Citrus Sinensis ID: 018554

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350----
Protein Sequence
MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEGFLSIYSVH
Secondary Structure (PSIPRED)
cccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHccccccccccccccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccEEccccccccEEEEccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccccccEEEEEcccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccEccEEEEEEccHHHHHHHHHHHcccEEcccccccEEEEEccccccHHHHHHHHHHHHHccccccccccccHccccccccccHHccccccccccccccccccccccccccHHHccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
maeskkekksSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVniikdkttrasrgccfvicpsrqeADKAVnachnkktlpgassplqvkyadgelERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDlqilrgsqqtskgcaFLKYETKEQALAALEAINgkhkmegssvpLVVKWADTEKERQARRAQKAQSqannlpnadsqhpslfgalpmgyappyngygyqasgsyglmqyrlppmqnqpgfhgiippvnqgnamrgaspdlssnmgprnyamppsgfvgsgypavpglqypmpypggmlghrplnnspgsvspavansnpstsssggtgsggqiEGFLSIYSVH
Flexible Loop (DISEMBL)
maeskkekksseervKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKdkttrasrgCCFVICPSRQEADKAVNACHNkktlpgassplqVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIngkhkmegssVPLVVKWADTEKERQARRAQKAqsqannlpnadSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPstsssggtgsggqiEGFLSIYSVH
Low Complexity Region (SEG)
MAeskkekksseeRVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKErqarraqkaqsqaNNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPstsssggtgsggQIEGFLSIYSVH
Disordered region (IsUnstruct)
***************KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ****AVNAC*************QVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING********VPLVVKW*******************************LFGALPMGYAPPYNGYGYQASGSYGLMQYRLP*******FHGI****************************************V**L********************************************************
Disordered Region (DISOPRED)
*****************FVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTL************************IGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV*************************************************************************************************************************************************************************LSIYSVH
Disordered Region (DISEMBL)
*************RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE********************ADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSP**********************GGQIEGFLSIYSVH
Disordered Region (DISPRO)
************ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVA******************EG*L**YSVH
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEGFLSIYSVH
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	354	2.2.26 [Sep-21-2011]
Q9IBD1	452	CUGBP Elav-like family me	yes	no	0.522	0.409	0.462	2e-43
A0JM51	486	CUGBP Elav-like family me	yes	no	0.579	0.421	0.421	5e-43
Q4R535	474	CUGBP Elav-like family me	N/A	no	0.528	0.394	0.452	6e-43
Q6DGV1	520	CUGBP Elav-like family me	no	no	0.531	0.361	0.446	1e-42
Q5SZQ8	465	CUGBP Elav-like family me	no	no	0.511	0.389	0.446	2e-42
Q08E07	461	CUGBP Elav-like family me	no	no	0.511	0.392	0.446	2e-42
O04425	747	Flowering time control pr	no	no	0.488	0.231	0.443	2e-42
Q8CIN6	465	CUGBP Elav-like family me	no	no	0.522	0.397	0.451	3e-42
Q7ZWM3	462	CUGBP Elav-like family me	N/A	no	0.511	0.391	0.440	4e-42
Q91579	462	CUGBP Elav-like family me	N/A	no	0.511	0.391	0.440	6e-42

>sp|Q9IBD1|CELF3_DANRE CUGBP Elav-like family member 3 OS=Danio rerio GN=celf3 PE=2 SV=2

 Score =  176 bits (447), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 86/186 (46%), Positives = 128/186 (68%), Gaps = 1/186 (0%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLF+GQ+P+++ E  L  +F++F  + E+ +IKDK T   +GC F+   +R+ A KA
Sbjct: 5   DAIKLFIGQIPRNLEEKDLKPIFEQFGKIYELTVIKDKYTGMHKGCAFLTYCARESALKA 64

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            NA H +KTLPG + P+QVK AD E  R + KLF+GML K +S+A+V  +F  +G+I++ 
Sbjct: 65  QNALHEQKTLPGMNRPIQVKPADSE-GRGDRKLFVGMLGKQLSDADVRKMFEPFGSIEEC 123

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG    SKGCAF+KY++  +A AA+ A++G   + G+S  LVVK+ADTEKER  RR 
Sbjct: 124 TVLRGPDGASKGCAFVKYQSNAEAQAAISALHGSRTLPGASSSLVVKFADTEKERGIRRM 183

Query: 193 QKAQSQ 198
           Q+  SQ
Sbjct: 184 QQVASQ 189

RNA-binding protein that may be involved in the regulation of pre-mRNA alternative splicing.
Danio rerio (taxid: 7955)

>sp|A0JM51|CELF5_XENTR CUGBP Elav-like family member 5 OS=Xenopus tropicalis GN=celf5 PE=2 SV=1

 Score =  175 bits (443), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 91/216 (42%), Positives = 136/216 (62%), Gaps = 11/216 (5%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLFVGQ+P+++ E  L  +F++F  + E+ ++KD+ T   +GC F+   +R  A KA
Sbjct: 45  DAIKLFVGQIPRNLEEKDLKPLFEQFGKIYELTVLKDRYTGMHKGCAFLTYCARDSAIKA 104

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             A H +KTLPG + P+QVK AD E    + KLF+GML K  SE EV+++F  +G+I++ 
Sbjct: 105 QTALHEQKTLPGMARPIQVKPADSESRGGDRKLFVGMLSKQQSEEEVTSMFQAFGSIEEC 164

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG   +SKGCAF+K+ +  +A AA++A++G   M G+S  LVVK+ADT+KER  RR 
Sbjct: 165 SVLRGPDGSSKGCAFVKFSSHAEAQAAIQALHGSQTMPGASSSLVVKFADTDKERTLRRM 224

Query: 193 QKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYG 228
           Q+   Q           PSL  ALP+    PY+ Y 
Sbjct: 225 QQMVGQLGIF------TPSL--ALPIS---PYSAYA 249

RNA-binding protein that may be implicated in the regulation of pre-mRNA alternative splicing.

Xenopus tropicalis (taxid: 8364)

>sp|Q4R535|CELF4_MACFA CUGBP Elav-like family member 4 OS=Macaca fascicularis GN=CELF4 PE=2 SV=1

 Score =  175 bits (443), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 85/188 (45%), Positives = 122/188 (64%), Gaps = 1/188 (0%)

Query: 11  SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
             + +KLF+GQ+P+++ E  L  +F+EF  + E+ ++KD+ T   +GC F+    R+ A 
Sbjct: 50  DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 109

Query: 71  KAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIK 130
           KA +A H +KTLPG + P+QVK AD E  R + KLF+GML K  SE +V  LF  +G I+
Sbjct: 110 KAQSALHEQKTLPGMNRPIQVKPADSE-SRGDRKLFVGMLNKQQSEDDVRRLFEAFGNIE 168

Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           +  ILRG    SKGCAF+KY +  +A AA+ A++G   M G+S  LVVK+ADT+KER  R
Sbjct: 169 ECTILRGPDGNSKGCAFVKYSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKERTMR 228

Query: 191 RAQKAQSQ 198
           R Q+   Q
Sbjct: 229 RMQQMAGQ 236

RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Promotes exclusion of both the smooth muscle (SM) and non-muscle (NM) exons in actinin pre-mRNAs. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Macaca fascicularis (taxid: 9541)

>sp|Q6DGV1|CELF4_DANRE CUGBP Elav-like family member 4 OS=Danio rerio GN=celf4 PE=2 SV=1

 Score =  174 bits (440), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 84/188 (44%), Positives = 121/188 (64%)

Query: 11  SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
             + +KLF+GQ+P+++ E  L  +F+EF  + E+ ++KD+ T   +GC F+   +R+ A 
Sbjct: 43  DHDAIKLFIGQIPRNLDEKDLRPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCARESAL 102

Query: 71  KAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIK 130
           KA  A H +KTLPG + P+QVK AD E    + KLF+GML K   E +V  LF  +G+I+
Sbjct: 103 KAQTALHEQKTLPGMNRPIQVKPADSESRGEDRKLFVGMLNKQQCEDDVRRLFESFGSIE 162

Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           +  ILRG    SKGCAF+KY T  +A AA+ A++G   M G+S  LVVK+ADT+KER  R
Sbjct: 163 ECTILRGPDGNSKGCAFVKYSTHAEAQAAISALHGSQTMPGASSSLVVKFADTDKERTIR 222

Query: 191 RAQKAQSQ 198
           R Q+   Q
Sbjct: 223 RMQQMAGQ 230

RNA-binding protein that may be implicated in the regulation of pre-mRNA alternative splicing.

Danio rerio (taxid: 7955)

>sp|Q5SZQ8|CELF3_HUMAN CUGBP Elav-like family member 3 OS=Homo sapiens GN=CELF3 PE=1 SV=1

 Score =  173 bits (438), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 83/186 (44%), Positives = 122/186 (65%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLFVGQ+P+H+ E  L  +F++F  + E+ +IKDK T   +GC F+   +R  A KA
Sbjct: 5   DAIKLFVGQIPRHLEEKDLKPIFEQFGRIFELTVIKDKYTGLHKGCAFLTYCARDSALKA 64

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            +A H +KTLPG + P+QVK AD E    + KLF+GML K  ++ +V  +F  +GTI + 
Sbjct: 65  QSALHEQKTLPGMNRPIQVKPADSESRGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDEC 124

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG   TSKGCAF+K++T  +A AA+  ++    + G+S  LVVK+ADTEKER  RR 
Sbjct: 125 TVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHSSRTLPGASSSLVVKFADTEKERGLRRM 184

Query: 193 QKAQSQ 198
           Q+  +Q
Sbjct: 185 QQVATQ 190

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Homo sapiens (taxid: 9606)

>sp|Q08E07|CELF3_BOVIN CUGBP Elav-like family member 3 OS=Bos taurus GN=CELF3 PE=2 SV=1

 Score =  173 bits (438), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 83/186 (44%), Positives = 122/186 (65%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLFVGQ+P+H+ E  L  +F++F  + E+ +IKDK T   +GC F+   +R  A KA
Sbjct: 5   DAIKLFVGQIPRHLEEKDLKPIFEQFGRIFELTVIKDKYTGLHKGCAFLTYCARDSALKA 64

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            +A H +KTLPG + P+QVK AD E    + KLF+GML K  ++ +V  +F  +GTI + 
Sbjct: 65  QSALHEQKTLPGMNRPIQVKPADSESRGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDEC 124

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG   TSKGCAF+K++T  +A AA+  ++    + G+S  LVVK+ADTEKER  RR 
Sbjct: 125 TVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHSSRTLPGASSSLVVKFADTEKERGLRRM 184

Query: 193 QKAQSQ 198
           Q+  +Q
Sbjct: 185 QQVATQ 190

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Bos taurus (taxid: 9913)

>sp|O04425|FCA_ARATH Flowering time control protein FCA OS=Arabidopsis thaliana GN=FCA PE=1 SV=2

 Score =  172 bits (437), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 78/176 (44%), Positives = 120/176 (68%), Gaps = 3/176 (1%)

Query: 15  VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
           VKLFVG VP+  TE ++   F++   V EV +IKDK T   +GCCFV   + ++AD+A+ 
Sbjct: 120 VKLFVGSVPRTATEEEIRPYFEQHGNVLEVALIKDKRTGQQQGCCFVKYATSKDADRAIR 179

Query: 75  ACHNKKTLPGASSPLQVKYADGELER---LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD 131
           A HN+ TLPG + P+QV+YADGE ER   LE KLF+G L K  +E EV  +F  +G ++D
Sbjct: 180 ALHNQITLPGGTGPVQVRYADGERERIGTLEFKLFVGSLNKQATEKEVEEIFLQFGHVED 239

Query: 132 LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKER 187
           + ++R   + S+GC F+KY +KE A+AA++ +NG + M G + PL+V++A+ ++ +
Sbjct: 240 VYLMRDEYRQSRGCGFVKYSSKETAMAAIDGLNGTYTMRGCNQPLIVRFAEPKRPK 295

Plays a major role in the promotion of the transition of the vegetative meristem to reproductive development. Plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. Required for RNA-mediated chromatin silencing of a range of loci in the genome. Cotranscriptionally recognizes aberrant RNA and marks it for silencing. Controls alternative cleavage and polyadenylation on pre-mRNAs and antisense RNAs. Acts redundantly with FPA to prevent the expression of distally polyadenylated antisense RNAs at the FLC locus.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8CIN6|CELF3_MOUSE CUGBP Elav-like family member 3 OS=Mus musculus GN=Celf3 PE=2 SV=1

 Score =  172 bits (437), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 84/186 (45%), Positives = 123/186 (66%), Gaps = 1/186 (0%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLFVGQ+P+H+ E  L  +F++F  + E+ +IKDK T   +GC F+   +R  A KA
Sbjct: 5   DAIKLFVGQIPRHLEEKDLKPIFEQFGRIFELTVIKDKYTGLHKGCAFLTYCARDSALKA 64

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            +A H +KTLPG + P+QVK AD E  R + KLF+GML K  ++ +V  +F  +GTI + 
Sbjct: 65  QSALHEQKTLPGMNRPIQVKPADSE-SRGDRKLFVGMLGKQQTDEDVRKMFEPFGTIDEC 123

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG   TSKGCAF+K++T  +A AA+  ++    + G+S  LVVK+ADTEKER  RR 
Sbjct: 124 TVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHSSRTLPGASSSLVVKFADTEKERGLRRM 183

Query: 193 QKAQSQ 198
           Q+  +Q
Sbjct: 184 QQVATQ 189

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Mus musculus (taxid: 10090)

>sp|Q7ZWM3|CEL3B_XENLA CUGBP Elav-like family member 3-B OS=Xenopus laevis GN=tnrc4-b PE=2 SV=1

 Score =  172 bits (436), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 82/186 (44%), Positives = 124/186 (66%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLF+GQ+P+++ E  L  +F++F  + E+ +IKDK T   +GC F+   +R+ A KA
Sbjct: 5   DAIKLFIGQIPRNLDEKDLKPIFEQFGKIYELTVIKDKFTGMHKGCAFLTYCARESALKA 64

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            +A H +KTLPG + P+QVK AD E    + KLF+GML K  ++ +V  +F  +G I + 
Sbjct: 65  QSALHEQKTLPGMNRPIQVKPADSESRGEDRKLFVGMLGKQQTDEDVRRMFETFGNIDEC 124

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG   TSKGCAF+K++T  +A AA+ A++G   + G+S  LVVK+ADTEKER  RR 
Sbjct: 125 TVLRGPDGTSKGCAFVKFQTHTEAQAAINALHGSRTLPGASSSLVVKFADTEKERGLRRM 184

Query: 193 QKAQSQ 198
           Q+  +Q
Sbjct: 185 QQVANQ 190

RNA-binding protein that may be involved in the regulation of pre-mRNA alternative splicing.

Xenopus laevis (taxid: 8355)

>sp|Q91579|CEL3A_XENLA CUGBP Elav-like family member 3-A OS=Xenopus laevis GN=tnrc4-a PE=2 SV=2

 Score =  171 bits (434), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 82/186 (44%), Positives = 124/186 (66%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           + +KLF+GQ+P+++ E  L  +F++F  + E+ +IKDK T   +GC F+   +R+ A KA
Sbjct: 5   DAIKLFIGQIPRNLDEKDLKPIFEQFGKIYELTVIKDKFTGMHKGCAFLTYCARESALKA 64

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            +A H +KTLPG + P+QVK AD E    + KLF+GML K  ++ +V  +F  +G I + 
Sbjct: 65  QSALHEQKTLPGMNRPIQVKPADSESRGEDRKLFVGMLGKQQTDEDVRRMFEPFGNIDEC 124

Query: 133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +LRG   TSKGCAF+K++T  +A AA+ A++G   + G+S  LVVK+ADTEKER  RR 
Sbjct: 125 TVLRGPDGTSKGCAFVKFQTHTEAQAAINALHGSRTLPGASSSLVVKFADTEKERGLRRM 184

Query: 193 QKAQSQ 198
           Q+  +Q
Sbjct: 185 QQVANQ 190

RNA-binding protein that may be involved in the regulation of pre-mRNA alternative splicing.

Xenopus laevis (taxid: 8355)

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	354
255559360	436	RNA binding protein, putative [Ricinus c	0.977	0.793	0.861	1e-166
225436819	437	PREDICTED: CUGBP Elav-like family member	0.977	0.791	0.809	1e-165
359479768	447	PREDICTED: CUGBP Elav-like family member	0.977	0.774	0.787	1e-162
224128620	432	predicted protein [Populus trichocarpa]	0.937	0.768	0.821	1e-160
356505495	431	PREDICTED: CUGBP Elav-like family member	0.966	0.793	0.812	1e-157
147772817	450	hypothetical protein VITISV_044358 [Viti	0.977	0.768	0.698	1e-156
449462310	438	PREDICTED: CUGBP Elav-like family member	0.966	0.780	0.781	1e-152
356572661	429	PREDICTED: CUGBP Elav-like family member	0.926	0.764	0.801	1e-150
356535559	429	PREDICTED: CUGBP Elav-like family member	0.870	0.717	0.796	1e-143
356500250	426	PREDICTED: CUGBP Elav-like family member	0.889	0.739	0.786	1e-141

>gi|255559360|ref|XP_002520700.1| RNA binding protein, putative [Ricinus communis] gi|223540085|gb|EEF41662.1| RNA binding protein, putative [Ricinus communis]

 Score =  591 bits (1523), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 299/347 (86%), Positives = 318/347 (91%), Gaps = 1/347 (0%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE KKEKKSSEE VKLFVGQVPKHMTE QLLAMFKEFALVDEVNIIKDKTTRASRGCCF
Sbjct: 1   MAEDKKEKKSSEESVKLFVGQVPKHMTEVQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVS 120
           VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLF+GMLPKNVSEAEVS
Sbjct: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFVGMLPKNVSEAEVS 120

Query: 121 ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180
            LFS YGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW
Sbjct: 121 ELFSTYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180

Query: 181 ADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQY 240
           ADTEKERQARRAQK QSQA+NLPNADSQHPSLFGALPMGY P YNGYGYQA G+YGLM Y
Sbjct: 181 ADTEKERQARRAQKVQSQASNLPNADSQHPSLFGALPMGYVPQYNGYGYQAPGTYGLMPY 240

Query: 241 RLPPMQNQPGFHGIIPPVNQGNAMR-GASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQ 299
           RLPP+Q+QP FH IIPPVNQGNA+R G  PDL  +MGPRNYA+PP+ +VGS YPAVPG+Q
Sbjct: 241 RLPPLQSQPAFHSIIPPVNQGNALRGGVRPDLGPSMGPRNYALPPASYVGSAYPAVPGIQ 300

Query: 300 YPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
           YPM YPGGM+  RPL++SPG+VSP V +SN +TSS   + SGGQ+EG
Sbjct: 301 YPMAYPGGMMSPRPLSSSPGAVSPTVGSSNSATSSGVSSSSGGQLEG 347

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436819|ref|XP_002270390.1| PREDICTED: CUGBP Elav-like family member 5 isoform 1 [Vitis vinifera] gi|296086641|emb|CBI32276.3| unnamed protein product [Vitis vinifera]

 Score =  586 bits (1511), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 281/347 (80%), Positives = 313/347 (90%), Gaps = 1/347 (0%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE+ K +K+SE+ VKLFVGQVPK+MTEAQLLAMFKEFALVDEVNIIKDK TRASRGCCF
Sbjct: 1   MAEAPKPRKASEDSVKLFVGQVPKNMTEAQLLAMFKEFALVDEVNIIKDKATRASRGCCF 60

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVS 120
           VICPSRQEADKAVNACHNK+TLPGASSPLQVKYADGELERLEHKLF+GMLPKNVSEAEVS
Sbjct: 61  VICPSRQEADKAVNACHNKRTLPGASSPLQVKYADGELERLEHKLFVGMLPKNVSEAEVS 120

Query: 121 ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180
           +LFS YGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW
Sbjct: 121 SLFSKYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180

Query: 181 ADTEKERQARRAQKAQSQANNLPNADS-QHPSLFGALPMGYAPPYNGYGYQASGSYGLMQ 239
           ADTEKERQAR+AQKAQSQA+NLP+ADS QHPSLFGALP+GY PPYNGYGYQA G+YGLMQ
Sbjct: 181 ADTEKERQARKAQKAQSQASNLPSADSGQHPSLFGALPLGYVPPYNGYGYQAPGAYGLMQ 240

Query: 240 YRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQ 299
           YR+PPMQ+Q  FH +IP VNQG+AMR  +PDL+  + PRNYA+P + ++GS YPA+PGLQ
Sbjct: 241 YRMPPMQSQAAFHNMIPQVNQGSAMRAIAPDLARAVAPRNYAVPSASYMGSAYPALPGLQ 300

Query: 300 YPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
           YPM Y GG++ H+PL+ SPGS  PA+  SN  T+S  G  SGGQ+EG
Sbjct: 301 YPMAYHGGIMSHQPLSGSPGSRPPAMMTSNSPTNSGAGASSGGQVEG 347

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479768|ref|XP_003632354.1| PREDICTED: CUGBP Elav-like family member 5 isoform 2 [Vitis vinifera]

 Score =  577 bits (1487), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 281/357 (78%), Positives = 313/357 (87%), Gaps = 11/357 (3%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE+ K +K+SE+ VKLFVGQVPK+MTEAQLLAMFKEFALVDEVNIIKDK TRASRGCCF
Sbjct: 1   MAEAPKPRKASEDSVKLFVGQVPKNMTEAQLLAMFKEFALVDEVNIIKDKATRASRGCCF 60

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----------EHKLFIGML 110
           VICPSRQEADKAVNACHNK+TLPGASSPLQVKYADGELERL          EHKLF+GML
Sbjct: 61  VICPSRQEADKAVNACHNKRTLPGASSPLQVKYADGELERLGVIFCHPCYPEHKLFVGML 120

Query: 111 PKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME 170
           PKNVSEAEVS+LFS YGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME
Sbjct: 121 PKNVSEAEVSSLFSKYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME 180

Query: 171 GSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADS-QHPSLFGALPMGYAPPYNGYGY 229
           GSSVPLVVKWADTEKERQAR+AQKAQSQA+NLP+ADS QHPSLFGALP+GY PPYNGYGY
Sbjct: 181 GSSVPLVVKWADTEKERQARKAQKAQSQASNLPSADSGQHPSLFGALPLGYVPPYNGYGY 240

Query: 230 QASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVG 289
           QA G+YGLMQYR+PPMQ+Q  FH +IP VNQG+AMR  +PDL+  + PRNYA+P + ++G
Sbjct: 241 QAPGAYGLMQYRMPPMQSQAAFHNMIPQVNQGSAMRAIAPDLARAVAPRNYAVPSASYMG 300

Query: 290 SGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
           S YPA+PGLQYPM Y GG++ H+PL+ SPGS  PA+  SN  T+S  G  SGGQ+EG
Sbjct: 301 SAYPALPGLQYPMAYHGGIMSHQPLSGSPGSRPPAMMTSNSPTNSGAGASSGGQVEG 357

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128620|ref|XP_002320377.1| predicted protein [Populus trichocarpa] gi|222861150|gb|EEE98692.1| predicted protein [Populus trichocarpa]

 Score =  569 bits (1467), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 277/337 (82%), Positives = 300/337 (89%), Gaps = 5/337 (1%)

Query: 11  SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
           +EE VKLFVGQVPK+MTEA+LLAMFK+FALVDEVNIIKDKTTRASRGCCF+ICPSRQEAD
Sbjct: 12  NEESVKLFVGQVPKNMTEAELLAMFKDFALVDEVNIIKDKTTRASRGCCFLICPSRQEAD 71

Query: 71  KAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIK 130
           KAVNACHNKKTLPGASSPLQVKYADGELERLEHKLF+GMLPKNVSEAEVS LFS YGTIK
Sbjct: 72  KAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFVGMLPKNVSEAEVSDLFSKYGTIK 131

Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           DLQILRGSQQTSK CAFLKYETKEQALAALE INGKHKMEGSSVPLVVKWADTEKERQAR
Sbjct: 132 DLQILRGSQQTSKSCAFLKYETKEQALAALEDINGKHKMEGSSVPLVVKWADTEKERQAR 191

Query: 191 RAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPG 250
           RAQKAQSQA  +PN DSQHPSLFGALPMGYAPPYNGYGYQA G YGLM YRLPPMQNQP 
Sbjct: 192 RAQKAQSQA--MPNTDSQHPSLFGALPMGYAPPYNGYGYQAPGVYGLMPYRLPPMQNQPA 249

