQRDKGFGFVRYSTHAEAALAIQMGN  321 (335)
Q Consensus       259 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~i~~v~~~~~~g~afV~f~~~~~a~~A~~~l~  321 (335)
                      .+...-||...+|......||.++|++||.+.|..|    +.-.|||...+.+.|..++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI----ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI----DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE----ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe----cCceEEEEecCHHHHHHHHHHhc
Confidence            344466999999999999999999999996555555    45589999999999998886653