Query: 251 FHGIIPPVNQGNAMRGA-SPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGML 309
           FH ++PPVNQGN +RG   PDLS N+ PRNYA  P+ ++GS YP V GLQYP+ YPG M+
Sbjct: 250 FHSMVPPVNQGNVLRGGIRPDLSPNISPRNYA--PATYMGSAYPTVTGLQYPVAYPGAMM 307

Query: 310 GHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
            HRPL++SPG++SP V +SN +T S  G  SG Q+EG
Sbjct: 308 THRPLSSSPGALSPTVVSSNSATPSGVGGSSGVQVEG 344

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505495|ref|XP_003521526.1| PREDICTED: CUGBP Elav-like family member 1-like [Glycine max]

 Score =  560 bits (1443), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 281/346 (81%), Positives = 304/346 (87%), Gaps = 4/346 (1%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE K+E KSSEE VKLFVGQVPKHMTE +LLAMFKEFALVDEVNIIKDK TRASRGCCF
Sbjct: 1   MAEGKEESKSSEESVKLFVGQVPKHMTEPELLAMFKEFALVDEVNIIKDKATRASRGCCF 60

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVS 120
           VICPSR+EADKAVNACHNK+TLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSE E+S
Sbjct: 61  VICPSREEADKAVNACHNKRTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEVEIS 120

Query: 121 ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180
           ALFS YGTIKDLQILRGSQQTSKGCAFLKYETKEQAL ALEAINGKHKMEGSSVPLVVKW
Sbjct: 121 ALFSKYGTIKDLQILRGSQQTSKGCAFLKYETKEQALTALEAINGKHKMEGSSVPLVVKW 180

Query: 181 ADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQY 240
           ADTEKERQARRAQKAQSQA+N+P+ DSQHPSLFGALPM Y PPYNGYGYQA   YGLM Y
Sbjct: 181 ADTEKERQARRAQKAQSQASNVPHTDSQHPSLFGALPMSYVPPYNGYGYQAPVGYGLMPY 240

Query: 241 RLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQY 300
           R+PPMQ+Q G+H ++P +NQGNA+R   PDL  NM PRNY +PP+ +VGS YPAVPGLQ+
Sbjct: 241 RMPPMQSQHGYHNMMPHMNQGNALR---PDLGPNMNPRNYHVPPASYVGS-YPAVPGLQH 296

Query: 301 PMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
           PM YP GM+  RP+N SPGSVSPA  N+N + SS     SGGQ EG
Sbjct: 297 PMAYPTGMISPRPMNTSPGSVSPASGNNNHAASSGASKNSGGQAEG 342

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772817|emb|CAN71673.1| hypothetical protein VITISV_044358 [Vitis vinifera]

 Score =  557 bits (1435), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 280/401 (69%), Positives = 313/401 (78%), Gaps = 55/401 (13%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE+ K +K+SE+ VKLFVGQVPK+MTEAQLLAMFKEFALVDEVNIIKDK TRASRGCCF
Sbjct: 1   MAEAPKPRKASEDSVKLFVGQVPKNMTEAQLLAMFKEFALVDEVNIIKDKATRASRGCCF 60

Query: 61  VICPSRQEADKAVNACH-NKKTLPG----------------------------------- 84
           VICPSRQEADKAVNACH +K+TLPG                                   
Sbjct: 61  VICPSRQEADKAVNACHSDKRTLPGKHVNISHIGFMWHDAAADAWKIKATIVANENQQRK 120

Query: 85  ------------------ASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIY 126
                             ASSPLQVKYADGELERLEHKLF+GMLPKNVSEAEVS+LFS Y
Sbjct: 121 KCTREHTNFGLRLAFQVSASSPLQVKYADGELERLEHKLFVGMLPKNVSEAEVSSLFSKY 180

Query: 127 GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 186
           GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE
Sbjct: 181 GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 240

Query: 187 RQARRAQKAQSQANNLPNADS-QHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPM 245
           RQAR+AQKAQSQA+NLP+ADS QHPSLFGALP+GY PPYNGYGYQA G+YGLMQYR+PPM
Sbjct: 241 RQARKAQKAQSQASNLPSADSGQHPSLFGALPLGYVPPYNGYGYQAPGAYGLMQYRMPPM 300

Query: 246 QNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYP 305
           Q+Q  FH +IP VNQG+AMR  +PDL+  + PRNYA+P + ++GS YPA+PGLQYPM Y 
Sbjct: 301 QSQAAFHNMIPQVNQGSAMRAIAPDLARAVAPRNYAVPSASYMGSAYPALPGLQYPMAYH 360

Query: 306 GGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
           GG++ H+PL+ SPGS  PA+  SN  T+S  G  SGGQ+EG
Sbjct: 361 GGIMSHQPLSGSPGSRPPAMMTSNSPTNSGAGASSGGQVEG 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462310|ref|XP_004148884.1| PREDICTED: CUGBP Elav-like family member 2-like [Cucumis sativus] gi|449491521|ref|XP_004158924.1| PREDICTED: CUGBP Elav-like family member 2-like [Cucumis sativus]

 Score =  543 bits (1398), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 276/353 (78%), Positives = 297/353 (84%), Gaps = 11/353 (3%)

Query: 1   MAESKK--EKKSS-----EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR 53
           MAE  +  E+K S     E+ VKLFVGQVPKHMTE QLL MF+EFALVDEVNII+DKTTR
Sbjct: 1   MAEGSRGGERKESSNQEEEDSVKLFVGQVPKHMTEPQLLTMFQEFALVDEVNIIRDKTTR 60

Query: 54  ASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKN 113
           ASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKN
Sbjct: 61  ASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKN 120

Query: 114 VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS 173
           VSE EVS LFS YGTIKDLQILRGSQQTSKGCAFLKYETK+QA+AALEAINGK KMEGSS
Sbjct: 121 VSEDEVSGLFSQYGTIKDLQILRGSQQTSKGCAFLKYETKDQAVAALEAINGKCKMEGSS 180

Query: 174 VPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASG 233
           VPLVVKWADTEKERQAR+AQKAQSQA N+ NADSQHPSLFGA+P+GY PPYNGYGYQA G
Sbjct: 181 VPLVVKWADTEKERQARKAQKAQSQATNVLNADSQHPSLFGAMPLGYVPPYNGYGYQAPG 240

Query: 234 SYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYP 293
           SYGLMQY LPPMQNQ GF  +IP +NQGNAMRG  PDL   M  RNYAMPP+ +  S YP
Sbjct: 241 SYGLMQYHLPPMQNQSGFPNMIPQLNQGNAMRGIPPDLGPGMATRNYAMPPASY--SAYP 298

Query: 294 AVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
            VP LQ+PM YPGGM+    +++SPG   P     N S +SS G GSGGQIEG
Sbjct: 299 GVPALQHPMAYPGGMMSPGVVSSSPGP-GPFTGGKN-SPTSSMGKGSGGQIEG 349

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572661|ref|XP_003554485.1| PREDICTED: CUGBP Elav-like family member 2-like [Glycine max]

 Score =  537 bits (1383), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 266/332 (80%), Positives = 291/332 (87%), Gaps = 4/332 (1%)

Query: 15  VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
           VKLFVGQVPKHMTE +LLAMFKEFALVDEVNIIKDK TRASRGCCF+ICPSR+EADKAVN
Sbjct: 13  VKLFVGQVPKHMTEPELLAMFKEFALVDEVNIIKDKATRASRGCCFLICPSREEADKAVN 72

Query: 75  ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
           ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSE E+SALFS YGTIKDLQI
Sbjct: 73  ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEVEISALFSKYGTIKDLQI 132

Query: 135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
           LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME SSVPLVVKWADTEKERQARRAQK
Sbjct: 133 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEDSSVPLVVKWADTEKERQARRAQK 192

Query: 195 AQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGI 254
           AQSQA+N+P+ DSQH S+FGALPM Y PPYNGY YQA G YGLM YR+PPMQ+Q G+H +
Sbjct: 193 AQSQASNVPHTDSQHLSMFGALPMSYVPPYNGYAYQAPGGYGLMPYRMPPMQSQHGYHNV 252

Query: 255 IPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPL 314
           +P +NQ NA+R   PDL  NM PRNY +PP+ +V S YPAVPGLQ+PM YP GM+  RP+
Sbjct: 253 MPHMNQVNALR---PDLGPNMNPRNYHVPPASYV-SSYPAVPGLQHPMAYPTGMISPRPM 308

Query: 315 NNSPGSVSPAVANSNPSTSSSGGTGSGGQIEG 346
           N SPGSVSPA  N++ + SS     SGGQ+EG
Sbjct: 309 NTSPGSVSPAGGNNSSAASSGASKNSGGQVEG 340

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535559|ref|XP_003536312.1| PREDICTED: CUGBP Elav-like family member 1-B-like [Glycine max]

 Score =  512 bits (1319), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 250/314 (79%), Positives = 273/314 (86%), Gaps = 6/314 (1%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE K+E K SEE VKLFVGQVPK M E ++LAMFKEFALVDEVNII+DK +RASRGCCF
Sbjct: 2   MAEGKEESKFSEESVKLFVGQVPKRMAEDEVLAMFKEFALVDEVNIIRDKASRASRGCCF 61

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVS 120
           VICPSR+EADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKN+SE EVS
Sbjct: 62  VICPSREEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNISEDEVS 121

Query: 121 ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180
            LFS+YGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH MEGSSVPLVVKW
Sbjct: 122 DLFSMYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHTMEGSSVPLVVKW 181

Query: 181 ADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQY 240
           ADTEKER ARRAQKAQSQ +N+P AD QHPSLFGALPMGY PPYNGYGYQA G YGLM Y
Sbjct: 182 ADTEKERLARRAQKAQSQVSNMPQADPQHPSLFGALPMGYVPPYNGYGYQAPGGYGLMAY 241

Query: 241 RLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQY 300
           R PPMQNQPGFH +   +NQ NA+R   PDL  ++ PRNY  PP+ ++G  YPAVPG+Q+
Sbjct: 242 RFPPMQNQPGFHNM--NMNQVNAVR---PDLGHSVNPRNYHAPPASYIGP-YPAVPGVQH 295

Query: 301 PMPYPGGMLGHRPL 314
           PM YP  ++  RP+
Sbjct: 296 PMVYPRRIVSPRPM 309

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500250|ref|XP_003518946.1| PREDICTED: CUGBP Elav-like family member 1-like [Glycine max]

 Score =  506 bits (1302), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 254/323 (78%), Positives = 278/323 (86%), Gaps = 8/323 (2%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           MAE K+E KSSEE VKLFVGQVPK M+E ++LAMFKE ALVDEVNII+DK TRASRGCCF
Sbjct: 1   MAEGKEESKSSEESVKLFVGQVPKRMSEDEVLAMFKELALVDEVNIIRDKATRASRGCCF 60

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVS 120
           VICPSR+EADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKN+SE EVS
Sbjct: 61  VICPSREEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNISEDEVS 120

Query: 121 ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180
            LFS YGTIKDLQILRGSQ TSKGCAFLKYETKEQA  ALEAINGKH MEGSSVPLVVKW
Sbjct: 121 NLFSKYGTIKDLQILRGSQHTSKGCAFLKYETKEQAFTALEAINGKHTMEGSSVPLVVKW 180

Query: 181 ADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQY 240
           ADTEKER ARRAQK QS+ +N P+AD QHPSLFGALPMGY PPYNGYGYQA G YGLM Y
Sbjct: 181 ADTEKERLARRAQKTQSRVSNAPHADPQHPSLFGALPMGYVPPYNGYGYQAPGGYGLMPY 240

Query: 241 RLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQY 300
           R PP+QNQPGFH +    NQ NA+R   PDL  +M PRNY  PP+ ++GS YPAVPG+Q+
Sbjct: 241 RFPPVQNQPGFHNM----NQANAVR---PDLGHSMNPRNYPAPPASYIGS-YPAVPGIQH 292

Query: 301 PMPYPGGMLGHRPLNNSPGSVSP 323
           PM YP G++  RP+++ PGSVSP
Sbjct: 293 PMVYPRGIVSPRPMSSCPGSVSP 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	354
TAIR|locus:2139340	441	RBP-DR1 "RNA-binding protein-d	0.943	0.757	0.648	2.4e-115
TAIR|locus:2825067	438	BRN2 "Bruno-like 2" [Arabidops	0.847	0.684	0.609	2.5e-97
DICTYBASE|DDB_G0291486	489	DDB_G0291486 "putative splicin	0.480	0.347	0.485	2.9e-46
UNIPROTKB|Q6K271	738	P0415D04.46-1 "FCA" [Oryza sat	0.483	0.231	0.431	1.5e-41
UNIPROTKB|Q6WQT6	738	Q6WQT6 "Flowering time control	0.483	0.231	0.431	1.5e-41
ZFIN|ZDB-GENE-040718-300	520	celf4 "CUGBP, Elav-like family	0.485	0.330	0.459	3.2e-41
FB|FBgn0262475	893	bru-2 "bruno-2" [Drosophila me	0.841	0.333	0.363	4.5e-41
ZFIN|ZDB-GENE-000501-2	452	celf3a "cugbp, Elav-like famil	0.483	0.378	0.465	7.8e-39
DICTYBASE|DDB_G0270634	368	DDB_G0270634 "putative splicin	0.477	0.459	0.426	2.2e-38
FB|FBgn0000114	810	aret "arrest" [Drosophila mela	0.483	0.211	0.485	3.5e-38

TAIR|locus:2139340 RBP-DR1 "RNA-binding protein-defense related 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1137 (405.3 bits), Expect = 2.4e-115, P = 2.4e-115
 Identities = 223/344 (64%), Positives = 263/344 (76%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             VKLFVGQ+PKHM+E+QLL +F+EFA+VDEVNIIKDK TRASRGCCF++CPSR+EADK VN
Sbjct:    18 VKLFVGQIPKHMSESQLLTLFQEFAVVDEVNIIKDKITRASRGCCFLLCPSREEADKLVN 77

Query:    75 ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
             ACHNKKTLPGA+S LQVKYADGELERLEHKLF+GMLPKNVSEAEV +LFS YGTIKDLQI
Sbjct:    78 ACHNKKTLPGANSLLQVKYADGELERLEHKLFVGMLPKNVSEAEVQSLFSKYGTIKDLQI 137

Query:   135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKEXXXXXXXX 194
             LRG+QQTSKGCAFLKYETKEQA++A+E+INGKHKMEGS+VPLVVKWADTE+E        
Sbjct:   138 LRGAQQTSKGCAFLKYETKEQAVSAMESINGKHKMEGSTVPLVVKWADTERERHTRRLQK 197

Query:   195 XXXXXNNLPNADSQHPSLFGALPMGYAPPYNGYGY-QASGSYGLMQYRLPPMQNQPGFHG 253
                    L N D  +PSLFGALPMGY PPYNGYGY Q  G+YG   Y LPP+QNQ  F  
Sbjct:   198 AQSHIARLGNGDPTNPSLFGALPMGYVPPYNGYGYHQPPGTYG---YMLPPIQNQAAFSN 254

Query:   254 IIPPVNQGN--AMRGASPD-LSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLG 310
             +I   NQGN  A++G SPD +   +  RN+ MPP  ++GSGYPA+ G  +P  YP G++ 
Sbjct:   255 MIAQPNQGNNNALQGTSPDSVPPRLARRNFPMPPGNYMGSGYPAMRGHPFPFAYPRGIVS 314

Query:   311 HRPLNNSPGSVSPAVANSNPXXXXXXXXXXXXQIEGF-LSIYSV 353
              RPL++SPGS+SP +  S P              EG  L IY++
Sbjct:   315 PRPLSSSPGSISPGM--STPLGIGLSSVVQTEGPEGANLFIYNI 356

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0080151 "positive regulation of salicylic acid mediated signaling pathway" evidence=IMP

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

TAIR|locus:2825067 BRN2 "Bruno-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 967 (345.5 bits), Expect = 2.5e-97, P = 2.5e-97
 Identities = 200/328 (60%), Positives = 240/328 (73%)

Query:    14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
             RVKLFVGQVPKHMTE QLL +F+EF++V+EVNIIK+KTTRA RGCCF+ CP+R++ADK +
Sbjct:    11 RVKLFVGQVPKHMTEIQLLTLFREFSIVNEVNIIKEKTTRAPRGCCFLTCPTREDADKVI 70

Query:    74 NACHNKKTLPGASSPLQVKYADGELERL---------EHKLFIGMLPKNVSEAEVSALFS 124
             N+ HNKKTLPGASSPLQVKYADGELERL         EHKLF+GMLPKNVSE EV +LFS
Sbjct:    71 NSFHNKKTLPGASSPLQVKYADGELERLDVLDCSCNPEHKLFVGMLPKNVSETEVQSLFS 130

Query:   125 IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE 184
              YGTIKDLQILRGS QTSKGC FLKYE+KEQA+AA+EA+NG+H MEG++VPL+VKWADTE
Sbjct:   131 EYGTIKDLQILRGSLQTSKGCLFLKYESKEQAVAAMEALNGRHIMEGANVPLIVKWADTE 190

Query:   185 KEXXXXXXXXXXXXXNNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPP 244
             KE             + L   D Q+PS+FGALPM Y PPYNGYGY   G+YG   Y LPP
Sbjct:   191 KERQARRLLKVQSHVSRL---DPQNPSMFGALPMSYVPPYNGYGYHVPGTYG---YMLPP 244

Query:   245 MQNQPGFHGIIPPVNQGN--AMRGASPDLSSNMGPRNYAMPPSGF-VGSGYPAVPGLQYP 301
             +Q Q  FH +I P NQGN  A++G +  L+ ++ PR    P   F    G     GLQYP
Sbjct:   245 IQTQHAFHNVISP-NQGNGRALQGTA--LTESVPPR--LAPRRNFPTALGNYGYHGLQYP 299

Query:   302 MPYPGGMLGHR-PLNNSPGSVSPAVANS 328
             M +P GM+  R PL     +VSP ++N+
Sbjct:   300 MAFPRGMIPPRLPLT----TVSPGISNN 323

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0291486 DDB_G0291486 "putative splicing regulator" [Dictyostelium discoideum (taxid:44689)]

 Score = 445 (161.7 bits), Expect = 2.9e-46, Sum P(2) = 2.9e-46
 Identities = 83/171 (48%), Positives = 118/171 (69%)

Query:    16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
             KLFVGQ+PK   E ++  +F   A ++ V++IK+KTT   +GC FV  PSR+EAD+A+  
Sbjct:     4 KLFVGQIPKSFNEEEIKNLFTNIANIESVSLIKNKTTNEPQGCAFVSVPSREEADRAIEQ 63

Query:    76 CHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
              HN K   G  + LQVKYAD E E+L  KLF+GMLP++  E ++  LF  +G ++D+ IL
Sbjct:    64 LHNSKKFQGVLNNLQVKYADSEQEKLASKLFVGMLPRSYEEEQIRELFEPHGVVEDICIL 123

Query:   136 RGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 186
             RG    SKGC F+K++ +E AL+A+  +NG  K++GS  PLVVK+ADTEK+
Sbjct:   124 RGPNSESKGCGFIKFDNRESALSAIATLNGM-KLDGSPNPLVVKFADTEKD 173

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q6K271 P0415D04.46-1 "FCA" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 409 (149.0 bits), Expect = 1.5e-41, Sum P(2) = 1.5e-41
 Identities = 75/174 (43%), Positives = 118/174 (67%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             VKLF+G VP+  TE  +  +F+E   V EV +IKD+ T   +GCCFV   + +EA++A+ 
Sbjct:   122 VKLFIGSVPRTATEDDVRPLFEEHGDVVEVALIKDRKTGEQQGCCFVKYATSEEAERAIR 181

Query:    75 ACHNKKTLPGASSPLQVKYADGELER---LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD 131
             A HN+ TLPGA  P+QV+YADGE ER   +EHKLF+  L K  +  E+  +F+ YG ++D
Sbjct:   182 ALHNQYTLPGAMGPIQVRYADGERERHGAIEHKLFVASLNKQATAKEIEEIFAPYGHVED 241

Query:   132 LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK 185
             + I++   + S+GC F+K+ ++E ALAA+ A++G + M G   PL++++AD ++
Sbjct:   242 VYIMKDGMRQSRGCGFVKFSSREPALAAMSALSGNYVMRGCEQPLIIRFADPKR 295

GO:0003723 "RNA binding" evidence=ISS

GO:0009909 "regulation of flower development" evidence=ISS

GO:0044428 "nuclear part" evidence=ISS

UNIPROTKB|Q6WQT6 Q6WQT6 "Flowering time control protein isoform OsFCA-1" [Oryza sativa Indica Group (taxid:39946)]

 Score = 409 (149.0 bits), Expect = 1.5e-41, Sum P(2) = 1.5e-41
 Identities = 75/174 (43%), Positives = 118/174 (67%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             VKLF+G VP+  TE  +  +F+E   V EV +IKD+ T   +GCCFV   + +EA++A+ 
Sbjct:   122 VKLFIGSVPRTATEDDVRPLFEEHGDVVEVALIKDRKTGEQQGCCFVKYATSEEAERAIR 181

Query:    75 ACHNKKTLPGASSPLQVKYADGELER---LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD 131
             A HN+ TLPGA  P+QV+YADGE ER   +EHKLF+  L K  +  E+  +F+ YG ++D
Sbjct:   182 ALHNQYTLPGAMGPIQVRYADGERERHGAIEHKLFVASLNKQATAKEIEEIFAPYGHVED 241

Query:   132 LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK 185
             + I++   + S+GC F+K+ ++E ALAA+ A++G + M G   PL++++AD ++
Sbjct:   242 VYIMKDGMRQSRGCGFVKFSSREPALAAMSALSGNYVMRGCEQPLIIRFADPKR 295

GO:0003723 "RNA binding" evidence=ISS

GO:0009909 "regulation of flower development" evidence=ISS

GO:0044428 "nuclear part" evidence=ISS

ZFIN|ZDB-GENE-040718-300 celf4 "CUGBP, Elav-like family member 4" [Danio rerio (taxid:7955)]

 Score = 405 (147.6 bits), Expect = 3.2e-41, Sum P(2) = 3.2e-41
 Identities = 79/172 (45%), Positives = 114/172 (66%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             +KLF+GQ+P+++ E  L  +F+EF  + E+ ++KD+ T   +GC F+   +R+ A KA  
Sbjct:    47 IKLFIGQIPRNLDEKDLRPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCARESALKAQT 106

Query:    75 ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
             A H +KTLPG + P+QVK AD E    + KLF+GML K   E +V  LF  +G+I++  I
Sbjct:   107 ALHEQKTLPGMNRPIQVKPADSESRGEDRKLFVGMLNKQQCEDDVRRLFESFGSIEECTI 166

Query:   135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 186
             LRG    SKGCAF+KY T  +A AA+ A++G   M G+S  LVVK+ADT+KE
Sbjct:   167 LRGPDGNSKGCAFVKYSTHAEAQAAISALHGSQTMPGASSSLVVKFADTDKE 218

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

FB|FBgn0262475 bru-2 "bruno-2" [Drosophila melanogaster (taxid:7227)]

 Score = 445 (161.7 bits), Expect = 4.5e-41, P = 4.5e-41
 Identities = 114/314 (36%), Positives = 168/314 (53%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             +K+FVGQ+PK   E +L  MF++F  V  +N+++DK T  SRGCCFV   +R+ A +A +
Sbjct:   295 IKMFVGQIPKTWDETRLRQMFEQFGPVHTLNVLRDKVTSISRGCCFVTYYTRKAALRAQD 354

Query:    75 ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
             A HN KTL G   P+Q+K AD E  R E KLF+GML K  +EA+V  LF+ +GTI++  +
Sbjct:   355 ALHNIKTLDGMHHPIQMKPADSE-NRNERKLFVGMLNKKYTEADVRQLFTGHGTIEECTV 413

Query:   135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKEXXXXXXXX 194
             LR     SKGCAF+ + TK+ A+ A++A++    MEG S PLVVK+ADT+KE        
Sbjct:   414 LRDQAGQSKGCAFVTFATKQNAIGAIKALHQSQTMEGCSAPLVVKFADTQKEKDQKKMQQ 473

Query:   195 XXXXXN-NLPN---ADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPG 250
                    N P+   A +  P++  A  +  APP  G   + + S       +P +Q Q G
Sbjct:   474 IHAFCGINTPSGATAGAATPTINAATALIAAPPSAG---RTNPSMAAALAAVPQVQ-QAG 529

Query:   251 FHGIIP----PVNQGNAMRGA-SPDLSSNMGPRNYAMPPSGFVGSGYPAVPGLQYPMPYP 305
                  P    P+N   A+  + +P+L +       A   + ++G+   A   LQ      
Sbjct:   530 SAATAPTTLVPLNSTTALSASLTPNLLATNAAHQGAAAAAAYLGADPAAAAHLQLYQQLH 589

Query:   306 GGMLGHRPLNNSPG 319
             G   G  P +  PG
Sbjct:   590 G--YGLSPAHYLPG 601

GO:0003729 "mRNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=ISA

ZFIN|ZDB-GENE-000501-2 celf3a "cugbp, Elav-like family member 3a" [Danio rerio (taxid:7955)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 80/172 (46%), Positives = 120/172 (69%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             +KLF+GQ+P+++ E  L  +F++F  + E+ +IKDK T   +GC F+   +R+ A KA N
Sbjct:     7 IKLFIGQIPRNLEEKDLKPIFEQFGKIYELTVIKDKYTGMHKGCAFLTYCARESALKAQN 66

Query:    75 ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
             A H +KTLPG + P+QVK AD E  R + KLF+GML K +S+A+V  +F  +G+I++  +
Sbjct:    67 ALHEQKTLPGMNRPIQVKPADSE-GRGDRKLFVGMLGKQLSDADVRKMFEPFGSIEECTV 125

Query:   135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 186
             LRG    SKGCAF+KY++  +A AA+ A++G   + G+S  LVVK+ADTEKE
Sbjct:   126 LRGPDGASKGCAFVKYQSNAEAQAAISALHGSRTLPGASSSLVVKFADTEKE 177

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

DICTYBASE|DDB_G0270634 DDB_G0270634 "putative splicing regulator" [Dictyostelium discoideum (taxid:44689)]

 Score = 380 (138.8 bits), Expect = 2.2e-38, Sum P(2) = 2.2e-38
 Identities = 73/171 (42%), Positives = 112/171 (65%)

Query:    17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
             +FVG +P  M E  +  +F +F  + ++ IIKDK T  S+GC F+   +++EAD A+N  
Sbjct:    20 VFVGHIPSSMNEEGVSQIFNKFGNILDITIIKDKRTNVSKGCAFITFSTKEEADNALNTT 79

Query:    77 HNKKT-LPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
             +   T L   + PLQVKY+D E+E++E KLFIGML  +  E ++  LF  YG I+DL I+
Sbjct:    80 NESGTFLENMNKPLQVKYSDNEIEKMERKLFIGMLGTS-DEDQIRILFGNYGIIEDLNIV 138

Query:   136 RGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKE 186
             R      KG  F+KY T++++  AL  I+GKH + GS++P++VK+ADTE++
Sbjct:   139 REKDGKPKGYGFIKYSTRDESENALREIDGKHTLPGSNLPIIVKFADTERQ 189

GO:0045335 "phagocytic vesicle" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

FB|FBgn0000114 aret "arrest" [Drosophila melanogaster (taxid:7227)]

 Score = 417 (151.9 bits), Expect = 3.5e-38, P = 3.5e-38
 Identities = 84/173 (48%), Positives = 118/173 (68%)

Query:    15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
             +K+FVGQVPK M E+QL  MF+E+  V  +N+++DK T  S+GCCFV   +R  A KA +
Sbjct:   357 IKMFVGQVPKSMDESQLREMFEEYGAVHSINVLRDKATGISKGCCFVTFYTRHAALKAQD 416

Query:    75 ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
             A HN KTL G   P+Q+K AD E  R E KLF+GML K ++E +V  LF ++G I++  +
Sbjct:   417 ALHNVKTLNGMYHPIQMKPADSE-NRNERKLFVGMLNKKLNENDVRKLFEVHGAIEECTV 475

Query:   135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHK-MEGSSVPLVVKWADTEKE 186
             LR     SKGCAF+ + TK  A++A++    ++K MEG + PLVVK+ADT+KE
Sbjct:   476 LRDQNGQSKGCAFVTFATKHAAISAIKVTLSQNKIMEGCTSPLVVKFADTQKE 528

GO:0048477 "oogenesis" evidence=IMP

GO:0007286 "spermatid development" evidence=IMP

GO:0007319 "negative regulation of oskar mRNA translation" evidence=IDA;NAS;TAS

GO:0003729 "mRNA binding" evidence=ISS;NAS;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0030727 "germarium-derived female germ-line cyst formation" evidence=TAS

GO:0042078 "germ-line stem cell division" evidence=NAS

GO:0046011 "regulation of oskar mRNA translation" evidence=TAS

GO:0006378 "mRNA polyadenylation" evidence=TAS

GO:0003730 "mRNA 3'-UTR binding" evidence=IDA;TAS

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0043186 "P granule" evidence=IDA

GO:0005634 "nucleus" evidence=IC

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

GO:0003723 "RNA binding" evidence=IDA

GO:0007281 "germ cell development" evidence=IMP

GO:0031536 "positive regulation of exit from mitosis" evidence=IMP

GO:0002121 "inter-male aggressive behavior" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	354
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	9e-38
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	8e-35
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-26
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-25
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	7e-24
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	9e-24
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	3e-23
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-22
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-19
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	8e-19
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-18
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-18
smart00360	73	smart00360, RRM, RNA recognition motif	1e-16
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-16
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-16
smart00360	73	smart00360, RRM, RNA recognition motif	6e-16
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-15
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-13
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-12
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-12
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-12
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-12
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	1e-11
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-11
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-11
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-11
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-11
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-11
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	5e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-11
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-10
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-09
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-09
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-08
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-08
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-08
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-08
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-08
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	6e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-08
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-08
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	8e-08
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	8e-08
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	1e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-07
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-07
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	3e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	5e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	5e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	6e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	6e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	7e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	9e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-06
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-06
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	2e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	3e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-06
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	5e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-06
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	6e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	7e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	7e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	7e-06
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	7e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	8e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	8e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-06
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	8e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	9e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-05
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	3e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	3e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	4e-05
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	4e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-05
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	5e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-05
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	5e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	6e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	6e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-05
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	7e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	8e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	9e-05
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	9e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	1e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	1e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-04
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	2e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-04
cd12289	93	cd12289, RRM_LARP6, RNA recognition motif in La-re	3e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	3e-04
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	3e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	3e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	3e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	4e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	4e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	4e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	4e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	5e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	5e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	5e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	6e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	6e-04
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	6e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	7e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	7e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	8e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	9e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	9e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.001
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.001
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.001
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.001
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.001
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.001
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.001
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.001
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.001
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.001
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	0.002
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.002
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.002
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	0.002
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.002
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.002
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.002
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.002
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.002
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.002
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.003
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.003
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.003
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.003
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.003
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.003
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	0.003
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.003
cd12624	91	cd12624, RRM_PRC, RNA recognition motif in peroxis	0.003
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.004
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.004
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	0.004
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.004
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.004
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.004
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.004
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.004
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.004
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.004
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.004
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.004
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	0.004

>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 =  129 bits (327), Expect = 9e-38
 Identities = 44/77 (57%), Positives = 56/77 (72%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVGQ+PK  TE  + A+F+E+  ++EV II+DK T  S+GC FV   SR+EA KA+ A
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 76 CHNKKTLPGASSPLQVK 92
           H K T+PGAS PLQVK
Sbjct: 61 LHGKVTMPGASRPLQVK 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|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 =  121 bits (307), Expect = 8e-35
 Identities = 38/77 (49%), Positives = 54/77 (70%), Gaps = 1/77 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEA 162
           KLF+G LPK  +E +V ALF  YG I+++ I+R      SKGCAF+K+ ++E+A  A+EA
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 163 INGKHKMEGSSVPLVVK 179
           ++GK  M G+S PL VK
Sbjct: 61  LHGKVTMPGASRPLQVK 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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score =  100 bits (249), Expect = 2e-26
 Identities = 45/80 (56%), Positives = 59/80 (73%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVG VP+ +TE ++  MF+E   V EV IIKDK T   +GCCFV   +R EAD+A+ A
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           HN++TLPG +SP+QV+YAD
Sbjct: 61 LHNQRTLPGGASPVQVRYAD 80

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 97.5 bits (243), Expect = 2e-25
 Identities = 36/81 (44%), Positives = 56/81 (69%)

Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          +KLFVGQ+P+++ E  L  +F++F  + E+ ++KDK T   +GC F+   +R+ A KA +
Sbjct: 6  IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65

Query: 75 ACHNKKTLPGASSPLQVKYAD 95
          A H +KTLPG + P+QVK AD
Sbjct: 66 ALHEQKTLPGMNRPIQVKPAD 86

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|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 = 93.3 bits (232), Expect = 7e-24
 Identities = 39/79 (49%), Positives = 54/79 (68%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLF+GML K  +E +V  LF  +GTI++  ILRG    SKGCAF+K+ +  +A AA+ A+
Sbjct: 3   KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINAL 62

Query: 164 NGKHKMEGSSVPLVVKWAD 182
           +G   M G+S  LVVK+AD
Sbjct: 63  HGSQTMPGASSSLVVKFAD 81

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 93.0 bits (231), Expect = 9e-24
 Identities = 35/81 (43%), Positives = 56/81 (69%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           E KLF+GML K  +E +V  +F+ +G+I++  +LR     S+GCAF+ + +++ AL A++
Sbjct: 1   ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIK 60

Query: 162 AINGKHKMEGSSVPLVVKWAD 182
           A++    MEG S PLVVK+AD
Sbjct: 61  AMHHSQTMEGCSSPLVVKFAD 81

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|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 91.8 bits (228), Expect = 3e-23
 Identities = 35/83 (42%), Positives = 57/83 (68%), Gaps = 2/83 (2%)

Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT--RASRGCCFVICPSRQEADKA 72
          +K+FVGQ+P+  +E  L  +F+++  V ++N+++D++     S+GCCFV   +R+ A +A
Sbjct: 2  IKMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61

Query: 73 VNACHNKKTLPGASSPLQVKYAD 95
           NA HN KTLPG   P+Q+K AD
Sbjct: 62 QNALHNMKTLPGMHHPIQMKPAD 84

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. 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) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The 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 binds specifically 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. 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 = 84

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 89.5 bits (222), Expect = 2e-22
 Identities = 37/79 (46%), Positives = 56/79 (70%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLF+G L K  +E EV  +FS YG ++D+ ++R   + S+GCAF+KY +KE A AA++A+
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 164 NGKHKMEGSSVPLVVKWAD 182
           NG + M G   PL+V++AD
Sbjct: 61  NGVYTMRGCDQPLIVRFAD 79

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

 Score = 89.9 bits (223), Expect = 1e-19
 Identities = 72/350 (20%), Positives = 128/350 (36%), Gaps = 37/350 (10%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           + + ++E    ++   L+V  +   + E +L  +F +F  +    ++KD + R SRG  F
Sbjct: 165 IKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGR-SRGFAF 223

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSP-----------------LQVKYADGELERLEH 103
           V     ++A KAV   + KK +  A                    L+ K+ + + ER   
Sbjct: 224 VNFEKHEDAAKAVEEMNGKK-IGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK 282

Query: 104 KLFIGMLPKN----VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 159
              + +  KN    V++ ++  LFS  G I   +++   +  S+G  F+ +   E+A  A
Sbjct: 283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRA 342

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQAR---RAQKAQSQANNLPNADSQHPSLFGAL 216
           +  ++G  +M G   PL V  A  +++R+A    +  + Q +   LP   S      G  
Sbjct: 343 VTEMHG--RMLGGK-PLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMG-SPMGGAMGQP 398

Query: 217 PMGYAPPYNGYGYQASGSYGLMQYRLPPMQN--QPGFHGIIPPVNQGNAMRGASPDLSSN 274
           P     P   +  Q  G +  M     PM        +G+ P        R A       
Sbjct: 399 PYYGQGPQQQFNGQPLG-WPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKP 457

Query: 275 MGPRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPA 324
                   P         P    L  P         ++ L     S +P 
Sbjct: 458 PMQPVMYPPNY----QSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQ 503

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 79.7 bits (196), Expect = 8e-19
 Identities = 35/81 (43%), Positives = 55/81 (67%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           + KLFIGM+ K  +E ++  +FS +G I++ +ILRG    S+GCAF+ + T+  A  A++
Sbjct: 1   DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 60

Query: 162 AINGKHKMEGSSVPLVVKWAD 182
           A++    MEG S P+VVK+AD
Sbjct: 61  AMHQAQTMEGCSSPIVVKFAD 81

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), 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 binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 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 preferentially binds 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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 = 81

>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 = 78.2 bits (193), Expect = 2e-18
 Identities = 35/80 (43%), Positives = 48/80 (60%), Gaps = 1/80 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVG + K  TE  +  +F+ F  ++E  I++      S+GC FV   S  EA  A+NA
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDG-NSKGCAFVKFSSHAEAQAAINA 61

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           H  +T+PGASS L VK+AD
Sbjct: 62 LHGSQTMPGASSSLVVKFAD 81

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 83.8 bits (207), Expect = 4e-18
 Identities = 54/248 (21%), Positives = 113/248 (45%), Gaps = 12/248 (4%)

Query: 12  EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
           E +  L V  +P+ MT+ ++ ++F     ++   +++DK T  S G  FV     ++A+K
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 72  AVNACHNKKTLPGASSPLQVKYADGELERLE-HKLFIGMLPKNVSEAEVSALFSIYGTIK 130
           AVN+ +    L   +  ++V YA    + ++   L++  LPK +++ E+ ++FS +G I 
Sbjct: 61  AVNSLNG---LRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQII 117

Query: 131 DLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT--EKER 187
             +IL  +    SKG  F++++ +++A  A++ +NG     G + P+ VK+A+       
Sbjct: 118 TSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT-TPSGCTEPITVKFANNPSSSNS 176

Query: 188 QARRAQKAQSQANNLPNADSQHPSLFGAL-PMGYAPP---YNGYGYQASGSYGLMQYRLP 243
           +   +Q    Q                 + PM +A      +   + A  ++   Q+ + 
Sbjct: 177 KGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVA 236

Query: 244 PMQNQPGF 251
                   
Sbjct: 237 QQHAAQRA 244

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|214636 smart00360, RRM, RNA recognition motif

 Score = 73.4 bits (181), Expect = 1e-16
 Identities = 25/65 (38%), Positives = 40/65 (61%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           LFVG +P   TE +L  +F +F  V+ V +++DK T  S+G  FV   S ++A+KA+ A
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 76 CHNKK 80
           + K+
Sbjct: 61 LNGKE 65

Length = 73

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 72.9 bits (179), Expect = 2e-16
 Identities = 37/83 (44%), Positives = 51/83 (61%), Gaps = 2/83 (2%)

Query: 13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
          ER KLFVG + K   E  +  MF  F  ++E  +++D+  + SRGC FV   SRQ A  A
Sbjct: 1  ER-KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQ-SRGCAFVTFASRQCALNA 58

Query: 73 VNACHNKKTLPGASSPLQVKYAD 95
          + A H+ +T+ G SSPL VK+AD
Sbjct: 59 IKAMHHSQTMEGCSSPLVVKFAD 81

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 71.9 bits (177), Expect = 4e-16
 Identities = 28/62 (45%), Positives = 43/62 (69%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+G LP + +E ++  LFS +G I+ ++I+R     SKG AF+++E +E A  ALEA+N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 165 GK 166
           GK
Sbjct: 61  GK 62

(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|214636 smart00360, RRM, RNA recognition motif

 Score = 71.5 bits (176), Expect = 6e-16
 Identities = 27/64 (42%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            LF+G LP + +E E+  LFS +G ++ ++++R  +   SKG AF+++E++E A  ALEA
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 163 INGK 166
           +NGK
Sbjct: 61  LNGK 64

Length = 73

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 70.5 bits (173), Expect = 2e-15
 Identities = 32/82 (39%), Positives = 51/82 (62%), Gaps = 3/82 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTS--KGCAFLKYETKEQALAALE 161
           KLF+G +P+N+ E ++  LF  +G I +L +L+  + T   KGCAFL Y  +E AL A  
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLK-DKYTGMHKGCAFLTYCARESALKAQS 65

Query: 162 AINGKHKMEGSSVPLVVKWADT 183
           A++ +  + G + P+ VK AD+
Sbjct: 66  ALHEQKTLPGMNRPIQVKPADS 87

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 69.3 bits (170), Expect = 3e-15
 Identities = 28/62 (45%), Positives = 43/62 (69%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+G LP + +E ++  LFS +G I+ ++I+R     SKG AF+++E+ E A  ALEA+N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 165 GK 166
           GK
Sbjct: 61  GK 62

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 64.7 bits (157), Expect = 2e-13
 Identities = 32/80 (40%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLF+G V K   E  +  MF  F  ++E  I++      SRGC FV   +R  A  A+ A
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAIKA 61

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           H  +T+ G SSP+ VK+AD
Sbjct: 62 MHQAQTMEGCSSPIVVKFAD 81

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), 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 binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 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 preferentially binds 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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 = 81

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

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFVG +P   TE  L  +F +F  ++ V I++DK  + S+G  FV   S ++A+KA+ A 
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK-SKGFAFVEFESPEDAEKALEAL 59

Query: 77 HNKK 80
          + K+
Sbjct: 60 NGKE 63

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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 62.2 bits (151), Expect = 1e-12
 Identities = 28/80 (35%), Positives = 48/80 (60%), Gaps = 1/80 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVG + K  TE ++  +F  +  V+++ +++D+  + SRGC FV   S++ A  A+ A
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAIKA 59

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           +   T+ G   PL V++AD
Sbjct: 60 LNGVYTMRGCDQPLIVRFAD 79

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 26/78 (33%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L+I  LP ++ E ++  +   YG +   +ILR S+  S+G  F + E++E+    +   N
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62

Query: 165 GKHKMEGSSVPLVVKWAD 182
           GK+ ++G   PL+VK+AD
Sbjct: 63  GKY-LKGEGEPLLVKFAD 79

This subfamily corresponds to the RRM2 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, they 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 = 79

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

 Score = 67.2 bits (164), Expect = 2e-12
 Identities = 56/212 (26%), Positives = 91/212 (42%), Gaps = 27/212 (12%)

Query: 5   KKEKKSSEERVKL--FVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
            KE  +  ER     FV Q+     E  L   F +   V +V  IKD+ +R S+G  +V 
Sbjct: 78  TKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVE 137

Query: 63  CPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER-------------LEHKLFIGM 109
               +   KA+      + L G   P+ V+ +  E  R                KL++G 
Sbjct: 138 FYDVESVIKALAL--TGQMLLGR--PIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGN 193

Query: 110 LPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEAINGKHK 168
           L  N++E E+  +F  +G I+D+Q+ R  +   SKG  F+++   E+A  ALE +NG   
Sbjct: 194 LHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNG--- 250

Query: 169 MEGSSVPLVVKWADTEKERQARRAQKAQSQAN 200
            E +  P+ V +A             A +  +
Sbjct: 251 FELAGRPIKVGYAQDSTYLLD----AANTFED 278

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

 Score = 61.5 bits (149), Expect = 2e-12
 Identities = 28/78 (35%), Positives = 49/78 (62%), Gaps = 2/78 (2%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAI 163
           L++  LP+ ++E E+  +F  YG I    +LR  S    +G AF++Y+ +E+A AA+ ++
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NG     GS++PL V++A
Sbjct: 63  NGTI-PPGSTMPLSVRYA 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFVG +P   TE  L  +F +F  ++ + I++D+T R S+G  FV     ++A+KA+ A 
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR-SKGFAFVEFEDEEDAEKALEAL 59

Query: 77 HNKK 80
          + K+
Sbjct: 60 NGKE 63

(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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 60.8 bits (148), Expect = 5e-12
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +PK MT+ +L A+F  +  +    I+ D  T  SRG  F+    R EA++A+ A 
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 77 HNKKTLPGASSPLQVKYA 94
           N    PGA+ P+ VK+A
Sbjct: 63 -NGTIPPGATEPITVKFA 79

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 59.6 bits (144), Expect = 1e-11
 Identities = 28/83 (33%), Positives = 53/83 (63%), Gaps = 7/83 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR----GSQQTSKGCAFLKYETKEQALAA 159
           KLF+G +P+ ++E EV  +F  +G + ++ I++    G QQ   GC F+KY T+++A  A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQ---GCCFVKYSTRDEADRA 57

Query: 160 LEAINGKHKMEGSSVPLVVKWAD 182
           + A++ +  + G + P+ V++AD
Sbjct: 58  IRALHNQRTLPGGASPVQVRYAD 80

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L++  +P HM E  L  M K +  V    I++D   + SRG  F    SR++ +  ++  
Sbjct: 3  LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQ-SRGVGFARMESREKCEDIISKF 61

Query: 77 HNKKTLPGASSPLQVKYAD 95
          +  K L G   PL VK+AD
Sbjct: 62 NG-KYLKGEGEPLLVKFAD 79

This subfamily corresponds to the RRM2 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, they 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 = 79

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

 Score = 59.5 bits (144), Expect = 1e-11
 Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +P+ +TE +L  +F+ +  + + N+++DK+T   RG  FV    R+EA  A+++ 
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 77 HNKKTLPGASSPLQVKYA 94
           N    PG++ PL V+YA
Sbjct: 63 -NGTIPPGSTMPLSVRYA 79

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

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 3/82 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ---TSKGCAFLKYETKEQALAAL 160
           K+F+G +P++ SE ++  LF  YG +  + +LR   Q    SKGC F+ + T++ AL A 
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 161 EAINGKHKMEGSSVPLVVKWAD 182
            A++    + G   P+ +K AD
Sbjct: 63  NALHNMKTLPGMHHPIQMKPAD 84

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. 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) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The 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 binds specifically 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. 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 = 84

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 27/78 (34%), Positives = 49/78 (62%), Gaps = 2/78 (2%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEAI 163
           L++  LPK +++ E+ ALFS YG I   +IL  +    S+G  F++++ + +A  A++A+
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NG     G++ P+ VK+A
Sbjct: 63  NG-TIPPGATEPITVKFA 79

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

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

 Score = 64.3 bits (156), Expect = 2e-11
 Identities = 58/209 (27%), Positives = 101/209 (48%), Gaps = 9/209 (4%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L V  +P+ MT+ +L A+F+    ++   I++D  T  S G  FV   S  ++ +A+   
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIK-- 167

Query: 77  HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
            N   +   +  L+V YA    E + +  L++  LP+ +++ ++  +F  YG I    IL
Sbjct: 168 -NLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNIL 226

Query: 136 RGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
           R     T +G AF+++  +E+A  A+ A+N     EG S PL V+ A+   E    +A  
Sbjct: 227 RDKLTGTPRGVAFVRFNKREEAQEAISALNNVIP-EGGSQPLTVRLAE---EHGKAKAHH 282

Query: 195 AQSQANNLPNADSQHPSLFGALPMGYAPP 223
             SQ  +    +  H ++  A   G  PP
Sbjct: 283 YMSQMGHGNMGNMGHGNMGMAGGSGMNPP 311

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

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 7/82 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL---RGSQQ-TSKGCAFLKYETKEQALAA 159
           +L+IG L   ++E  +  LFS YG IK    L    G  +   +G  F+ +ETKE+A  A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 160 LEAINGKHKMEGSSVPLVVKWA 181
           L+++NG  K       LVV+WA
Sbjct: 61  LKSLNG--KTALGKK-LVVRWA 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|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 = 57.2 bits (139), Expect = 8e-11
 Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFV  +    TE +L A+F +F  V+EV ++KD  T  SRG  FV   S ++AD A+  
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 76 CHNKKTLPG 84
            N K L G
Sbjct: 63 L-NGKELEG 70

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

 Score = 56.9 bits (137), Expect = 1e-10
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +PK MT+ +L  +F ++  +    I++D+ T  SRG  F+    R EA++A+   
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 77 HNKKTLPGASSPLQVKYA 94
          + +K   GAS P+ VK+A
Sbjct: 63 NGQKPE-GASEPITVKFA 79

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

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

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 19/70 (27%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++  LP +V+E ++   FS YG ++ ++++R ++   +G AF+++ + E A AAL+   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR-NKDRPRGFAFVEFASPEDAEAALKK-L 58

Query: 165 GKHKMEGSSV 174
               ++G ++
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 61.4 bits (149), Expect = 2e-10
 Identities = 45/150 (30%), Positives = 73/150 (48%), Gaps = 2/150 (1%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L+VG +   +TEA+L  +FK F  V  V + +D  TR S G  +V   +  +A++A+   
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 77  HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
            N K L G    +     D  L R     +F+  L K+V    +   FS +G I   ++ 
Sbjct: 63  -NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVA 121

Query: 136 RGSQQTSKGCAFLKYETKEQALAALEAING 165
                 S+G  F+ +E +E A AA++ +NG
Sbjct: 122 TDENGKSRGYGFVHFEKEESAKAAIQKVNG 151

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 = 60.3 bits (145), Expect = 2e-10
 Identities = 44/191 (23%), Positives = 78/191 (40%), Gaps = 10/191 (5%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 160
            + LF+G LP +V+E ++  LF  +G +K ++++R  +   S+G AF+++E++E A  A+
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174

Query: 161 EAINGKHKMEGSSVPLVVKWA-DTEKERQARRAQKAQSQANNLPNADSQHP-----SLFG 214
           E +NGK ++EG   PL V+ A    + R         S A  L    +           G
Sbjct: 175 EELNGK-ELEGR--PLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 215 ALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSN 274
            LP+  A       +++ G               P     +      +A+   S      
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKK 291

Query: 275 MGPRNYAMPPS 285
           +  R      S
Sbjct: 292 ILGRGPRKAFS 302

Length = 306

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

 Score = 54.9 bits (133), Expect = 4e-10
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +P  +TE  L   F  +  V+ V ++++K     RG  FV   S ++A+ A+   
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 77 HNKK 80
          +   
Sbjct: 59 NGLV 62

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

>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 = 6e-10
 Identities = 22/64 (34%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           KLF+  L    +E E+ ALFS +G ++++ +++  +   S+G  F+ +E+ E A AA+  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 163 INGK 166
           +NGK
Sbjct: 63  LNGK 66

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|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 = 54.2 bits (131), Expect = 7e-10
 Identities = 22/70 (31%), Positives = 43/70 (61%), Gaps = 6/70 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +++G LP  ++E E+   FS +G I+++++ +      KG AF++++T E A  A+ A+N
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAVN 57

Query: 165 GKHKMEGSSV 174
           G   + G +V
Sbjct: 58  G-TSINGQTV 66

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

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

 Score = 54.2 bits (130), Expect = 1e-09
 Identities = 31/79 (39%), Positives = 52/79 (65%), Gaps = 4/79 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           L++  LPK +++ E+  LFS YG I   +ILR  Q T  S+G  F++++ + +A  A++ 
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILR-DQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +NG+ K EG+S P+ VK+A
Sbjct: 62  LNGQ-KPEGASEPITVKFA 79

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

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

 Score = 57.6 bits (138), Expect = 2e-09
 Identities = 53/199 (26%), Positives = 79/199 (39%), Gaps = 29/199 (14%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
               K  +KS EE   LFVG +P  +TE  L  +FK+F  V  V +++D+ T  SRG  F
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAF 161

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHK---------------- 104
           V   S + A+KA+    N K L     PL+V+ A    +                     
Sbjct: 162 VEFESEESAEKAIEE-LNGKEL--EGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGK 218

Query: 105 ---------LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKE 154
                    L++G LP   +E E++ LF   G I    +         K  +F+  E  +
Sbjct: 219 ALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASK 278

Query: 155 QALAALEAINGKHKMEGSS 173
            AL +    N K  +    
Sbjct: 279 DALESNSRGNKKKILGRGP 297

Length = 306

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 17 LFVGQVPKHMTEAQLL-AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          L++G +   M EA +  A  +   +   V II++K T  S G  FV   + + A++A+ +
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVT-SVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 76 CHNKKTLPGA 85
            N K +P  
Sbjct: 61 -LNGKPIPNT 69

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

>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 = 52.0 bits (125), Expect = 6e-09
 Identities = 20/63 (31%), Positives = 38/63 (60%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           HKLF+  LP +V++ E+  LF  +G +K ++++       KG A+++YE +  A  A+  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 163 ING 165
           ++G
Sbjct: 63  MDG 65

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|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 = 51.6 bits (124), Expect = 7e-09
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 9/80 (11%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L++G + K +TE  L  +F+E+  +  +++I        RGC +V   +RQ+A +A+   
Sbjct: 5  LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQKL 58

Query: 77 HNKKTLPGASSPLQVKYADG 96
           N K    A   ++V +A  
Sbjct: 59 RNVK---LAGKKIKVAWAPN 75

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 23/65 (35%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            L++G LP NV+E ++  LF  +G +   +++  R + + S+G  F++ ET E+A AA+E
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGR-SRGFGFVEMETAEEANAAIE 59

Query: 162 AINGK 166
            +NG 
Sbjct: 60  KLNGT 64

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 23/64 (35%), Positives = 39/64 (60%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          ++V  +P  +T   L  +F ++  V +V I+KDK TR S+G  F++   R++A K V A 
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 77 HNKK 80
          +NK+
Sbjct: 64 NNKE 67

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 23/61 (37%), Positives = 30/61 (49%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFVG +P   T   LLA FK       V ++ DK T  S+GC FV   + +   KA+   
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 77 H 77
          H
Sbjct: 63 H 63

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

 Score = 55.2 bits (133), Expect = 2e-08
 Identities = 46/201 (22%), Positives = 85/201 (42%), Gaps = 18/201 (8%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN-- 74
           +FV  + K +    L   F +F  +    +  D+  + SRG  FV     + A  A+   
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGFVHFEKEESAKAAIQKV 149

Query: 75  ---ACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD 131
                ++K+   G       +  +    +    L++  L  +V+E ++  LF+ +G I  
Sbjct: 150 NGMLLNDKEVYVGRFIKKHER--EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITS 207

Query: 132 LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH-KMEGSSVPLVVKWADTEKERQA- 189
             +++     S+G AF+ +E  E A  A+E +NGK   +      L V  A    ER+A 
Sbjct: 208 AAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAE 267

Query: 190 --------RRAQKAQSQANNL 202
                   ++ +K ++Q  NL
Sbjct: 268 LRRKFEELQQERKMKAQGVNL 288

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 26/76 (34%), Positives = 47/76 (61%), Gaps = 3/76 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           +LFI +  K+V+E ++   F+ +G I+D+ +++  Q + SKG A++K+     A  A+E 
Sbjct: 5   RLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEE 63

Query: 163 INGKHKMEGSSVPLVV 178
           +NGK  + G + PL V
Sbjct: 64  MNGK-CLGGDTKPLKV 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++  LP  +S  E+  LF  YG I+  QI  G+ + ++G AF+ YE    A  A + ++
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIR--QIRIGNTKETRGTAFVVYEDIYDAKNACDHLS 62

Query: 165 G 165
           G
Sbjct: 63  G 63

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

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 50.8 bits (121), Expect = 2e-08
 Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +PK M++ ++  +F ++  +    I+ D+ T  SRG  F+    R EA++A+   
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 77 HNKKTLPGASSPLQVKYAD 95
          + +K L GA+ P+ VK+A+
Sbjct: 64 NGQKPL-GAAEPITVKFAN 81

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

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 3/63 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIK--DLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           L +G L +NV++  +  +FS YGT+K  DL I R      +G A++++E+ E A  A++ 
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREV-NLPRGYAYVEFESPEDAEKAIKH 59

Query: 163 ING 165
           ++G
Sbjct: 60  MDG 62

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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 50.6 bits (120), Expect = 2e-08
 Identities = 27/79 (34%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +PK MT+ +L  +F ++  +    I+ D+ T  SRG  F+    R EA++A+   
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 77 HNKKTLPGASSPLQVKYAD 95
          + +K  PGA+ P+ VK+A+
Sbjct: 68 NGQKP-PGATEPITVKFAN 85

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 50.4 bits (120), Expect = 3e-08
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L++  +P+ MT+  +  MF  F  +    ++ D+ T  SRG  F+    R EA++A+ + 
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 77 HNKKTLPGASSPLQVKYA 94
          +  K  PG+S P+ VK+A
Sbjct: 63 NGHKP-PGSSEPITVKFA 79

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +LF+G LP +++E E   LFS YG + ++ + +      KG  F++ +T+  A  A   +
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAEL 57

Query: 164 NGK 166
           +G 
Sbjct: 58  DGI 60

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|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 = 49.9 bits (120), Expect = 3e-08
 Identities = 19/64 (29%), Positives = 39/64 (60%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KL +  +P   ++ E+  LFS +G +K +++ +    + +G AF+++ TK++A  A+EA+
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 164 NGKH 167
              H
Sbjct: 62  KSTH 65

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           L++G L + V E  + A F  +G IKD+QI    + Q  +G AF+++E  E A AA++ +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 164 NG 165
           N 
Sbjct: 61  NE 62

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 23/62 (37%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 163
           ++IG LP  ++E ++  +FS YG I D+ ++R  +   SKG AFL YE +   + A++ +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 164 NG 165
           NG
Sbjct: 72  NG 73

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 21/60 (35%), Positives = 33/60 (55%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L+VG +P ++TE  L  +F +F  V    +I D+ T  SRG  FV   + +EA+ A+  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

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

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 14/90 (15%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +++  L +++ + ++  LF  YG I   ++++  +  SKG  F+ +E  E A  A+E +N
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 165 GKHKMEGSSVPLVVKWADTEKERQARRAQK 194
           GK ++ G             K+    RAQK
Sbjct: 64  GK-EVNG-------------KKLYVGRAQK 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L V  +P+ MT+ +L ++F+    ++   I++D+ T  S G  FV      +A KA+N  
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 77 HNKKTLPGASSPLQVKYA 94
          +  +     +  L+V YA
Sbjct: 63 NGFEIR---NKRLKVSYA 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|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 = 27/78 (34%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +L +  LP   +EA++  LFS +G + ++ I R      KG AF+++ +K  A  A++ +
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NGK K++G   P+ V WA
Sbjct: 61  NGK-KIKGR--PVAVDWA 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 49.0 bits (117), Expect = 6e-08
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 3/78 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+ +  LP   ++ +V  LFS YG +K +++ +   Q+++G AF+++ T ++AL A+ A+
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNAL 61

Query: 164 NGKHKMEGSSVPLVVKWA 181
              H +      LV+++A
Sbjct: 62  KDTHLL---GRRLVLQYA 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|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 = 48.8 bits (117), Expect = 6e-08
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           +LF+  LP   +E E+  LF  +G I ++ +    + + SKG AF+ +   E A+ A   
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 163 INGK 166
           ++G 
Sbjct: 61  LDGS 64

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
            +LFV  +PK  TE  L   FKEF  ++ V+I+KDK T  S+G  +V      +A  A+
Sbjct: 1  LTRLFV-VIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

Query: 74 NAC 76
            C
Sbjct: 60 ENC 62

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|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 = 48.5 bits (116), Expect = 8e-08
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 8/79 (10%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             L+IG L K V+E ++  LF  YG I+ + ++       +GCA++  ET++ A  AL+ 
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI-----PPRGCAYVCMETRQDAHRALQK 57

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +    K+ G  +   V WA
Sbjct: 58  LRN-VKLAGKKIK--VAWA 73

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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 48.9 bits (116), Expect = 8e-08
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +PK MT+ +L  +F ++  +    I+ D+ T  SRG  F+    R EA++A+   
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 77 HNKKTLPGASSPLQVKYA 94
          + +K   GA+ P+ VK+A
Sbjct: 65 NGQKP-SGAAEPITVKFA 81

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 29/79 (36%), Positives = 51/79 (64%), Gaps = 4/79 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           L+I  LP+ +++ +V  +FS +G I + ++L   Q T  S+G AF++++ + +A  A+ +
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLV-DQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 163 INGKHKMEGSSVPLVVKWA 181
            NG HK  GSS P+ VK+A
Sbjct: 62  FNG-HKPPGSSEPITVKFA 79

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

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILR-GSQQTSKGCAFLKYETKEQALAALEAI 163
           +++  LPKN +   + A+FS YGT+  + + R       KG AF+++ET E+A  A + +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 164 N 164
           N
Sbjct: 62  N 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
          K+FVG +P H T+  L   F +F  ++E  +I D+ T  SRG  FV    ++ A++A
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 22/58 (37%), Positives = 29/58 (50%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          KLFVG + + +TE  L   F ++  V+ V I+ DK T   RG  FV        DK V
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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|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 = 48.3 bits (115), Expect = 1e-07
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 13/88 (14%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +     E  L  +F ++  + EV ++KD+ T+ SRG  FV   +  +A  A+ A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 76  CHNKKTLPGASSPLQVKYADGELERLEH 103
            + K               DG   R++ 
Sbjct: 62  MNGKSV-------------DGRQIRVDQ 76

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 3/65 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            LF+G L  +V +  + A F  +GT+   +++  R + + S+G  ++ +E+ E A  A+E
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGR-SRGFGYVDFESPEDAKKAIE 59

Query: 162 AINGK 166
           A++GK
Sbjct: 60  AMDGK 64

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 18/61 (29%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +F+G L  +V++ E++  FS +G I ++ +++ +  T+   AF+K+E ++ A  A+E+ N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 165 G 165
            
Sbjct: 65  H 65

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           L +G LP   ++ +   L S +G ++   ++  S+ T  SKG  F++Y +K  AL A   
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVY-SESTGESKGYGFVEYASKASALKAKNQ 60

Query: 163 INGK 166
           ++GK
Sbjct: 61  LDGK 64

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 163
           L++G L  N++E ++  +F  +G I+ +Q+ R  +   SKG  F+++   E A  ALE +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 164 NG 165
           NG
Sbjct: 61  NG 62

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 105 LFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           LF+  LPK     + +  LFS  G     Q+        +G AF++Y T E A  A +A+
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 164 NGKHKMEGSSV 174
           NG H ++GS +
Sbjct: 65  NG-HSLQGSPI 74

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 6/69 (8%)

Query: 115 SEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGS 172
            E +V   F+ +G IK+L  L   ++T   KG A ++YETK++A AA+E +NGK  +   
Sbjct: 19  QEEDVHDKFAEFGEIKNLH-LNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLG-- 75

Query: 173 SVPLVVKWA 181
              + V WA
Sbjct: 76  -QTISVDWA 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|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 = 47.2 bits (112), Expect = 3e-07
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           KLFIG L  + +E  +  +FS YG I ++ +++  + Q S+G  F+ +E  + A  A+ A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 163 INGK 166
           +NGK
Sbjct: 62  MNGK 65

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 7/63 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLF+G LP   +  E+ ALF  YGT+ +  ++       K   F+  E +E A  A++A+
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKAL 53

Query: 164 NGK 166
           NG 
Sbjct: 54  NGY 56

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

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

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 3/63 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           ++IG LP    E E+   FS +GT+K++++ R S++T  SK   F+++   E A  A ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVAR-SKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 163 ING 165
           +N 
Sbjct: 61  MNN 63

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 21/59 (35%), Positives = 31/59 (52%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          K+FVG +P ++TE  L   F +F  V EV ++ D   +  RG  F+   S    D+ VN
Sbjct: 4  KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTS----KGCAFLKYETKEQALA 158
            ++++  L   + E ++  +FS +G ++ ++I +   +       G AF+ ++    A  
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 159 ALEAINGK 166
           AL+  NG 
Sbjct: 61  ALQL-NGT 67

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

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 17/63 (26%), Positives = 39/63 (61%), Gaps = 7/63 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +L++   P + SE+ +  +FS YG +K+++++          AF+++E+ E A+ A +++
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISNF-------AFVEFESLESAIRAKDSV 53

Query: 164 NGK 166
           +GK
Sbjct: 54  HGK 56

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 = 46.8 bits (111), Expect = 4e-07
 Identities = 22/58 (37%), Positives = 29/58 (50%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          KLFVG +   + E  L   F +F  V++  +I DK T   RG  FV   +   ADKA 
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 25 HMTEAQLLAMFKEFAL--VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            TE  +L      A   + +V +I+DK T  SRG  FV  PS ++A + ++A
Sbjct: 13 LTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDA 65

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|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 46.5 bits (110), Expect = 5e-07
 Identities = 28/80 (35%), Positives = 51/80 (63%), Gaps = 4/80 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           L++  LPK +S+ E+  LFS YG I   +IL   Q T  S+G  F++++ + +A  A++ 
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILV-DQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 163 INGKHKMEGSSVPLVVKWAD 182
           +NG+  + G++ P+ VK+A+
Sbjct: 63  LNGQKPL-GAAEPITVKFAN 81

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|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 = 46.5 bits (111), Expect = 5e-07
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFS-IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           +L +  LP +++EAE+   FS   G I D+++LR     S+  AF+ Y+T+E+A  A + 
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 163 ING 165
            N 
Sbjct: 62  FNN 64

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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 46.3 bits (109), Expect = 6e-07
 Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 2/78 (2%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 163
           L++  LPK +++ E+  LFS YG I   +IL       S+G  F++++ + +A  A++ +
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NG+ K  G++ P+ VK+A
Sbjct: 65  NGQ-KPSGAAEPITVKFA 81

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

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 4/79 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILR-GSQQTSKGCAFLKYETKEQALAALEAI 163
           LF+  LP + ++ ++   FS  G IK   +++    +  +G  ++ +  +E A  ALE  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 164 NGKHKMEGSSVPLVVKWAD 182
               K  G    + V++A 
Sbjct: 62  KKT-KFGGR--KIHVEFAK 77

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

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

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 7/63 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+F+G +    +  E+  LF  +G + +   +       K  AF+  E +E+ALAA+EA+
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEAL 54

Query: 164 NGK 166
           NGK
Sbjct: 55  NGK 57

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

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 21/60 (35%), Positives = 32/60 (53%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLF+G +    T+  L   F ++  + +  ++KD  T+ SRG  FV   S  E D A+NA
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 20/64 (31%), Positives = 35/64 (54%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L V  +    T   L  +F+++  V +V I +D+ TR SRG  FV    +++A+ A++A 
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 77 HNKK 80
            K+
Sbjct: 61 DGKE 64

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

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 10/77 (12%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++  LP + +E ++  LFS YG ++ ++ +       K  AF+ +E ++ A+ A+E +N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKI-------KDYAFVHFEERDDAVKAMEEMN 56

Query: 165 GKHKMEGSSVPLVVKWA 181
           GK ++EGS  P+ V  A
Sbjct: 57  GK-ELEGS--PIEVSLA 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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 6/82 (7%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRA---SRGCCFVICPSRQEADKA 72
          +L++G +   +TE  LL +F ++  + + + +  K+       RG CFV   +++EA+KA
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 73 VNACHNKKTLPGASSPLQVKYA 94
          +    N KT  G    L V++A
Sbjct: 61 L-KSLNGKTALGKK--LVVRWA 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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 26/84 (30%), Positives = 51/84 (60%), Gaps = 2/84 (2%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 163
           L++  LPK +++ E+  LFS YG I   +IL       S+G  F++++ + +A  A++ +
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 164 NGKHKMEGSSVPLVVKWADTEKER 187
           NG+ K  G++ P+ VK+A+   ++
Sbjct: 68  NGQ-KPPGATEPITVKFANNPSQK 90

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 13/45 (28%), Positives = 30/45 (66%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          +++G +P  +TE  +L +F ++  + ++N+++DK T  S+G  F+
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFL 56

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|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 = 45.4 bits (108), Expect = 1e-06
 Identities = 21/64 (32%), Positives = 33/64 (51%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +LFV  +P   TE +L  +F+ F  + EV++  DK T+ S+G  FV     + A KA + 
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 76 CHNK 79
              
Sbjct: 61 LDGS 64

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           ++ G  P +   ++V  LF   G ++ + +L    +T +  AF+ +E  E A  A+E +N
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML---SRTVQPHAFITFENLEAAQLAIETLN 58

Query: 165 GKH 167
           G  
Sbjct: 59  GAS 61

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|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 = 21/77 (27%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L + V+E ++   F  +G I+ + ++       + CAF+ + T+E A  A E + 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVV-----PRQQCAFVTFTTREAAEKAAERLF 58

Query: 165 GKHKMEGSSVPLVVKWA 181
            K  + G    L +KW 
Sbjct: 59  NKLIINGRR--LKLKWG 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|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTI-KDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           LFIG L   V E  +   FS +G I +  +I+R      SKG AF+ Y++ E + AA+EA
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 163 ING 165
           +NG
Sbjct: 64  MNG 66

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           L +  LP+++++ E+ +LF   G I+  +I+R  + T  S G  F+ Y  +  A  A+  
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVR-DRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 163 ING 165
           +NG
Sbjct: 62  LNG 64

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALE 161
             +FI  LP + +E E+  LFS +G +K  +I++      SKG AF+K++TKE A   LE
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 162 A 162
           A
Sbjct: 61  A 61

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 22/70 (31%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQA--LAA 159
            +++F+G +P + +E E+   FS +G++KD++I+      SKG  F+ +ET+E A  + A
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILA 61

Query: 160 LEAINGKHKM 169
           +  +N + K 
Sbjct: 62  MGNLNFRGKK 71

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             LF+  LP+  ++  +  LF+ +   K+++++       +G AF+++ET+EQA  AL+A
Sbjct: 3   KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-----RGIAFVEFETEEQATVALQA 57

Query: 163 INGKHKMEG 171
           + G     G
Sbjct: 58  LQGFKITPG 66

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

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 5/83 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L+I  LP ++ E E+ ++   +G +   +ILR +  TS+G  F + E+ E+  A +   N
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHFN 62

Query: 165 GKHKMEGSSV-----PLVVKWAD 182
           GK+      V     PL+ K+AD
Sbjct: 63  GKYIKTPPGVPAPTEPLLCKFAD 85

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is 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 = 86

>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 = 43.8 bits (104), Expect = 3e-06
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVG +P   T  +L A+F+++  V E +++K+          FV     ++A+ A+ A
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNYG--------FVHMEEEEDAEDAIKA 52

Query: 76 CHNKKTLPGASSPLQVK 92
           +      G    + V+
Sbjct: 53 LNG-YEFMG--KRINVE 66

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

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

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 19/68 (27%), Positives = 39/68 (57%), Gaps = 5/68 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL-RGSQQTSKGCAFLKYETKEQALAAL-- 160
           K+F+G LP NV+E ++   FS +GT+ ++ ++    ++  +G  F+ +E+++     +  
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

Query: 161 --EAINGK 166
               INGK
Sbjct: 64  HFHDINGK 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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 48.8 bits (116), Expect = 3e-06
 Identities = 84/348 (24%), Positives = 131/348 (37%), Gaps = 66/348 (18%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDE--VNII-----KDKTTRASRGCCFVICPSRQE 68
           +LFVG +PK+    ++L   +EF+ V E  V++I      DK    +RG  FV   S + 
Sbjct: 140 RLFVGGIPKNKKREEIL---EEFSKVTEGVVDVIVYHSAADKKK--NRGFAFVEYESHRA 194

Query: 69  ADKAVNACHNKKTLPGA----SSPLQVKYADGELERLEHK------LFIGMLPKNVSEAE 118
           A  A      +K +PG        + V +A+ E E  E        L++  L    +E  
Sbjct: 195 AAMA-----RRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEI 249

Query: 119 VSALFSIY--GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL 176
           +   FS +  G ++ ++ +R         AF+ +E +E A+ A++ +NGK ++EGS   +
Sbjct: 250 IEKSFSEFKPGKVERVKKIRDY-------AFVHFEDREDAVKAMDELNGK-ELEGS--EI 299

Query: 177 VVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYG 236
            V  A    ++   R  +          A  Q        P   +  Y  Y Y    +  
Sbjct: 300 EVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYD-PASRSLAYEDYYYHPPYAPS 358

Query: 237 LMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVP 296
           L   R+P            P   +G   RG +P  S   G R       G+   GY A  
Sbjct: 359 LHFPRMPG-----------PIRGRG---RGGAP--SRAAGGR-------GYPPYGYEAYY 395

Query: 297 GLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSGGTGSGGQI 344
           G  Y      G    +     PG     +   NP     GG G    I
Sbjct: 396 GDYYGYHDYRGKYEDKYYGYDPGMELTPM---NPVRGKPGGRGGRPAI 440

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 48.5 bits (115), Expect = 3e-06
 Identities = 45/182 (24%), Positives = 94/182 (51%), Gaps = 28/182 (15%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           ++FVG++P+ + E +L+ +F++   + E+ ++ D + + +RG  FV    ++EA +AV  
Sbjct: 60  EVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ-NRGYAFVTFCGKEEAKEAVKL 118

Query: 76  CHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFS----------I 125
            +N +  PG    + +   +        +LF+G +PKN    E+   FS          +
Sbjct: 119 LNNYEIRPGRLLGVCISVDN-------CRLFVGGIPKNKKREEILEEFSKVTEGVVDVIV 171

Query: 126 YGTIKDLQILRGSQQTSKGCAFLKYET-KEQALAALEAINGKHKMEGSSVPLVVKWADTE 184
           Y +  D       ++ ++G AF++YE+ +  A+A  + + G+ ++ G  +   V WA+ E
Sbjct: 172 YHSAAD-------KKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVI--AVDWAEPE 222

Query: 185 KE 186
           +E
Sbjct: 223 EE 224

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|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 = 44.2 bits (105), Expect = 3e-06
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 5/61 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +F+G L   V+E E+ +LF  +G I  ++I  G     KGC F+++  +  A AA++ + 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG-----KGCGFVQFVHRAAAEAAIQQLQ 58

Query: 165 G 165
           G
Sbjct: 59  G 59

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 13/90 (14%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR----GSQQTSKGCAFLKYETKEQAL 157
              LF+G L    +E  +  +FS YG I+ L+++R    G    SKG AF++YE +  AL
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGF---SKGYAFVEYEHERDAL 59

Query: 158 AALEAINGKHKMEGSSVPLVVKWADTEKER 187
            A    + K  ++GS +  V    D E+ER
Sbjct: 60  RAYRDAH-KLVIDGSEI-FV----DFERER 83

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALE 161
           +K+FIG LP  +SE +V  L   +G +K   +++ S    SKG AF +Y        A+ 
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 162 AINGK 166
            +NG 
Sbjct: 61  GLNGM 65

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

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++ V  +PK++TE +L   F+    V +V +++ +  + SR   FV   S ++A +AV  
Sbjct: 2  RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGK-SRRFGFVGFKSEEDAQQAVKY 60

Query: 76 CHNKKTLPGASSPLQVKYA 94
           +        +S + V+ A
Sbjct: 61 FNKTFID---TSKISVELA 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFV  +P   T+ QL   F E   +    ++KDK ++  RG  +V     ++A +A+   
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE-- 59

Query: 77 HNKKTLPGASSPLQVKYAD 95
            KK        + V++A 
Sbjct: 60 -EKKKTKFGGRKIHVEFAK 77

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

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 10/67 (14%)

Query: 110 LPKNVSEAEVSALFSI---------YGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL 160
           LP  V E ++  L  +          G I  + +       +KG AF+++ T E+A  A+
Sbjct: 9   LPV-VGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAV 67

Query: 161 EAINGKH 167
           +A+NG  
Sbjct: 68  KALNGYK 74

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 26/84 (30%), Positives = 47/84 (55%), Gaps = 7/84 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           LF+  L  + +E+++   F  YG IK ++++R  +    +G AF+++E +    AA +  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 164 NGKHKMEGSSVPLVVKWADTEKER 187
           +GK K++G  V LV    D E+ R
Sbjct: 64  DGK-KIDGRRV-LV----DVERGR 81

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 43.9 bits (103), Expect = 5e-06
 Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L+I  LP ++ E E+  +   +G +   +ILR S  TS+G  F + E+ E+  A +   N
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHFN 62

Query: 165 GK--HKMEGSSV---PLVVKWAD 182
           GK      G S    PL+ K+AD
Sbjct: 63  GKFIKTPPGVSAPAEPLLCKFAD 85

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is 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 = 85

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

 Score = 42.9 bits (102), Expect = 5e-06
 Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 4/48 (8%)

Query: 119 VSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK 166
           +  LFS +G ++ +++L+       G AF+++ T+E A  A++ +NG 
Sbjct: 1   LYKLFSPFGNVEKIKLLK----KKPGFAFVEFSTEEAAEKAVQYLNGV 44

(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|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 27/77 (35%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVG +P  +   +L   F +F  V   N+  DK T  S+G  FV   SR   + A+  
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ- 59

Query: 76 CHNKKTLPGASSPLQVK 92
             K  L G    LQV+
Sbjct: 60 -KQKHILEGN--KLQVQ 73

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL---- 160
           +F+  L  +V E E+  LFS  G I D+++++  +  SKG A++++E +E    AL    
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDR 61

Query: 161 EAINGK 166
           E I G+
Sbjct: 62  ELIKGR 67

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 43.4 bits (102), Expect = 6e-06
 Identities = 19/69 (27%), Positives = 42/69 (60%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++FVG++P+ + E +L+ +F++   + ++ ++ D  T  +RG  FV   +++ A +AV  
Sbjct: 3  EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 76 CHNKKTLPG 84
           +N +  PG
Sbjct: 63 YNNHEIRPG 71

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

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL-RGSQQTSKGCAFLKYETKEQALAAL 160
            H+LF+G LP +++E E+   F  +G + +++I  +G         F+ ++  E     L
Sbjct: 3   SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62

Query: 161 EA----INGKHKM 169
                   G H++
Sbjct: 63  ANKPIYFRGDHRL 75

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.3 bits (103), Expect = 7e-06
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +F+G +P+++ E E+  LF   G I +L+++      ++G AF+ Y  KE   AA  A+ 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKE---AAQRAVK 60

Query: 165 GKHKMEGSS 173
             H  E   
Sbjct: 61  QLHNYEIRP 69

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

 Score = 42.9 bits (102), Expect = 7e-06
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 3/63 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           ++IG LP    E E+   FS +GT+  L++ R S++T  SKG AF+++E+ E A    E 
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSR-SKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 163 ING 165
           +N 
Sbjct: 61  MNN 63

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

 Score = 42.9 bits (101), Expect = 7e-06
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          VKLFVG +P   TE ++ ++F+++  V E +IIK+          FV    +  AD+A+ 
Sbjct: 1  VKLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYG--------FVHMDDKTAADEAIR 52

Query: 75 ACHNKK 80
            H+ K
Sbjct: 53 NLHHYK 58

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

 Score = 43.3 bits (102), Expect = 7e-06
 Identities = 19/61 (31%), Positives = 37/61 (60%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++F+G +P+++ E E+  LF   G I + +++      ++G AF+ Y TKE+A  A+  +
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 164 N 164
           N
Sbjct: 63  N 63

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

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 14/64 (21%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALE 161
           +++++  +  ++SE ++ ++F  +G IK   +    +    KG  F++YE  + A  A+ 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 162 AING 165
           ++N 
Sbjct: 61  SMNL 64

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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 43.2 bits (102), Expect = 8e-06
 Identities = 19/62 (30%), Positives = 33/62 (53%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+G L   ++E E+   F  YG ++D+ I R  +      AF+K+   + A  A  A++
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMS 64

Query: 165 GK 166
           G+
Sbjct: 65  GQ 66

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

 Score = 43.2 bits (102), Expect = 8e-06
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEA 162
           +LF+  LP +  E ++  LFS +G + ++ + +      SKG A++ +   E A+ A + 
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 163 INGKH 167
           ++GK 
Sbjct: 64  LDGKV 68

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 43.2 bits (102), Expect = 8e-06
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR--GSQQTSKGCAFLKYETKEQALAALE 161
           K+ +  +P   +  E+  LFS +G +K +++ +      + +G  F+ + TK+ A  A +
Sbjct: 2   KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

Query: 162 AINGKHKMEGSSVPLVVKWA 181
           A+     + G    LV++WA
Sbjct: 62  ALCHSTHLYGRR--LVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 17/58 (29%), Positives = 32/58 (55%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          L+VG +  ++TE  L  +F+ F  ++ V + +D  T  S+G  F+     ++A KA+ 
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALE 58

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|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 = 42.7 bits (101), Expect = 9e-06
 Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 106 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE---A 162
            +G +  ++SE ++   FS  G +  +++  G +Q S   AF+++   E AL+AL     
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLC-GDRQHSARFAFVEFADAESALSALNLSGT 62

Query: 163 INGKHKM 169
           + G H +
Sbjct: 63  LLGGHPL 69

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

 Score = 42.7 bits (101), Expect = 9e-06
 Identities = 18/57 (31%), Positives = 28/57 (49%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
          K+FVG +    TE ++   F +F  + E+ +  DK T   RG CF+   S +   K 
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

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

 Score = 42.9 bits (102), Expect = 9e-06
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 19 VGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          V  + +   E  L  +F+ F  +  V + KDK T  SRG  FV   +R++A++A+ 
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 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|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 = 42.2 bits (100), Expect = 1e-05
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          ++VG +P  +TE +L   F  F  ++EV + KDK      G  FV   + + A  A+ A 
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAV 56

Query: 77 HNK 79
          +  
Sbjct: 57 NGT 59

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

 Score = 42.1 bits (100), Expect = 1e-05
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 10/76 (13%)

Query: 110 LPKNVSEAEVSALFSIYGTIKDLQILR-GSQQTSKGCAFLKYETKEQALAALEAING--- 165
           L ++  E ++  LF  +G I  + + +      S+G AF+ + T+E A  A+E +NG   
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGY 66

Query: 166 KHKMEGSSVPLVVKWA 181
            + +      L V+WA
Sbjct: 67  DNLI------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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L++  L  ++ +  +   FS +GTI   +++   +  SKG  F+ + + E+A  A+  +
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NG  ++ G   PL V  A
Sbjct: 63  NG--RIIGGK-PLYVALA 77

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

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 8/64 (12%)

Query: 104 KLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           ++F+G L  + VS+ ++  +FS YG I  + +        KG  F++++ +E A AA+  
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLH-------KGYGFVQFDNEEDARAAVAG 54

Query: 163 INGK 166
            NG+
Sbjct: 55  ENGR 58

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           LFI  LP   ++ ++  LF+ +G +   ++        SK   F+ Y+  E A AA++A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 164 NG 165
           NG
Sbjct: 61  NG 62

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 7/67 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL---RGSQQTSKGCAFLKYETKEQALAAL 160
           +L +  +P    + ++  +F  +G I D++I+   RGS    KG  F+ +     A  A 
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS----KGFGFVTFANSADADRAR 57

Query: 161 EAINGKH 167
           E ++G  
Sbjct: 58  EKLHGTV 64

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          R +LFVG +P  +TE +   +F ++  V EV + K+K      G  F+   +R  A+KA 
Sbjct: 1  RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAK 54

Query: 74 NACHNKKTLPGASSPLQVKY 93
                         L+V++
Sbjct: 55 AELDGI---MRKGRQLRVRF 71

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

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 20/59 (33%), Positives = 27/59 (45%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          LF+G +    TE  L   F ++  V +  I+KD  T  SRG  FV        DK + A
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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 20/58 (34%), Positives = 32/58 (55%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          +FVG +   +T+A L A F  F    +  ++ D  +  SRG  FV   S+Q+A+ A+N
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN 59

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 110 LPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING 165
           LPK + E ++  LF  +GTI D+Q+        +   F+ Y+T+E+A  AL+  N 
Sbjct: 8   LPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNN 63

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          +FVG +   +    L A F  F  + +  ++KD  T  S+G  FV    +++A+ A+
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58

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

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 18/64 (28%), Positives = 33/64 (51%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+VG +  + TE Q+  +F     +  + +  D+ T+   G CFV   +R++A+ AV   
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 77 HNKK 80
          +  K
Sbjct: 61 NGTK 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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/58 (32%), Positives = 28/58 (48%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          K+FVG +  + TE  +   F +F  V++  ++ DK T   RG  FV   S    DK  
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVC 58

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTS-KGCAFLKYETKEQALAALEAI 163
           LF+G L  +  E  +   F  YG I  +++         KG  ++++ ++E A AAL+A+
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 164 NG 165
            G
Sbjct: 61  GG 62

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

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+  +P++V+E+ +  LF +YG ++ +Q  R     S+G   + +     A  A+  + 
Sbjct: 4   LFVINVPRDVTESTLRRLFEVYGDVRGVQTER----ISEGIVTVHFYDIRDAKRAVRELC 59

Query: 165 GKH 167
           G+H
Sbjct: 60  GRH 62

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 16/65 (24%), Positives = 33/65 (50%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+F+G +P +++E Q+  + + F  +   N++KD  T  S+G  F         D+A+  
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 76 CHNKK 80
           +  +
Sbjct: 62 LNGMQ 66

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

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 15/62 (24%), Positives = 33/62 (53%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++ +  LPK V+E  +   F   G + D++++R     S+   F+ ++++E A  A++  
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 164 NG 165
           N 
Sbjct: 62  NK 63

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           +F+G L   +    + A F+ +G I D ++++  Q   SKG  F+ +  KE A  A++++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 164 NGK 166
           NG+
Sbjct: 62  NGQ 64

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 163
           L++G L    +E ++  LFS  G IK + + L    +T  G  F++Y T+E A  A++ +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 164 NG 165
           NG
Sbjct: 61  NG 62

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 25 HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH 77
          + TE  L  +F  +  +++V ++ D+ T  SRG  FV   S ++A +A    +
Sbjct: 10 YTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 106 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEAIN 164
           F+G LP ++ E E+   F   G ++ ++I+R  +    KG  ++ ++TK+    AL  +N
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLN 61

Query: 165 GKHKMEG 171
           G  K++G
Sbjct: 62  GI-KLKG 67

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|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 6/64 (9%)

Query: 114 VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK-HKMEGS 172
           VS  E+  +F  YGT++DL +  G     K   F+ Y + E A AA +A+NGK  ++   
Sbjct: 15  VSREELLRVFEKYGTVEDLVMPPG-----KPYCFVSYSSIEDAAAAYDALNGKELELPQQ 69

Query: 173 SVPL 176
           + PL
Sbjct: 70  NKPL 73

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +FI  L K++    +   FS +G I   ++       SKG  F+ +ET+E A+ A+E +N
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 165 GK 166
           G 
Sbjct: 65  GM 66

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+ I  +P +V   ++ +L S YGT+K+ + +    +T+     + YE+ EQA  A+  +
Sbjct: 2   KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETAT--VNVTYESPEQAQQAVNKL 59

Query: 164 NGKHKMEGSS 173
           NG H+ EGS 
Sbjct: 60  NG-HEYEGSK 68

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

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 20/58 (34%), Positives = 28/58 (48%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          KLFVG + +   E  L   F+E+  +D + II D+ +   RG  FV        DK V
Sbjct: 2  KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 21/60 (35%), Positives = 32/60 (53%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           LFVG +   + +  L A F++F  V    +I D+ T  SRG  +V   S ++A KA+ A
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 25/68 (36%), Positives = 38/68 (55%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           +R    LFIG L  NVSE E+   F  YG I+++ I R ++      AFLK++  + A  
Sbjct: 5   QRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHR 64

Query: 159 ALEAINGK 166
           A  A++G+
Sbjct: 65  AKVAMSGR 72

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L+I  LP ++ E E+  +   +G +   +ILR +   S+G  F + E+ E+    ++  N
Sbjct: 4   LYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFN 63

Query: 165 GKH-----KMEGSSVPLVVKWAD 182
           GK+      +   + PL+ K+AD
Sbjct: 64  GKYLKTPPGVPAPTEPLLCKFAD 86

This subgroup corresponds to the RRM2 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 contain 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 = 88

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

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 9/84 (10%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          +  L V  +P++MT+ ++ ++F     ++   +I+DK T  S G  FV     ++A+KA+
Sbjct: 1  KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 74 NACHNKKTLPGA---SSPLQVKYA 94
          N      TL G    +  ++V YA
Sbjct: 61 N------TLNGLRLQNKTIKVSYA 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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS--QQTSKGCAFLKYETKEQA 156
           +R    LF+G L   V+E ++   F  +G I ++ I R    Q ++ G  FLK+E  + A
Sbjct: 4   QRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYG--FLKFENLDMA 61

Query: 157 LAALEAINGK 166
             A  A++GK
Sbjct: 62  HRAKLAMSGK 71

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L + V+E  ++ LFS  G IK  +++R  +  +   AF++Y     A AAL+ +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIR--EHGNDPYAFVEYYDHRSAAAALQTMN 58

Query: 165 GKHKMEGSSVPLVVKWA 181
           G+  +      + V WA
Sbjct: 59  GRLILGQ---EIKVNWA 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 20/62 (32%), Positives = 37/62 (59%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           +++F+G +    +E ++   FS YGT+K+++I+      SKG  F+ +ET+E A   L+ 
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62

Query: 163 IN 164
            N
Sbjct: 63  AN 64

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|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 6/56 (10%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
          L+VGQV K  T+  L  +F+EF  ++ +N+I        RGC +V    RQ+A +A
Sbjct: 5  LWVGQVDKKATQQDLTNLFEEFGQIESINMI------PPRGCAYVCMVHRQDAYRA 54

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), 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. 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, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

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

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA- 75
          ++V  +PK+ T   L A+F ++  V  V++ + K T   +G  F+   + +EA KA    
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 76 CHNKKTLPGASSPL 89
           +  +T        
Sbjct: 62 NNPPETATDKPGKF 75

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|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 = 40.3 bits (95), Expect = 6e-05
 Identities = 17/59 (28%), Positives = 26/59 (44%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          LF+  +P   T+  L  +F  F  V    +  DK T  S+   FV   + + A  A+ A
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

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

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 5/60 (8%)

Query: 106 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING 165
           ++G +P   ++A++  LF  +G I + +      Q  +G AF+K +T EQA  A+  + G
Sbjct: 4   YVGNIPPYTTQADLIPLFQNFGYILEFRH-----QPDRGFAFVKLDTHEQAAMAIVQLQG 58

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

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+F+G + ++ S+ E+ ALF  YG +    ++R         AF+    +  A  A+E +
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQF-------AFVHLRGEAAADRAIEEL 54

Query: 164 NGK 166
           NG+
Sbjct: 55  NGR 57

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+++G L    ++ E+   F  YG ++ + + R       G AF+++E    A  A+ A+
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR----NPPGFAFVEFEDPRDAEDAVRAL 56

Query: 164 NGK 166
           +G+
Sbjct: 57  DGR 59

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

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 17/57 (29%), Positives = 30/57 (52%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           LF+G L  +  + ++   F   G + D++I +     SKG   +++ T+E A  ALE
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE 58

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

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTS-KGCAFLKYETKEQALAALEAI 163
           LF+G L  +V+E+++   FS +GT+ D++I++       +G A++   T E  L   ++ 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 164 NGKHKMEGS 172
               K +GS
Sbjct: 62  LNGTKWKGS 70

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

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 18/69 (26%), Positives = 41/69 (59%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++FVG++P+ + E +L+ +F++   + ++ ++ D  +  +RG  F+    ++ A +AV  
Sbjct: 3  EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62

Query: 76 CHNKKTLPG 84
          C N +  PG
Sbjct: 63 CDNYEIRPG 71

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

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 12/81 (14%)

Query: 15 VK-LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          VK L+V  +P   TE QL  +F E+  V+ V  IKD          FV    R +A KA+
Sbjct: 1  VKVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDY--------AFVHFEERDDAVKAM 52

Query: 74 NACHNKKTLPGASSPLQVKYA 94
              N K L G  SP++V  A
Sbjct: 53 EE-MNGKELEG--SPIEVSLA 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|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 110 LPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL 160
           LPK+ +E ++   F   G I++++I+          A +++ET+++ALAAL
Sbjct: 8   LPKDTTENKIRQFFKDCGEIREVKIVESEGGLV---AVIEFETEDEALAAL 55

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

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

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKG--CAFLKYETKEQALAAL 160
           L++G L   V+E  +   F  +G +  ++I+  R  ++  +   C F+ +  +  A  AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 161 EAINGKHKMEGSSVPLVVKWA 181
           + ++GK  M      L + W 
Sbjct: 64  DELDGKDVMG---YELKLGWG 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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 39.9 bits (93), Expect = 9e-05
 Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++FVG++P+ + E +L+ +F+    + E+ ++ D   + +RG  FV+   + EA +AV  
Sbjct: 3  EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGK-NRGYAFVMYTQKHEAKRAVRE 61

Query: 76 CHNKKTLPG 84
           +N +  PG
Sbjct: 62 LNNYEIRPG 70

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

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 162
           ++++G +   + E  +   FS +G IK + +         KG AF++YE  E A  ALE 
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 163 ING 165
           +NG
Sbjct: 62  MNG 64

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFV  +   +T+  L   F + A +    ++ D  T  SRG  FV     ++A +A+   
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 77 HNKK 80
           NKK
Sbjct: 62 KNKK 65

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 9/77 (11%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV-- 73
          K+FVG + +   E  L   F+++  ++ + +++D+ +   RG  FV        DK V  
Sbjct: 2  KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 74 -------NACHNKKTLP 83
                 + C  KK L 
Sbjct: 62 KYHTINGHNCEVKKALS 78

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDE----VNIIKDKTTRASRGCCFVICPSRQEADKA 72
          L++G +  +M E  +    + FA + E    V II++K T    G CFV       A++ 
Sbjct: 2  LWMGDLEPYMDENFIK---RAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERC 58

Query: 73 VNACHNKKTLPGASSPLQVK 92
          ++   N K +PG++ P + K
Sbjct: 59 LHKL-NGKPIPGSNPPKRFK 77

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEAI 163
           L++G L   + EA + + F+  G +  ++I+R  Q   S G  F+++ T E A  AL+++
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 164 NGK 166
           NGK
Sbjct: 62  NGK 64

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|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 = 19/59 (32%), Positives = 35/59 (59%), Gaps = 3/59 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
           LF+G LP + +  ++ A F   G    +++L  + + + SKGCAF++++T E    AL+
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGK-SKGCAFVEFDTAEAMTKALK 60

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 24 KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP 83
          K +TE  L   F  F  + ++ ++KDK T+ S+G  +V       A +A+   +  K L 
Sbjct: 12 KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNG-KCLG 70

Query: 84 GASSPLQV 91
          G + PL+V
Sbjct: 71 GDTKPLKV 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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          ++FVG +P   TE +L   F  F  V +V II D+    S+G  FV   ++++A+K +
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAG-VSKGYGFVTFETQEDAEKIL 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLF+G LP   +E E+ +LF  YG + +  I+       K   F+  + K  A  A+  +
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAADEAIRNL 54

Query: 164 NGKHKMEGSSV 174
           +  +K+ G ++
Sbjct: 55  H-HYKLHGVAI 64

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 113 NVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEAING 165
             +E ++  +FS YG I+ +Q++   Q+T  S+G  F+ +E+ E A  A E +NG
Sbjct: 10  YTTERDLREVFSRYGPIEKVQVVY-DQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 2/81 (2%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFV  +P   TE  L   F +F  V     + DK+T  ++G  FV    +   +  +   
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 77 --HNKKTLPGASSPLQVKYAD 95
                +L   SS       D
Sbjct: 64 PAAGSTSLLSGSSLTADIGDD 84

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 20/60 (33%), Positives = 35/60 (58%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   S +E D A+NA
Sbjct: 4  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEA 162
           KLFIG L    ++  + + F  +GT+ D  ++R  + + S+G  F+ Y + E+  AA+ A
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 163 INGKHKMEGSSV 174
               HK++G  V
Sbjct: 64  --RPHKVDGRVV 73

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 11/78 (14%)

Query: 105 LF-IGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           LF +G  P    E ++  LF  +G +    I        K  AF+++E  E A  ALEA+
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI-------RKTFAFVEFEDSEDATKALEAL 54

Query: 164 NGKHKMEGSSVPLVVKWA 181
           +G  +++GS   L V++ 
Sbjct: 55  HGS-RIDGSV--LTVEFV 69

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

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

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAAL 160
           + +++IG LP  + E ++  L   +G +K   +++      SKG AF +Y+       A+
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354

Query: 161 EAINGK 166
            A+NGK
Sbjct: 355 AALNGK 360

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

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

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 44/221 (19%), Positives = 83/221 (37%), Gaps = 49/221 (22%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
               + + ++++G +P ++ E Q+  + + F  +   N+IKD  T  S+G  F       
Sbjct: 289 TTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPS 348

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYA-----DGELERLEHKLFIGMLPKNVSEA----- 117
             D A+ A + K T     + L V+ A        ++       + +L K +S++     
Sbjct: 349 VTDVAIAALNGKDT---GDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIG 405

Query: 118 -----------------------------EVSALFSIYGTIKDLQILR--GSQQTSKGCA 146
                                        +V   FS YG + ++ I R  G + ++ G  
Sbjct: 406 GKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVG 465

Query: 147 --FLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK 185
             FL+Y     A  A+E +NG+ K     V  V  +   + 
Sbjct: 466 KVFLEYADVRSAEKAMEGMNGR-KFNDRVV--VAAFYGEDC 503

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
          + +  L V  +P++MT+ +  ++F     ++   +++DK T  S G  FV      +ADK
Sbjct: 1  DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 72 AVNACHNKKTLPGASSPLQVKYA 94
          A+N  +  K     +  ++V YA
Sbjct: 61 AINTLNGLKL---QTKTIKVSYA 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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L ++V+EA +  LFS  G  K  +++  +      C F+++     A A+L A+N
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYC-FVEFFEHRHAAASLAAMN 60

Query: 165 GKHKMEGSSVPLVVKWA 181
           G+ K+ G  V   V WA
Sbjct: 61  GR-KIMGKEVK--VNWA 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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L    S AE+   F  +G I+ +    G     +  A+++YE+ E A AA EA+ 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG-----RNYAYIEYESIEAAQAAKEALR 55

Query: 165 G 165
           G
Sbjct: 56  G 56

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEAI 163
           L I  LP+ +++ E  +LF   G +K+ +I+R  +   S G  F+ Y++ E A  A+  +
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62

Query: 164 NG 165
           NG
Sbjct: 63  NG 64

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|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 6/58 (10%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          L+VGQ+ K  T+  + ++ +EF  ++ +N+I        RGC +++   RQ+A +A+ 
Sbjct: 7  LWVGQLDKRTTQQDVTSLLEEFGPIESINMI------PPRGCAYIVMVHRQDAYRALQ 58

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 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) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +F+  +P   TE +L  +F +F  V    I+KDK T  S+G  FV   +++ A K + A
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L++  +P  M E +L +M K F  V    I++D  +  SRG  F    S ++ +  +   
Sbjct: 3  LYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIITHF 61

Query: 77 HNK--KTLPGA---SSPLQVKYADG 96
          + K  KT PG    + PL  K+ADG
Sbjct: 62 NGKYIKTPPGVPAPTEPLLCKFADG 86

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is 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 = 86

>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 = 38.3 bits (90), Expect = 3e-04
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           LFIG L  + +E  +   FS YG + D  I++      S+G  F+ +         L A 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA- 59

Query: 164 NGKHKMEGSSV 174
              H ++G  +
Sbjct: 60  -KPHVLDGREI 69

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|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 15/68 (22%)

Query: 119 VSALFSIYGTIKDLQILRG---------------SQQTSKGCAFLKYETKEQALAALEAI 163
           V  LFS  G I  ++ILR                 Q  +K CA +++E  E A  A+E +
Sbjct: 18  VLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVVEFEKLEAARKAVEEL 77

Query: 164 NGKHKMEG 171
           + +     
Sbjct: 78  SARDDWRD 85

This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 16/71 (22%)

Query: 110 LPKNVSEAEVSALFSIYGT---------IKDLQILR-------GSQQTSKGCAFLKYETK 153
           LPK+V E ++  LF    +         IK ++I+R         +  SKG  F+++   
Sbjct: 8   LPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNH 67

Query: 154 EQALAALEAIN 164
           E AL AL A+N
Sbjct: 68  EHALKALRALN 78

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 8/79 (10%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             +  G   K + E  +   F  +G I+D+++L      SKG AF++Y+ +  A  A EA
Sbjct: 7   GGIKAGSALKQIEEI-LRRHFGEWGDIEDIRVL-----PSKGIAFVRYKYRASAEFAKEA 60

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +  +  ++G  V L V+WA
Sbjct: 61  MADQ-SLDGGEV-LNVRWA 77

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 106 FIGMLPKNVSEAEVSALFSIYGTIKDLQILR-GSQQTSKGCAFLKYETKEQALAALEAIN 164
           F+  L   V E ++   FS  G ++D++I+R  + + SKG A++++  +E    AL  + 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLT 61

Query: 165 GKHKMEGSSVPLVVK 179
           G+  +     P++V+
Sbjct: 62  GQRLL---GQPIMVQ 73

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|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+  L  N +E E+  LFS     + L++            F+++E    A  AL ++ 
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGP---VCFVEFEDVSFATQALNSLQ 61

Query: 165 G 165
           G
Sbjct: 62  G 62

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 9/67 (13%)

Query: 115 SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV 174
           SE E+  +FS YG + D+ +        KG A +++ +K+ A AA+E   G       S 
Sbjct: 17  SEDELRKIFSKYGDVSDVVVS----SKKKGSAIVEFASKKAAEAAVENECGL-----PSN 67

Query: 175 PLVVKWA 181
           PL+V W 
Sbjct: 68  PLLVSWL 74

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 5/72 (6%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASR---GCCFVICPSRQEADKA 72
          +++V  +   + E  L  +F +F  V+ + I K +  +  R   G  FV       A+ A
Sbjct: 2  EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 73 VNACHNKKTLPG 84
          +    N   L G
Sbjct: 62 LQL--NGTELGG 71

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           KLFIG L    ++  +   FS +G I D  +++    + S+G  F+ + +  +  AA+ A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 163 INGKHKMEGSSV 174
               HK++G  V
Sbjct: 61  --RPHKVDGREV 70

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

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 19/69 (27%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++FVG++P+ M E +L+ +F+    + E  ++ + +   +RG  FV+  +++EA  A+  
Sbjct: 3  EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGE-NRGYAFVMYTTKEEAQLAIRI 61

Query: 76 CHNKKTLPG 84
           +N +  PG
Sbjct: 62 LNNYEIRPG 70

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

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

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 17/61 (27%), Positives = 36/61 (59%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++F+G +P++V E E+  +F   G I +++++      ++G AF+ Y  K +A  A+  +
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVREL 62

Query: 164 N 164
           N
Sbjct: 63  N 63

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 5/53 (9%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQA 156
           +LF+G LP +++E E+  LF  YG   ++ I        KG  F++ ET+  A
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFI-----HKDKGFGFIRLETRTLA 50

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
          K+FVG +P  +TE +    F +F  V +  +++D  T  SRG  FV   S    ++
Sbjct: 1  KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVER 56

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 17 LFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +FVG +   +T+  L   F+  +  V    ++ D  T  S+G  FV      E D+A+  
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 76 C 76
           
Sbjct: 64 M 64

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 17/63 (26%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           +++  LP +++  ++  +FS YG +  + I++  + + SKG AF+ +  +E A   ++A+
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 164 NGK 166
           N K
Sbjct: 64  NNK 66

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

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

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 13/83 (15%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALE- 161
           K+F+G LP + ++  +   FS +G I++  ++   Q   S+G  F+ ++ KE A  A + 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 162 ---AINGKHKMEGSSVPLVVKWA 181
               I+G+           V  A
Sbjct: 62  PNPIIDGRK--------ANVNLA 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 14/45 (31%), Positives = 26/45 (57%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          LFV ++    TE++L   F+E+  +  + +++DK T   RG  F+
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFI 48

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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++++G LP +V E ++  LF  YG I+D+++   +++     AF+++E    A  A+   
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL--KNRRGLVPFAFVRFEDPRDAEDAVFGR 58

Query: 164 NG 165
           NG
Sbjct: 59  NG 60

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

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 17/61 (27%), Positives = 37/61 (60%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++FIG LP+++ E E+  L    G I +++++      ++G AF+ +  K++A  A++ +
Sbjct: 3   EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 164 N 164
           N
Sbjct: 63  N 63

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|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 5/55 (9%)

Query: 112 KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK 166
           +N+ E E+      YG I+ ++ILR      K CAF+ +     A+AAL+ +NGK
Sbjct: 17  RNLPEKELRKECEKYGEIESIRILR-----EKACAFINFMNIPNAIAALQTLNGK 66

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALE 161
           +LF+ ++PK+ +E ++   F  +G I+ + I++  +   SKG  ++K+    QA  ALE
Sbjct: 3   RLFV-VIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 18/62 (29%), Positives = 31/62 (50%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KL +  L   VS+ ++  LF+ +G +K   +       S G A + +E +  AL A++  
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQY 61

Query: 164 NG 165
           NG
Sbjct: 62  NG 63

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, 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. THOC4 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. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTS-KGCAFLKYETKEQALAALE 161
           +++G +P   +E E+ + FS  G I++L ++        +G AF+ ++T+E A  AL 
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA 58

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|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++FIG +P++V E  +  LF   GT+ + +++      ++G A+ KY  +  A AA+  +
Sbjct: 3   EVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATL 62

Query: 164 NGKHKMEGSSVPLVV 178
           +     EG    L+V
Sbjct: 63  HNYELPEGC--CLLV 75

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 22 VPKHMTEAQLLAMFKEFALV-DEVNIIKDKTTRASRGCCFVICPSRQEADK 71
          +P  +TE  +        +   +V +++ KTT ASRG  FV   S +EA +
Sbjct: 10 LPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60

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

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAI 163
           L +  LP+N+++ E+ +LFS  G I+  +++R      S G  F+ Y   E A  A+  +
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 164 NG 165
           NG
Sbjct: 64  NG 65

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 = 37.8 bits (87), Expect = 7e-04
 Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
          + +  L V  +P++MT+ +L ++F     ++   +++DK T  S G  FV     ++A+K
Sbjct: 2  DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 72 AVNACHNKKTLPGASSPLQVKYA 94
          A+N  +  +     +  ++V YA
Sbjct: 62 AINTLNGLRL---QTKTIKVSYA 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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 21/70 (30%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+  LP N++  E+  +F       D+++  G   +SKG A+++++T+ +A  ALE   
Sbjct: 6   LFVKNLPYNITVDELKEVFE---DAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 165 GKHKMEGSSV 174
           G  +++G S+
Sbjct: 63  GA-EVDGRSI 71

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

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

 Score = 37.5 bits (88), Expect = 7e-04
 Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 163
           L++G L  +V+EA +  +FS  G +  +++ R    + S G A++ ++    A  AL+ +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 164 N 164
           N
Sbjct: 62  N 62

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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 37.8 bits (87), Expect = 8e-04
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 3/81 (3%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          R  L V  +P++MT+ +L ++F     V+   +I+DK    S G  FV   + ++A++A+
Sbjct: 1  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 74 NACHNKKTLPGASSPLQVKYA 94
          N  +  +     S  ++V YA
Sbjct: 61 NTLNGLRL---QSKTIKVSYA 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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          +FV  +P    E+ L  +F  F  V  V +I+D TT   +G  FV   + +EA  A+   
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA-S 62

Query: 77 HNKKTLPGASSPLQVKY 93
           N   L G    LQV +
Sbjct: 63 LNGYRLGG--RVLQVSF 77

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

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

 Score = 37.5 bits (87), Expect = 9e-04
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 160
             KLF+G L    S++ +   F+ YG + +  ++     + S+G  F+ + + ++A  A+
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 161 EAINGKHKMEGSSVPL 176
           EA    H ++G+ + L
Sbjct: 62  EAQ--PHSIDGNQIEL 75

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

 Score = 37.0 bits (86), Expect = 9e-04
 Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++++G LP ++ E ++  LF  YG IK + +   +++     AF+++E    A  A+   
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL--KNRRRGPPFAFVEFEDPRDAEDAVRGR 58

Query: 164 NG 165
           +G
Sbjct: 59  DG 60

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L VG +P   T+ Q   +   F  V+   ++  ++T  S+G  FV   S+  A KA N  
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 77 HNKKTLPGASSPLQVKYAD 95
            K+        LQV +AD
Sbjct: 62 DGKQIGGRK---LQVDWAD 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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 6/84 (7%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L++  +P  M E +L  M K F  V    I++D ++  SRG  F    S ++ +  ++  
Sbjct: 3  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 77 HNK--KTLPGASS---PLQVKYAD 95
          + K  KT PG S+   PL  K+AD
Sbjct: 62 NGKFIKTPPGVSAPAEPLLCKFAD 85

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is 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 = 85

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 162
           ++F+G +P+++ E E+  LF   G I DL+++       ++G AF+ + TKE A  A++ 
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 163 IN------GKH 167
            N      GKH
Sbjct: 63  YNNHEIRPGKH 73

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G L  N +E +V   FS +G ++D  ++   Q    +G  F+ +E+++      E 
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 163 ----INGK 166
               IN K
Sbjct: 61  HFHEINNK 68

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNII---KDKTTRASRGCCFVICPSRQEADKA 72
          L+VG +   +TE  L   F  F  +  V I+    ++  R +R C FV   +R +A++A
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

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|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 = 20/60 (33%), Positives = 32/60 (53%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLFVG +    +++ L   F  +  + E  ++ D  T+ SRG  F+   S  EAD+A+ A
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 4/84 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L ++V+E  +  LFS  G  K  +++         C F+++     A AAL A+N
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYC-FVEFYEHRDAAAALAAMN 60

Query: 165 GKHKMEGSSVPLVVKWADTEKERQ 188
           G+ K+ G  V   V WA T   ++
Sbjct: 61  GR-KILGKEVK--VNWATTPSSQK 81

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L   V+E  +  +F + G +++++I+           F++Y     A  AL+ +N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 165 GKHKMEGSSVPLVVKWA 181
           G+ ++E + +   V WA
Sbjct: 61  GR-QIENNEIR--VNWA 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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 7/63 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +++IG LP    E +V   F  YG I+++ +         G  F+++E    A  A+  +
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL-------KNGFGFVEFEDPRDADDAVYEL 53

Query: 164 NGK 166
           NGK
Sbjct: 54  NGK 56

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           KLFIG L    ++  +   F  +GT+ D  ++R  Q + S+G  F+ Y   E+  AA+ A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 163 INGKHKMEGSSV 174
               HK++G  V
Sbjct: 64  --RPHKVDGRVV 73

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 8/56 (14%)

Query: 111 PKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL---EAI 163
           P+  +  +++  FS +GTI ++Q+       +   A +++ T E+A  A    EA+
Sbjct: 11  PELNNITKLNEHFSKFGTIVNIQV-----NYNPESALVQFSTSEEAKKAYRSPEAV 61

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

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G LP+NV E  +S  F  YG ++ ++IL          AF+ +   + A  A  A+N
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61

Query: 165 GKHKMEG 171
              KM  
Sbjct: 62  ---KMGD 65

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 13/46 (28%), Positives = 28/46 (60%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKY 150
           +F+G +   + E E+ + F+ YG++K+++I+      SKG  F+ +
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSF 53

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLK---YETKEQALAA 159
           KLF+G L ++V+E ++   FS YG ++ ++I+   +    +G AF+    Y+  ++ +  
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 160 -LEAINGKH 167
               ING  
Sbjct: 61  KYHTINGHR 69

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 4/64 (6%)

Query: 110 LPKNVSEAEVSALFSIYGTIKDLQILR--GSQQTSKGCAFLKYETKEQALAALEAINGKH 167
           L    +  ++  +F  YG + D+ I R   +++ S+G AF+++  K  A  A++A++G  
Sbjct: 6   LTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRE-SRGFAFVRFYDKRDAEDAMDAMDG-K 63

Query: 168 KMEG 171
           +++G
Sbjct: 64  ELDG 67

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 6/63 (9%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+VG + + +TE  L   F +F  +  + ++        + C FV   +R+ A+KA    
Sbjct: 4  LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAERL 57

Query: 77 HNK 79
           NK
Sbjct: 58 FNK 60

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
           KLF+G LP  V   E+   FS +G +K   +    ++T  SKG  F+ + +++    AL+
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPF-DKETGLSKGYGFVSFSSRDGLENALQ 59

Query: 162 AINGKHKMEGSSV 174
               KH +EG+ +
Sbjct: 60  --KQKHILEGNKL 70

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +LFV  +P    E  L  +F +F  + EV++  DK +  S+G  +V      + + AV A
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYV---LFLDPEDAVKA 60

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +L V  +P    +  L  MF +F  + +V II ++  R S+G  FV   +  +AD+A   
Sbjct: 2  RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNE--RGSKGFGFVTFANSADADRAREK 59

Query: 76 CHNK 79
           H  
Sbjct: 60 LHGT 63

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           +F+G L   V++A + A FS + +  D +++    ++  S+G  F+ + +++ A  A+  
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVM-WDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 163 INGKHKMEGSSVPLVVKW 180
           +NGK      S P+   W
Sbjct: 61  MNGKWL---GSRPIRCNW 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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILR------GSQQTSKGCAFLKYETKEQALA 158
           LF+  L    +E  +   F   G ++ + I +        +  S G  F+++++KE A  
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 159 ALEAINGK----HKME 170
           AL+ + G     H +E
Sbjct: 63  ALKRLQGTVLDGHALE 78

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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 126 YGTIKDLQILRGSQQTSK----GCAFLKYETKEQALAALEAINGKHKMEGSSV 174
           YG +  + I R   +       G  F+++   E A  A  A+ G+ K +G +V
Sbjct: 35  YGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGR-KFDGRTV 86

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 15/83 (18%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          R +LFVG +P  +TE     +F+++    EV I +D      RG  F+   SR  A+ A 
Sbjct: 1  RCRLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIA- 53

Query: 74 NACHNKKTLPGA---SSPLQVKY 93
               K  L G    + PL++++
Sbjct: 54 -----KAELDGTILKNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +LF+G LP +++E +   LF  YG   ++ I R      +G  F++ E++  A  A   +
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAEL 57

Query: 164 NG 165
           +G
Sbjct: 58  DG 59

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|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 = 20/56 (35%), Positives = 32/56 (57%), Gaps = 5/56 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 159
           +LF+G LP +++E E   LF+ YG   ++ I +G     KG  F+K E++  A  A
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFINKG-----KGFGFIKLESRALAEIA 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 3/81 (3%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          +  L V  +P++MT+ +  ++F     ++   +++DK T  S G  FV     ++A+KA+
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 74 NACHNKKTLPGASSPLQVKYA 94
          N  +  +     +  ++V YA
Sbjct: 62 NTLNGLRL---QTKTIKVSYA 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|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 14/77 (18%)

Query: 114 VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS 173
           + E ++   F  +G  K + +   ++     C F+++ET+E A     AI+      G S
Sbjct: 14  LPEYKIRDYFEQFGKSKSVIVNHRAK-----CGFVRFETREAAEKFAAAISENGLNAGLS 68

Query: 174 ---------VPLVVKWA 181
                     PL V W 
Sbjct: 69  RGGLLVLEGCPLRVAWG 85

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 20/77 (25%), Positives = 44/77 (57%), Gaps = 4/77 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALF-SIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           ++FI  +P ++   ++  LF    G +  +++ +  +  S+GC  ++++ KE    ALE 
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 163 INGKHKMEGSSVPLVVK 179
           +N +++++G    LVVK
Sbjct: 61  MN-RYELKGR--KLVVK 74

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

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 15/62 (24%), Positives = 32/62 (51%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L VG++ +++ +  L  +F  +  V +V++  D+     RG  +V   S ++A+KA+   
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 77 HN 78
            
Sbjct: 61 DG 62

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          LFVG++    TE  L  +F  +  +  + +++D  T  S+G  FV     ++A +A    
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 77 HN 78
          H 
Sbjct: 66 HK 67

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 16/57 (28%), Positives = 30/57 (52%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          +FVG +   +T   + A F  F  + +  ++KD  T  S+G  FV   ++ +A+ A+
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 15/64 (23%), Positives = 29/64 (45%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          +++  +P + T+  L  + + F  +     I DK T   +G  FV   S + A KA+   
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 77 HNKK 80
          + + 
Sbjct: 63 NGRG 66

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 20/46 (43%), Positives = 26/46 (56%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          KLFVG +    T+  L   F ++  V +  I+KDKTT  SRG  FV
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFV 46

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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 5/54 (9%)

Query: 113 NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK 166
            ++E  +   FS +G I ++     S +  K C F+ +E  E A  A+  +NG 
Sbjct: 13  GLTEEILKKAFSPFGNIINI-----SMEKEKNCGFVTFEKMESADRAIAELNGT 61

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 112 KNVSEAEVSALFSIYGTIK--DLQILRGSQQTSKGCAFLKYETKEQALAALEAING 165
           K+V++ ++  LF I   ++  DL+    + + SKG A++ Y     A+ A E +NG
Sbjct: 9   KSVTQEQLHRLFDIIPGLEYCDLKRDPYTGK-SKGFAYVTYSNPASAIYAKEKLNG 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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 11/91 (12%)

Query: 12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
          E RV ++VG++P   T ++L   F+ F  ++E+ +   +    + G  FV      +A +
Sbjct: 1  ERRV-IYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-RDDGDNYG--FVTYRYACDAFR 56

Query: 72 AVNACHNKKTLP-------GASSPLQVKYAD 95
          A+   ++  T P       G     Q  YAD
Sbjct: 57 AIEHGNDDPTEPKYDLCFGGRRQFCQSSYAD 87

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|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           ++IG +P  ++ +E+   FS++G I++  I   S+  + G  F+ Y   E+A AA+E  N
Sbjct: 5   VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYG--FVTYRYTEEAFAAIE--N 60

Query: 165 GKHKM 169
           G HK+
Sbjct: 61  G-HKL 64

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 34.8 bits (81), Expect = 0.004
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 8/64 (12%)

Query: 31 LLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ 90
          L  +F  F  V+++ ++K K      G  FV   + + A+KAV   +          PL+
Sbjct: 1  LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGR---PLR 52

Query: 91 VKYA 94
          V Y+
Sbjct: 53 VDYS 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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +L V  +PK + E +L  +F+ F  + +V +   K  +  R   FV   + +EA KA+  
Sbjct: 2  RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKF-RKFGFVGYKTEEEAQKALKH 60

Query: 76 CHN 78
           +N
Sbjct: 61 FNN 63

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 15/44 (34%), Positives = 24/44 (54%)

Query: 18 FVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          FV Q+   + E  L   F +   V +V II+D+ +R S+G  +V
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYV 46

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
           K+F+G LP +V+E E    FS +G + D Q++    + + S+G  F+ ++++    +A+E
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGR-SRGFGFVTFDSE----SAVE 55

Query: 162 AI--NGKHKMEGSSV 174
            +   G  ++ G  V
Sbjct: 56  RVFSAGMLELGGKQV 70

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++F+G++P+ + E +L+ + ++   + E+ ++ D     +RG  FV   ++QEA  A+  
Sbjct: 3  EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQ 61

Query: 76 CHN 78
           +N
Sbjct: 62 LNN 64

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|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCC--FVICPSRQEADKAVN 74
          L+VG +P+++ E ++   FK +  V+ V I+  + +         FV   S Q+A  AVN
Sbjct: 2  LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAA 159
           E+ LF+  L    ++ ++  +FS +G IK  +++R  ++T  S   AF+++ETKE    A
Sbjct: 3   ENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIR-DKKTGDSLQYAFIEFETKEDCEEA 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|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 = 35.7 bits (83), Expect = 0.004
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 106 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEAI 163
           F+G +P + +E ++  +FS  G +   +++   + T   KG  F ++E  E A +A+  +
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVT-DRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NG    E +   L V +A
Sbjct: 61  NGY---EFNGRALRVDFA 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|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 14/37 (37%), Positives = 24/37 (64%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ 139
           H+LF+G LP +V ++E+   F  YG + +L+I  G +
Sbjct: 4   HQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGK 40

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 18/64 (28%), Positives = 33/64 (51%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
            +L +  L  +V+E ++  LF   G +K ++I       S+G A + +E +E A  A++ 
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 163 INGK 166
            NG 
Sbjct: 61  FNGV 64

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 4/79 (5%)

Query: 104 KLFIGMLPKNVSEAE-VSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           KL I  LP ++ +   +  +F  YG +++  I R       G AF+  + ++ A  ALE 
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61

Query: 163 INGKHKMEGSSVPLVVKWA 181
            NG   +E    P+ V WA
Sbjct: 62  TNG---LEIDGRPVAVDWA 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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 8/74 (10%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           LF+  L   V+E  +   FS +G ++ ++ L       K  AF+ +E ++ A+ A++ +N
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKL-------KDYAFVHFEERDAAVRAMDEMN 56

Query: 165 GKHKMEGSSVPLVV 178
           GK ++EG  + +V+
Sbjct: 57  GK-EIEGEEIEIVL 69

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|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQ-ILRGSQQTSKG-CAFLKYETKEQALAALEA 162
           LF+  LP +V E E++ LF  +   +  + + +  +   K    F+ + + + A AA++A
Sbjct: 3   LFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMDA 62

Query: 163 ING 165
           + G
Sbjct: 63  LQG 65

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	354
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.98
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.98
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.98
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.94
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.94
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.91
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.9
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.87
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.86
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.86
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.86
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.84
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.82
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.79
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.78
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.75
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.72
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.72
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.71
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.71
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.71
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.68
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.66
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.65
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.65
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.64
KOG0122	270	consensus Translation initiation factor 3, subunit	99.63
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.61
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.61
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.61
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.59
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.58
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.57
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.56
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.56
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.54
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.54
KOG0122	270	consensus Translation initiation factor 3, subunit	99.53
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.53
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.52
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.51
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.51
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.51
PLN03120	260	nucleic acid binding protein; Provisional	99.5
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.5
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.49
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.47
PLN03120	260	nucleic acid binding protein; Provisional	99.47
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.46
PLN03213	759	repressor of silencing 3; Provisional	99.45
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.44
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.44
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.42
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.42
smart00362	72	RRM_2 RNA recognition motif.	99.41
PLN03121	243	nucleic acid binding protein; Provisional	99.4
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.4
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.4
PLN03213	759	repressor of silencing 3; Provisional	99.38
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.38
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.38
smart00360	71	RRM RNA recognition motif.	99.38
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.38
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.36
smart00362	72	RRM_2 RNA recognition motif.	99.36
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.36
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.34
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.34
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.33
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.33
PLN03121	243	nucleic acid binding protein; Provisional	99.31
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.3
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.28
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.27
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.27
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.25
smart00360	71	RRM RNA recognition motif.	99.24
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.23
smart00361	70	RRM_1 RNA recognition motif.	99.22
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.21
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.21
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.2
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.2
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.19
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.18
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.17
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.16
KOG0226	290	consensus RNA-binding proteins [General function p	99.15
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.13
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.12
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.11
smart00361	70	RRM_1 RNA recognition motif.	99.09
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.08
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	99.06
KOG4210	285	consensus Nuclear localization sequence binding pr	99.0
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.96
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.96
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.95
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.93
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.92
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.88
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.85
KOG0226	290	consensus RNA-binding proteins [General function p	98.81
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.79
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.78
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.77
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.75
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.74
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.61
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.59
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.58
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.55
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.5
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.5
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.48
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.44
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.42
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.4
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.38
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.36
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.34
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.31
KOG0151	877	consensus Predicted splicing regulator, contains R	98.22
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.14
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.1
KOG0151	877	consensus Predicted splicing regulator, contains R	98.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.03
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.02
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.91
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.83
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.78
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.71
KOG4210	285	consensus Nuclear localization sequence binding pr	97.71
KOG2314	698	consensus Translation initiation factor 3, subunit	97.67
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.62
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.61
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.57
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.56
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.48
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.39
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.36
KOG2314	698	consensus Translation initiation factor 3, subunit	97.35
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.27
KOG3152	278	consensus TBP-binding protein, activator of basal	97.26
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.24
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.02
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.0
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.0
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.98
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.97
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.95
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.89
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.81
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.8
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.7
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.68
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.54
KOG3152	278	consensus TBP-binding protein, activator of basal	96.48
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.42
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.06
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.73
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.73
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.61
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.6
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.58
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.54
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.46
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.07
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.78
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.76
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	94.68
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.64
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.45
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.32
KOG2893	341	consensus Zn finger protein [General function pred	94.28
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.08
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.0
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.98
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.94
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.85
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.31
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	93.3
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.49
KOG2236	483	consensus Uncharacterized conserved protein [Funct	92.45
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	91.67
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	91.33
KOG2893	341	consensus Zn finger protein [General function pred	90.25
KOG2135	526	consensus Proteins containing the RNA recognition	89.34
KOG2236	483	consensus Uncharacterized conserved protein [Funct	88.7
KOG2318	650	consensus Uncharacterized conserved protein [Funct	88.33
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.07
COG5180	654	PBP1 Protein interacting with poly(A)-binding prot	86.68
PRK14548	84	50S ribosomal protein L23P; Provisional	86.05
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.53
KOG2135	526	consensus Proteins containing the RNA recognition	84.89
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	83.74
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	83.69
TIGR03636	77	L23_arch archaeal ribosomal protein L23. This mode	83.53
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	82.32
KOG4483	528	consensus Uncharacterized conserved protein [Funct	80.5

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=1.3e-48  Score=350.99  Aligned_cols=225  Identities=48%  Similarity=0.786  Sum_probs=200.4

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      +.+..+.+..+||||.||+.++|+||+++|++||.|.+|.|++||.|+.++|||||.|.+.++|++|+++||+...+.|.
T Consensus        26 ~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~  105 (510)
T KOG0144|consen   26 HTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGM  105 (510)
T ss_pred             CCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCC
Confidence            44455678889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cccceeeccccccccc--cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 018554           86 SSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI  163 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~~--~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l  163 (354)
                      ..+++|++++.++++.  +++||||.|+..+||.||+++|++||.|++|.|++|..+.+||||||+|+++|.|..||++|
T Consensus       106 ~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~  185 (510)
T KOG0144|consen  106 HHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKAL  185 (510)
T ss_pred             CcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhh
Confidence            9999999999998886  89999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccCCCceeEEEEecCChHHHHHHHH-HHHhhhccCCCCCCC-CCCCccCCCCCCCCCCCCCCCCC
Q 018554          164 NGKHKMEGSSVPLVVKWADTEKERQARRA-QKAQSQANNLPNADS-QHPSLFGALPMGYAPPYNGYGYQ  230 (354)
Q Consensus       164 ~g~~~~~g~~~~l~v~~a~~~~~~~~~~~-~~~~~~~~~~p~~~~-~~~~~~~~~~~~~~p~~~~~~~~  230 (354)
                      ||.+.++|++.+|.|+|||++++|..++. +..+.+...+.+... .....++...++|.+++.++.+.
T Consensus       186 ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~s  254 (510)
T KOG0144|consen  186 NGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQS  254 (510)
T ss_pred             ccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhcccc
Confidence            99999999999999999999988876665 444444444444422 23666777777777666665543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=1.1e-36  Score=282.21  Aligned_cols=174  Identities=28%  Similarity=0.500  Sum_probs=157.1

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+....++|||+|||+++||++|+++|++||+|++|+|++|+.|++++|||||+|.++++|++||+.|++.. +.+  +
T Consensus       101 ~~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~-l~g--r  177 (346)
T TIGR01659       101 NDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGIT-VRN--K  177 (346)
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCc-cCC--c
Confidence            3466688999999999999999999999999999999999999999999999999999999999999998866 444  7


Q ss_pred             cceeeccccccc-cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554           88 PLQVKYADGELE-RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus        88 ~l~v~~~~~~~~-~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      .|+|.+++.... ...++|||+||++++|+++|+++|++||+|++++|++|+ ++++|+||||+|+++++|++||+.||+
T Consensus       178 ~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng  257 (346)
T TIGR01659       178 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN  257 (346)
T ss_pred             eeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            888988765432 236789999999999999999999999999999999985 899999999999999999999999999


Q ss_pred             CcccCCCceeEEEEecCChH
Q 018554          166 KHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       166 ~~~~~g~~~~l~v~~a~~~~  185 (354)
                      .. +++..+.|+|+||+...
T Consensus       258 ~~-~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       258 VI-PEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             Cc-cCCCceeEEEEECCccc
Confidence            76 67777899999998653

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).

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

Probab=100.00  E-value=2.9e-33  Score=279.31  Aligned_cols=180  Identities=26%  Similarity=0.422  Sum_probs=155.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC--CCCc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP--GASS   87 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~--g~~~   87 (354)
                      .....++|||+||+.++|+++|+++|++||+|.++.+++|. +++++|||||+|.+.++|.+|++.+++..+ .  ...+
T Consensus       174 ~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i-~~~~~g~  251 (562)
T TIGR01628       174 PLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKI-GLAKEGK  251 (562)
T ss_pred             cccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEe-cccccce
Confidence            44566889999999999999999999999999999999996 589999999999999999999999988774 3  0136


Q ss_pred             cceeecccccccc-------------------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEE
Q 018554           88 PLQVKYADGELER-------------------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFL  148 (354)
Q Consensus        88 ~l~v~~~~~~~~~-------------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV  148 (354)
                      .+.|.++..+.++                   ..++|||+||++++|+++|+++|+.||.|++|+|+.|.++.++|||||
T Consensus       252 ~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV  331 (562)
T TIGR01628       252 KLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFV  331 (562)
T ss_pred             eeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEE
Confidence            6777766544332                   246899999999999999999999999999999999999999999999


Q ss_pred             EeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChHHHHHHHHHH
Q 018554          149 KYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQK  194 (354)
Q Consensus       149 ~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~~~~~~~~~~  194 (354)
                      +|++.++|.+|++.|||+. ++|  ++|.|+||+.+..+......+
T Consensus       332 ~f~~~~~A~~A~~~~~g~~-~~g--k~l~V~~a~~k~~~~~~~~~~  374 (562)
T TIGR01628       332 CFSNPEEANRAVTEMHGRM-LGG--KPLYVALAQRKEQRRAHLQDQ  374 (562)
T ss_pred             EeCCHHHHHHHHHHhcCCe-eCC--ceeEEEeccCcHHHHHHHHHH
Confidence            9999999999999999976 666  689999999887776554443

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>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=8.2e-35  Score=247.78  Aligned_cols=168  Identities=23%  Similarity=0.512  Sum_probs=150.7

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ++.+......|||+.|..+++-|+|++.|.+||+|.+++|+||..|+++|||+||.|.+.++|++||..++|+. |.+  
T Consensus        55 sk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqW-lG~--  131 (321)
T KOG0148|consen   55 SKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQW-LGR--  131 (321)
T ss_pred             CCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCee-ecc--
Confidence            33444557789999999999999999999999999999999999999999999999999999999999998865 555  


Q ss_pred             ccceeeccccccccc-----------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEE
Q 018554           87 SPLQVKYADGELERL-----------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLK  149 (354)
Q Consensus        87 ~~l~v~~~~~~~~~~-----------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~  149 (354)
                      +.|+-.|+..+..+.                 .++|||||++.-+||++||+.|+.||.|.+|+|+++     +||+||+
T Consensus       132 R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVr  206 (321)
T KOG0148|consen  132 RTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVR  206 (321)
T ss_pred             ceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEE
Confidence            788888886554332                 789999999999999999999999999999999998     8999999


Q ss_pred             eCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChH
Q 018554          150 YETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       150 f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~  185 (354)
                      |++.|+|.+||..+|++. ++|  -.|+|.|.++..
T Consensus       207 F~tkEaAahAIv~mNnte-i~G--~~VkCsWGKe~~  239 (321)
T KOG0148|consen  207 FETKEAAAHAIVQMNNTE-IGG--QLVRCSWGKEGD  239 (321)
T ss_pred             ecchhhHHHHHHHhcCce-eCc--eEEEEeccccCC
Confidence            999999999999999998 666  589999997653

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=3.6e-33  Score=252.66  Aligned_cols=173  Identities=25%  Similarity=0.474  Sum_probs=148.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....|.||||.||.|+.|+||+-+|++.|+|.+++||+|+.+|.+||||||+|.+.++|++||+.||+..+-.|+...+
T Consensus        79 ~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   79 PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             CCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence            44678999999999999999999999999999999999999999999999999999999999999999887666633333


Q ss_pred             eeeccc--------------------------------------------------------------------------
Q 018554           90 QVKYAD--------------------------------------------------------------------------   95 (354)
Q Consensus        90 ~v~~~~--------------------------------------------------------------------------   95 (354)
                      +++.++                                                                          
T Consensus       159 c~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn  238 (506)
T KOG0117|consen  159 CVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGN  238 (506)
T ss_pred             EEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCC
Confidence            333221                                                                          


Q ss_pred             --------cccccc------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHH
Q 018554           96 --------GELERL------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE  161 (354)
Q Consensus        96 --------~~~~~~------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~  161 (354)
                              ++.+..      .+.|||+||..++|+|.|+++|++||.|++|+.++|       ||||.|.++++|.+|++
T Consensus       239 ~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~  311 (506)
T KOG0117|consen  239 AITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMK  311 (506)
T ss_pred             cceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHH
Confidence                    111110      457999999999999999999999999999999966       99999999999999999


Q ss_pred             HhCCCcccCCCceeEEEEecCChHHHHHHHH
Q 018554          162 AINGKHKMEGSSVPLVVKWADTEKERQARRA  192 (354)
Q Consensus       162 ~l~g~~~~~g~~~~l~v~~a~~~~~~~~~~~  192 (354)
                      .+||+. |+|  ..|.|.+|++..+++..+.
T Consensus       312 ~~ngke-ldG--~~iEvtLAKP~~k~k~~r~  339 (506)
T KOG0117|consen  312 ETNGKE-LDG--SPIEVTLAKPVDKKKKERK  339 (506)
T ss_pred             HhcCce-ecC--ceEEEEecCChhhhccchh
Confidence            999998 788  5899999999877766653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.3e-32  Score=259.74  Aligned_cols=169  Identities=27%  Similarity=0.530  Sum_probs=154.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +.++|||+|||.+++|++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++||+.|++.. +.+  +.|+|.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~-l~g--~~i~v~   78 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLR-LQN--KTIKVS   78 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEE-ECC--eeEEEE
Confidence            57899999999999999999999999999999999999999999999999999999999999998866 555  788998


Q ss_pred             cccccccc-ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554           93 YADGELER-LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus        93 ~~~~~~~~-~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ++++.... ..++|||+||+.++++++|+++|+.||.|..++++.+. ++.++|||||+|++.++|++|++.|||.. +.
T Consensus        79 ~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~-~~  157 (352)
T TIGR01661        79 YARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTT-PS  157 (352)
T ss_pred             eecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCc-cC
Confidence            88765432 46789999999999999999999999999999999884 78889999999999999999999999976 77


Q ss_pred             CCceeEEEEecCChH
Q 018554          171 GSSVPLVVKWADTEK  185 (354)
Q Consensus       171 g~~~~l~v~~a~~~~  185 (354)
                      |+..+|.|+|++...
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            777899999997654

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

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=5.5e-32  Score=263.44  Aligned_cols=168  Identities=20%  Similarity=0.343  Sum_probs=147.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++||||||+++++|++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++|++.||+.. +.|  +.|+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~-i~G--R~Ik  180 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQM-LGG--RNIK  180 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeE-Eec--ceee
Confidence            3567899999999999999999999999999999999999999999999999999999999999998865 555  6677


Q ss_pred             eecccccc------------ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHH
Q 018554           91 VKYADGEL------------ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQAL  157 (354)
Q Consensus        91 v~~~~~~~------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~  157 (354)
                      |.++....            ....++|||+||+.++++++|+++|+.||.|++++|.+|. ++.+||||||+|++.++|.
T Consensus       181 V~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       181 VGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             ecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence            76543211            1124789999999999999999999999999999999985 6789999999999999999


Q ss_pred             HHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          158 AALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       158 ~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      +||+.||+.. ++|  +.|+|.++...
T Consensus       261 kAI~amNg~e-lgG--r~LrV~kAi~p  284 (612)
T TIGR01645       261 EAIASMNLFD-LGG--QYLRVGKCVTP  284 (612)
T ss_pred             HHHHHhCCCe-eCC--eEEEEEecCCC
Confidence            9999999986 666  68889888653

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.98  E-value=4.8e-32  Score=229.57  Aligned_cols=171  Identities=26%  Similarity=0.521  Sum_probs=157.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .++..+.|.|.-||.++|+|||+.+|...|+|++|+++|||.||.+.||+||.|.++++|++||+.|||.++   ..+.|
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrL---Q~KTI  113 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRL---QNKTI  113 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceee---ccceE
Confidence            356677899999999999999999999999999999999999999999999999999999999999999774   56899


Q ss_pred             eeecccccccc-ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 018554           90 QVKYADGELER-LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus        90 ~v~~~~~~~~~-~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                      +|+|+++..+. ...+|||.+||..+|..||.++|++||.|..-+|+.|. ++.+||++||+|+.+++|++||+.|||..
T Consensus       114 KVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  114 KVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             EEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            99999886554 36799999999999999999999999999998998884 89999999999999999999999999975


Q ss_pred             ccCCCceeEEEEecCCh
Q 018554          168 KMEGSSVPLVVKWADTE  184 (354)
Q Consensus       168 ~~~g~~~~l~v~~a~~~  184 (354)
                       -.|+..+|.|+||...
T Consensus       194 -P~g~tepItVKFannP  209 (360)
T KOG0145|consen  194 -PSGCTEPITVKFANNP  209 (360)
T ss_pred             -CCCCCCCeEEEecCCc
Confidence             7888899999999876

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.98  E-value=3.5e-31  Score=249.85  Aligned_cols=171  Identities=25%  Similarity=0.447  Sum_probs=150.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||.++++++|+++|++||.|..++++.|..++.++|||||+|.+.++|++|++.||+.. +.+....+.
T Consensus        86 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~-~~g~~~~i~  164 (352)
T TIGR01661        86 SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTT-PSGCTEPIT  164 (352)
T ss_pred             ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCc-cCCCceeEE
Confidence            4467799999999999999999999999999999999999889999999999999999999999999865 556566777


Q ss_pred             eeccccccc-----------------------------------------------------------------------
Q 018554           91 VKYADGELE-----------------------------------------------------------------------   99 (354)
Q Consensus        91 v~~~~~~~~-----------------------------------------------------------------------   99 (354)
                      +.+++....                                                                       
T Consensus       165 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (352)
T TIGR01661       165 VKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRA  244 (352)
T ss_pred             EEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccC
Confidence            777642220                                                                       


Q ss_pred             ----------------------cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHH
Q 018554          100 ----------------------RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQA  156 (354)
Q Consensus       100 ----------------------~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A  156 (354)
                                            ....+|||+||++++++++|+++|++||.|++++|++|. ++.+||||||+|.+.++|
T Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A  324 (352)
T TIGR01661       245 SPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEA  324 (352)
T ss_pred             CCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHH
Confidence                                  001259999999999999999999999999999999995 899999999999999999


Q ss_pred             HHHHHHhCCCcccCCCceeEEEEecCChH
Q 018554          157 LAALEAINGKHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       157 ~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~  185 (354)
                      .+|++.|||.. ++|  +.|+|.|+..+.
T Consensus       325 ~~Ai~~lnG~~-~~g--r~i~V~~~~~~~  350 (352)
T TIGR01661       325 AMAILSLNGYT-LGN--RVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHhCCCE-ECC--eEEEEEEccCCC
Confidence            99999999987 666  789999987653

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

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.98  E-value=6.1e-30  Score=248.88  Aligned_cols=165  Identities=26%  Similarity=0.490  Sum_probs=136.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC----
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS----   86 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~----   86 (354)
                      ....++|||+|||++++|++|+++|++||.|.+|+|++| .+|++||||||+|.+.++|++||+.||+..+..++.    
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            445699999999999999999999999999999999999 689999999999999999999999998755332211    


Q ss_pred             ------------------------------------------------------------------------------cc
Q 018554           87 ------------------------------------------------------------------------------SP   88 (354)
Q Consensus        87 ------------------------------------------------------------------------------~~   88 (354)
                                                                                                    +.
T Consensus       134 ~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~  213 (578)
T TIGR01648       134 ISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHV  213 (578)
T ss_pred             ccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCce
Confidence                                                                                          01


Q ss_pred             ceeeccccccc------cccceEEEecCCCCCCHHHHHHhhccC--CCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHH
Q 018554           89 LQVKYADGELE------RLEHKLFIGMLPKNVSEAEVSALFSIY--GTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus        89 l~v~~~~~~~~------~~~~~l~V~~l~~~~t~~~l~~~F~~~--G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                      |.|.|+..+.+      ...++|||+||++++|+|+|+++|++|  |+|++|+++       ++||||+|++.++|++|+
T Consensus       214 I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e~A~kAi  286 (578)
T TIGR01648       214 IAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDREDAVKAM  286 (578)
T ss_pred             EEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHHHHHHHH
Confidence            11222221111      013579999999999999999999999  999999987       459999999999999999


Q ss_pred             HHhCCCcccCCCceeEEEEecCChHH
Q 018554          161 EAINGKHKMEGSSVPLVVKWADTEKE  186 (354)
Q Consensus       161 ~~l~g~~~~~g~~~~l~v~~a~~~~~  186 (354)
                      ++||+.. ++|  +.|+|+||++...
T Consensus       287 ~~lnG~~-i~G--r~I~V~~Akp~~~  309 (578)
T TIGR01648       287 DELNGKE-LEG--SEIEVTLAKPVDK  309 (578)
T ss_pred             HHhCCCE-ECC--EEEEEEEccCCCc
Confidence            9999987 666  7899999987543

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

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

Probab=99.97  E-value=6.3e-30  Score=255.36  Aligned_cols=160  Identities=27%  Similarity=0.459  Sum_probs=142.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD   95 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~   95 (354)
                      +|||||||.++||++|+++|++||+|.+|+|++|+.|++++|||||+|.+.++|++|++.+++.. +.+  +.|+|.|+.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~-i~g--k~i~i~~s~   78 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKR-LGG--KPIRIMWSQ   78 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--eeEEeeccc
Confidence            79999999999999999999999999999999999999999999999999999999999998765 444  778888875


Q ss_pred             cccc---cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC
Q 018554           96 GELE---RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS  172 (354)
Q Consensus        96 ~~~~---~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  172 (354)
                      .+..   ....+|||+||+.++++++|+++|+.||.|++|+|..+.+++++|||||+|++.++|.+|++.|||.. +++ 
T Consensus        79 ~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~-~~~-  156 (562)
T TIGR01628        79 RDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGML-LND-  156 (562)
T ss_pred             ccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccE-ecC-
Confidence            4322   22568999999999999999999999999999999999999999999999999999999999999976 555 


Q ss_pred             ceeEEEEec
Q 018554          173 SVPLVVKWA  181 (354)
Q Consensus       173 ~~~l~v~~a  181 (354)
                       +.|.|...
T Consensus       157 -~~i~v~~~  164 (562)
T TIGR01628       157 -KEVYVGRF  164 (562)
T ss_pred             -ceEEEecc
Confidence             45665443

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.97  E-value=1.9e-29  Score=246.13  Aligned_cols=167  Identities=31%  Similarity=0.496  Sum_probs=145.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||.++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+ |++.. +.+  +.|.
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~-~~g--~~i~  161 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQM-LLG--RPII  161 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCE-ECC--eeeE
Confidence            3457899999999999999999999999999999999999999999999999999999999996 66765 444  6666


Q ss_pred             eecccccccc-------------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHH
Q 018554           91 VKYADGELER-------------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQA  156 (354)
Q Consensus        91 v~~~~~~~~~-------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A  156 (354)
                      |.++..+...             ..++|||+||+..+|+++|+++|+.||.|+.|.|+++. ++.++|||||+|.+.++|
T Consensus       162 v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A  241 (457)
T TIGR01622       162 VQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEA  241 (457)
T ss_pred             EeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHH
Confidence            6654322111             14789999999999999999999999999999999985 678999999999999999


Q ss_pred             HHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          157 LAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       157 ~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      .+|++.|||.. +.|  +.|.|.|+...
T Consensus       242 ~~A~~~l~g~~-i~g--~~i~v~~a~~~  266 (457)
T TIGR01622       242 KEALEVMNGFE-LAG--RPIKVGYAQDS  266 (457)
T ss_pred             HHHHHhcCCcE-ECC--EEEEEEEccCC
Confidence            99999999966 555  78999998743

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.

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=1.3e-28  Score=209.54  Aligned_cols=177  Identities=32%  Similarity=0.525  Sum_probs=162.7

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .+++.+..+.++||||-|.+.-+|||++.+|..||+|++|.+.+..+ |.+||||||+|.+..+|..||+.||+...+.|
T Consensus        10 adsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpG   88 (371)
T KOG0146|consen   10 ADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPG   88 (371)
T ss_pred             cccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCC
Confidence            34455556889999999999999999999999999999999999886 89999999999999999999999999999999


Q ss_pred             CCccceeeccccccccc---------------------------------------------------------------
Q 018554           85 ASSPLQVKYADGELERL---------------------------------------------------------------  101 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~~~---------------------------------------------------------------  101 (354)
                      ....|-|++++.++++.                                                               
T Consensus        89 ASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA  168 (371)
T KOG0146|consen   89 ASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAA  168 (371)
T ss_pred             CccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHH
Confidence            99999999999988875                                                               


Q ss_pred             --------------------------------------------------------------------------------
Q 018554          102 --------------------------------------------------------------------------------  101 (354)
Q Consensus       102 --------------------------------------------------------------------------------  101 (354)
                                                                                                      
T Consensus       169 ~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~  248 (371)
T KOG0146|consen  169 LNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYA  248 (371)
T ss_pred             HhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhh
Confidence                                                                                            


Q ss_pred             ------------------------------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcce
Q 018554          102 ------------------------------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKG  144 (354)
Q Consensus       102 ------------------------------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g  144 (354)
                                                          .|+|||-.||.+..+.||.+.|-.||.|.+.+++-|+ ++.||+
T Consensus       249 g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKC  328 (371)
T KOG0146|consen  249 GVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKC  328 (371)
T ss_pred             hHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccc
Confidence                                                6899999999999999999999999999999999995 889999


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChH
Q 018554          145 CAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       145 ~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~  185 (354)
                      |+||.|++..+|+.||.++||..+   ..++|+|.+.+++.
T Consensus       329 FGFVSfDNp~SaQaAIqAMNGFQI---GMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  329 FGFVSFDNPASAQAAIQAMNGFQI---GMKRLKVQLKRPKD  366 (371)
T ss_pred             eeeEecCCchhHHHHHHHhcchhh---hhhhhhhhhcCccc
Confidence            999999999999999999999875   45778888766654

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.95  E-value=3.5e-27  Score=230.40  Aligned_cols=161  Identities=18%  Similarity=0.283  Sum_probs=135.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcC-CccCCCCCcccee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHN-KKTLPGASSPLQV   91 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~-~~~~~g~~~~l~v   91 (354)
                      ++++|||+|||++++|++|+++|++||.|.+|.|+++      +|||||+|.+.++|++||+.++. ...+.+  +.|+|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g--~~l~v   72 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRG--QPAFF   72 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcC--eEEEE
Confidence            4789999999999999999999999999999999864      36999999999999999997632 233555  78888


Q ss_pred             ecccccc-cc------------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHH
Q 018554           92 KYADGEL-ER------------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA  158 (354)
Q Consensus        92 ~~~~~~~-~~------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~  158 (354)
                      .|+..+. .+            ...+|||+||++++|+++|+++|+.||+|++|.|+++..   +++|||+|++.++|.+
T Consensus        73 ~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~---~~~afVef~~~~~A~~  149 (481)
T TIGR01649        73 NYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN---VFQALVEFESVNSAQH  149 (481)
T ss_pred             EecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC---ceEEEEEECCHHHHHH
Confidence            8875332 11            123789999999999999999999999999999988643   4689999999999999


Q ss_pred             HHHHhCCCcccCCCceeEEEEecCChH
Q 018554          159 ALEAINGKHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       159 Ai~~l~g~~~~~g~~~~l~v~~a~~~~  185 (354)
                      |++.|||..+.++ .+.|+|.|++...
T Consensus       150 A~~~Lng~~i~~~-~~~l~v~~sk~~~  175 (481)
T TIGR01649       150 AKAALNGADIYNG-CCTLKIEYAKPTR  175 (481)
T ss_pred             HHHHhcCCcccCC-ceEEEEEEecCCC
Confidence            9999999985554 4789999987654

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).

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.95  E-value=5.1e-28  Score=195.18  Aligned_cols=169  Identities=27%  Similarity=0.436  Sum_probs=147.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +.....|||||||+..++++.|.++|-+.|+|.++.+.+|+.|...+|||||+|.++|+|+.|++.|+.-+ +-|  ++|
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~Vk-LYg--rpI   81 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVK-LYG--RPI   81 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHH-hcC--cee
Confidence            34567899999999999999999999999999999999999999999999999999999999999998433 555  788


Q ss_pred             eeeccc--cccccccceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554           90 QVKYAD--GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGS-QQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus        90 ~v~~~~--~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      +|..+.  .+......+|||+||..+++|..|.+.|+.||.+.. -+|+++. ++.+++|+||.|++.+.+.+|++.+||
T Consensus        82 rv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ng  161 (203)
T KOG0131|consen   82 RVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNG  161 (203)
T ss_pred             EEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhcc
Confidence            887765  233344689999999999999999999999998655 5888884 689999999999999999999999999


Q ss_pred             CcccCCCceeEEEEecCCh
Q 018554          166 KHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       166 ~~~~~g~~~~l~v~~a~~~  184 (354)
                      ..+   ++++++|+++..+
T Consensus       162 q~l---~nr~itv~ya~k~  177 (203)
T KOG0131|consen  162 QYL---CNRPITVSYAFKK  177 (203)
T ss_pred             chh---cCCceEEEEEEec
Confidence            764   4478888888544

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=2e-26  Score=195.49  Aligned_cols=174  Identities=25%  Similarity=0.460  Sum_probs=154.2

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      +...+..+...|||.+||+.+|..||+.+|+.||.|..-+|..|..||.+||.+||.|+..++|+.||+.|||.. -.+.
T Consensus       119 RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~-P~g~  197 (360)
T KOG0145|consen  119 RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK-PSGC  197 (360)
T ss_pred             cCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC-CCCC
Confidence            455667788899999999999999999999999999999999999999999999999999999999999999876 6677


Q ss_pred             Cccceeeccccccccc----------------------------------------------------------------
Q 018554           86 SSPLQVKYADGELERL----------------------------------------------------------------  101 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~~----------------------------------------------------------------  101 (354)
                      ..+|.|+|+.......                                                                
T Consensus       198 tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~  277 (360)
T KOG0145|consen  198 TEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGG  277 (360)
T ss_pred             CCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCC
Confidence            8899999985432221                                                                


Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .-+|||-||..+.+|..|+++|..||.|..|+|++| .+.+.|||+||.+.+-++|..||..|||.. +.+  +.|.|+|
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~-lg~--rvLQVsF  354 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYR-LGD--RVLQVSF  354 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCcc-ccc--eEEEEEE
Confidence            237999999999999999999999999999999999 468999999999999999999999999987 544  6788887


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      ...
T Consensus       355 Ktn  357 (360)
T KOG0145|consen  355 KTN  357 (360)
T ss_pred             ecC
Confidence            543

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=6.2e-26  Score=221.70  Aligned_cols=162  Identities=22%  Similarity=0.350  Sum_probs=136.2

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ...++|||+||++ ++|+++|+++|+.||.|.+|+|++++     +|||||+|.+.++|++||+.||+.. +.|  +.|+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~-l~g--~~l~  344 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVK-LFG--KPLR  344 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCE-ECC--ceEE
Confidence            4678999999997 69999999999999999999999974     5899999999999999999999876 555  6777


Q ss_pred             eeccccccc--------------------------------------cccceEEEecCCCCCCHHHHHHhhccCCC--ee
Q 018554           91 VKYADGELE--------------------------------------RLEHKLFIGMLPKNVSEAEVSALFSIYGT--IK  130 (354)
Q Consensus        91 v~~~~~~~~--------------------------------------~~~~~l~V~~l~~~~t~~~l~~~F~~~G~--v~  130 (354)
                      |.+++.+..                                      ...++|||+|||.++|+++|+++|+.||.  |+
T Consensus       345 v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~  424 (481)
T TIGR01649       345 VCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVK  424 (481)
T ss_pred             EEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccce
Confidence            776532210                                      11358999999999999999999999998  88


Q ss_pred             EEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc----eeEEEEecCC
Q 018554          131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS----VPLVVKWADT  183 (354)
Q Consensus       131 ~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~----~~l~v~~a~~  183 (354)
                      .++++.+.++ .+++|||+|++.++|.+|+..||+.. ++++.    ..|+|+|+++
T Consensus       425 ~ik~~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~-l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       425 KFKFFPKDNE-RSKMGLLEWESVEDAVEALIALNHHQ-LNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             EEEEecCCCC-cceeEEEEcCCHHHHHHHHHHhcCCc-cCCCCCCccceEEEEeccC
Confidence            8988765544 47899999999999999999999987 66542    2478888765

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).

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=8.1e-27  Score=210.61  Aligned_cols=173  Identities=30%  Similarity=0.508  Sum_probs=157.4

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .++++-.++++||||-|++.+||.|++++|++||.|++|.|++|.. +.+||||||+|.+.|.|..||++||+...+.|.
T Consensus       116 ~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGc  194 (510)
T KOG0144|consen  116 GERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGC  194 (510)
T ss_pred             hhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccC
Confidence            3444456789999999999999999999999999999999999987 899999999999999999999999999999999


Q ss_pred             Cccceeeccccccccc----------------------------------------------------------------
Q 018554           86 SSPLQVKYADGELERL----------------------------------------------------------------  101 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~~----------------------------------------------------------------  101 (354)
                      ..+|-|+|++.++++.                                                                
T Consensus       195 s~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~  274 (510)
T KOG0144|consen  195 SQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQL  274 (510)
T ss_pred             CCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHH
Confidence            9999999999887765                                                                


Q ss_pred             --------------------------------------------------------------------------------
Q 018554          102 --------------------------------------------------------------------------------  101 (354)
Q Consensus       102 --------------------------------------------------------------------------------  101 (354)
                                                                                                      
T Consensus       275 qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a  354 (510)
T KOG0144|consen  275 QQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGA  354 (510)
T ss_pred             HHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccc
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------------------cceEEEecCCC
Q 018554          102 ---------------------------------------------------------------------EHKLFIGMLPK  112 (354)
Q Consensus       102 ---------------------------------------------------------------------~~~l~V~~l~~  112 (354)
                                                                                           ..+|||.+||.
T Consensus       355 ~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPq  434 (510)
T KOG0144|consen  355 GTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQ  434 (510)
T ss_pred             cccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCch
Confidence                                                                                 45899999999


Q ss_pred             CCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          113 NVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       113 ~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      +.-+.||-..|..||.|+..+++-|+ ++.+++|+||.|++..+|..||..+||.. +..  ++++|.+..
T Consensus       435 efgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQ-ig~--KrlkVQlk~  502 (510)
T KOG0144|consen  435 EFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQ-IGS--KRLKVQLKR  502 (510)
T ss_pred             hhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchh-hcc--ccceEEeee
Confidence            99999999999999999999999884 89999999999999999999999999987 444  557776543

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=1.4e-25  Score=207.94  Aligned_cols=169  Identities=28%  Similarity=0.446  Sum_probs=144.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +.-+|+|+||||.|.+++|+.+|+.||.|.+|.|.+.+.++.+ |||||.|.+..+|.+|++.+|+.. +.|  +++-|+
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~-i~g--R~VAVD  191 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNK-IDG--RPVAVD  191 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCce-ecC--ceeEEe
Confidence            3778999999999999999999999999999999988875544 999999999999999999998866 555  888888


Q ss_pred             ccccccccc-----------------------------------------------------------------------
Q 018554           93 YADGELERL-----------------------------------------------------------------------  101 (354)
Q Consensus        93 ~~~~~~~~~-----------------------------------------------------------------------  101 (354)
                      |+..+..-.                                                                       
T Consensus       192 WAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S  271 (678)
T KOG0127|consen  192 WAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESS  271 (678)
T ss_pred             eecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccccccccccc
Confidence            873211000                                                                       


Q ss_pred             --------------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHH
Q 018554          102 --------------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus       102 --------------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                                          ..+|||+||++++|+++|.++|++||+|..+.|+.+ .++.++|+|||.|.+..+|..||
T Consensus       272 ~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci  351 (678)
T KOG0127|consen  272 GKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCI  351 (678)
T ss_pred             ccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHH
Confidence                                358999999999999999999999999999999998 58999999999999999999999


Q ss_pred             HHh-----CCCcccCCCceeEEEEecCChHHH
Q 018554          161 EAI-----NGKHKMEGSSVPLVVKWADTEKER  187 (354)
Q Consensus       161 ~~l-----~g~~~~~g~~~~l~v~~a~~~~~~  187 (354)
                      +..     .|..+|+|  +.|.|..|-.+++.
T Consensus       352 ~~Aspa~e~g~~ll~G--R~Lkv~~Av~RkeA  381 (678)
T KOG0127|consen  352 EAASPASEDGSVLLDG--RLLKVTLAVTRKEA  381 (678)
T ss_pred             HhcCccCCCceEEEec--cEEeeeeccchHHH
Confidence            887     34466787  67888888766543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.94  E-value=1.4e-26  Score=199.49  Aligned_cols=147  Identities=26%  Similarity=0.533  Sum_probs=132.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .+|||||||.++++.+|+.+|++||+|.+|.|+++        ||||..+|...|+.||..||+-+ |.|  ..|+|.-+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYt-Lhg--~nInVeaS   71 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYT-LHG--VNINVEAS   71 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccce-ecc--eEEEEEec
Confidence            57999999999999999999999999999999986        99999999999999999998876 555  77888877


Q ss_pred             ccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554           95 DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus        95 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      +.+ .+.+.+|+|+||...++.+||++.|++||.|.+++|++       +|+||.|+..++|..|++.||+.. +.|  +
T Consensus        72 ksK-sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk-------dy~fvh~d~~eda~~air~l~~~~-~~g--k  140 (346)
T KOG0109|consen   72 KSK-SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK-------DYAFVHFDRAEDAVEAIRGLDNTE-FQG--K  140 (346)
T ss_pred             ccc-CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec-------ceeEEEEeeccchHHHHhcccccc-ccc--c
Confidence            766 55678999999999999999999999999999999994       599999999999999999999987 677  5


Q ss_pred             eEEEEecCC
Q 018554          175 PLVVKWADT  183 (354)
Q Consensus       175 ~l~v~~a~~  183 (354)
                      +++|.+..+
T Consensus       141 ~m~vq~sts  149 (346)
T KOG0109|consen  141 RMHVQLSTS  149 (346)
T ss_pred             eeeeeeecc
Confidence            677766544

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.93  E-value=2.5e-25  Score=220.05  Aligned_cols=167  Identities=23%  Similarity=0.362  Sum_probs=138.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||.++++++|+++|+.||.|..+.|++|..||.++|||||+|.+.++|..||+.|++.. +.+  +.|.|
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~-~~~--~~l~v  369 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD-TGD--NKLHV  369 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999999998877 444  56666


Q ss_pred             ecccccc-----------------------------ccccceEEEecCCCC--C--------CHHHHHHhhccCCCeeEE
Q 018554           92 KYADGEL-----------------------------ERLEHKLFIGMLPKN--V--------SEAEVSALFSIYGTIKDL  132 (354)
Q Consensus        92 ~~~~~~~-----------------------------~~~~~~l~V~~l~~~--~--------t~~~l~~~F~~~G~v~~i  132 (354)
                      .++....                             ....++|+|.||...  +        ..++|+++|++||.|++|
T Consensus       370 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v  449 (509)
T TIGR01642       370 QRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINI  449 (509)
T ss_pred             EECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEE
Confidence            6652110                             012467899888531  1        236799999999999999


Q ss_pred             EEeeCC----CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          133 QILRGS----QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       133 ~i~~~~----~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      .|+++.    .+..+|++||+|++.++|++|+++|||.. ++|  +.|.|.|.+..
T Consensus       450 ~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~-~~g--r~v~~~~~~~~  502 (509)
T TIGR01642       450 VIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRK-FND--RVVVAAFYGED  502 (509)
T ss_pred             EeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEEEeCHH
Confidence            998762    24557999999999999999999999987 666  68899987654

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.93  E-value=6.4e-25  Score=217.13  Aligned_cols=162  Identities=23%  Similarity=0.422  Sum_probs=131.4

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhc------------CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHh
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEF------------ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC   76 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~------------G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l   76 (354)
                      ......++|||||||.++|+++|+++|..+            +.|..+.+      .+.+|||||+|.+.++|.+|| +|
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al-~l  242 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAM-AL  242 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhh-cC
Confidence            345678899999999999999999999985            23333433      456789999999999999999 58


Q ss_pred             cCCccCCCCCccceeecccccc------------------------------ccccceEEEecCCCCCCHHHHHHhhccC
Q 018554           77 HNKKTLPGASSPLQVKYADGEL------------------------------ERLEHKLFIGMLPKNVSEAEVSALFSIY  126 (354)
Q Consensus        77 ~~~~~~~g~~~~l~v~~~~~~~------------------------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~  126 (354)
                      ++.. +.+  ..|+|.......                              ....++|||+||+..+|+++|+++|+.|
T Consensus       243 ~g~~-~~g--~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~  319 (509)
T TIGR01642       243 DSII-YSN--VFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESF  319 (509)
T ss_pred             CCeE-eeC--ceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            7754 444  566665322110                              1124689999999999999999999999


Q ss_pred             CCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCC
Q 018554          127 GTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       127 G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~  183 (354)
                      |.|+.+.|+++ .++.++|||||+|.+.++|.+||+.|||.. +.|  ..|.|.++..
T Consensus       320 G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~-~~~--~~l~v~~a~~  374 (509)
T TIGR01642       320 GDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD-TGD--NKLHVQRACV  374 (509)
T ss_pred             CCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEEECcc
Confidence            99999999998 578999999999999999999999999987 555  5788888853

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.93  E-value=1.1e-25  Score=202.84  Aligned_cols=170  Identities=25%  Similarity=0.427  Sum_probs=142.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +.++||||+|+|++++|.|+++|+.||+|.+|.+++|+.|+++|||+||+|++.+.+.++|..  ..+.++++....+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~--~~h~~dgr~ve~k~a   82 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA--RTHKLDGRSVEPKRA   82 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc--cccccCCccccceec
Confidence            899999999999999999999999999999999999999999999999999999999999877  335566644444444


Q ss_pred             ccccccccc-----cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCC
Q 018554           93 YADGELERL-----EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGK  166 (354)
Q Consensus        93 ~~~~~~~~~-----~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  166 (354)
                      .++.+..+.     ..+|||++|+.++++++++++|++||.|.++.++.| .+...++|+||.|++++++.+++..  ..
T Consensus        83 v~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~--~f  160 (311)
T KOG4205|consen   83 VSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ--KF  160 (311)
T ss_pred             cCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc--ce
Confidence            444322222     458999999999999999999999999999999998 5788899999999999999998753  22


Q ss_pred             cccCCCceeEEEEecCChHHHH
Q 018554          167 HKMEGSSVPLVVKWADTEKERQ  188 (354)
Q Consensus       167 ~~~~g~~~~l~v~~a~~~~~~~  188 (354)
                      +.+.+  +.+.|+.|.++....
T Consensus       161 ~~~~g--k~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  161 HDFNG--KKVEVKRAIPKEVMQ  180 (311)
T ss_pred             eeecC--ceeeEeeccchhhcc
Confidence            33555  678899888775544

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=9.5e-25  Score=202.36  Aligned_cols=164  Identities=26%  Similarity=0.457  Sum_probs=145.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .||||++||++++.++|.++|+.+|.|..|.++.++.++++|||+||.|.-.+++..|+..+++.. +.|  +.|+|..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~k-f~G--r~l~v~~A   82 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSK-FEG--RILNVDPA   82 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCc-ccc--eecccccc
Confidence            899999999999999999999999999999999999999999999999999999999999987765 555  66666665


Q ss_pred             ccccccc---------------------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEE
Q 018554           95 DGELERL---------------------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAF  147 (354)
Q Consensus        95 ~~~~~~~---------------------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~af  147 (354)
                      ..+....                           .-+|.|+||||.+.+.+|+.+|+.||.|.+|.|.+...+.-.||||
T Consensus        83 ~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaF  162 (678)
T KOG0127|consen   83 KKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAF  162 (678)
T ss_pred             cccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEE
Confidence            3221110                           3479999999999999999999999999999999888777789999


Q ss_pred             EEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          148 LKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       148 V~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      |.|....+|.+|++.+|+.. ++|  ++|-|.||-.+
T Consensus       163 V~fk~~~dA~~Al~~~N~~~-i~g--R~VAVDWAV~K  196 (678)
T KOG0127|consen  163 VQFKEKKDAEKALEFFNGNK-IDG--RPVAVDWAVDK  196 (678)
T ss_pred             EEEeeHHHHHHHHHhccCce-ecC--ceeEEeeeccc
Confidence            99999999999999999987 666  78999999554

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.91  E-value=3.2e-23  Score=202.32  Aligned_cols=163  Identities=25%  Similarity=0.426  Sum_probs=136.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ..++|||+|||.++++++|+++|+.||.|..|.|++|..+|+++|||||+|.+.++|.+|++.|++.. +.+  +.|.|.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~-i~g--~~i~v~  261 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFE-LAG--RPIKVG  261 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcE-ECC--EEEEEE
Confidence            36899999999999999999999999999999999999999999999999999999999999999855 444  677777


Q ss_pred             ccccc---------------------------------------------------------------------------
Q 018554           93 YADGE---------------------------------------------------------------------------   97 (354)
Q Consensus        93 ~~~~~---------------------------------------------------------------------------   97 (354)
                      |+...                                                                           
T Consensus       262 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (457)
T TIGR01622       262 YAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYAT  341 (457)
T ss_pred             EccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccc
Confidence            73210                                                                           


Q ss_pred             ----------------cccccceEEEecCCCCCC----------HHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeC
Q 018554           98 ----------------LERLEHKLFIGMLPKNVS----------EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYE  151 (354)
Q Consensus        98 ----------------~~~~~~~l~V~~l~~~~t----------~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~  151 (354)
                                      ......+|+|.||-...+          .+||++.|++||.|+.|.|...   ...|++||+|+
T Consensus       342 ~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~  418 (457)
T TIGR01622       342 GALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFS  418 (457)
T ss_pred             cccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEEC
Confidence                            001135688888854433          3689999999999999999743   23799999999


Q ss_pred             CHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          152 TKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       152 ~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      +.++|.+|++.|||.. ++|  +.|.|.+....
T Consensus       419 ~~e~A~~A~~~lnGr~-f~g--r~i~~~~~~~~  448 (457)
T TIGR01622       419 SVDAALAAFQALNGRY-FGG--KMITAAFVVND  448 (457)
T ss_pred             CHHHHHHHHHHhcCcc-cCC--eEEEEEEEcHH
Confidence            9999999999999987 777  68888887654

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.

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.90  E-value=4.7e-23  Score=192.37  Aligned_cols=158  Identities=27%  Similarity=0.468  Sum_probs=141.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      ..||||   +++||+.|.++|+.+|+|.+|+|.+|. |  +.|||||.|.+.++|++||+++|... +.|  +.+++-|+
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~-~~~--~~~rim~s   72 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDV-LKG--KPIRIMWS   72 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcc-cCC--cEEEeehh
Confidence            468999   999999999999999999999999999 7  99999999999999999999997644 555  88888888


Q ss_pred             ccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554           95 DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus        95 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      ..+...    |||.||+.++|..+|.+.|+.||+|.+|++..+.+| ++|| ||+|+++++|.+|++.+||.. +.+  .
T Consensus        73 ~rd~~~----~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~l-l~~--k  143 (369)
T KOG0123|consen   73 QRDPSL----VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGML-LNG--K  143 (369)
T ss_pred             ccCCce----eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcc-cCC--C
Confidence            765443    999999999999999999999999999999999888 8999 999999999999999999976 555  6


Q ss_pred             eEEEEecCChHHHHHH
Q 018554          175 PLVVKWADTEKERQAR  190 (354)
Q Consensus       175 ~l~v~~a~~~~~~~~~  190 (354)
                      .|.|.....+.++...
T Consensus       144 ki~vg~~~~~~er~~~  159 (369)
T KOG0123|consen  144 KIYVGLFERKEEREAP  159 (369)
T ss_pred             eeEEeeccchhhhccc
Confidence            7888888777766533

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=2.4e-23  Score=184.45  Aligned_cols=162  Identities=20%  Similarity=0.370  Sum_probs=140.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      -|+||||.|.+++.|+.|+..|..||+|++|.+-+|..|++++|||||+|+-.|.|..|++.+|+.. +.|  +.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~m-lGG--RNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQM-LGG--RNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhcccc-ccC--ccccccC
Confidence            4899999999999999999999999999999999999999999999999999999999999998754 666  6777765


Q ss_pred             cccc------------cccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHH
Q 018554           94 ADGE------------LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus        94 ~~~~------------~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                      ...-            ..+.-++|||..+..+++|+||+.+|+.||+|.+|++-++. ...+|||+||+|.+..+..+||
T Consensus       190 PsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAi  269 (544)
T KOG0124|consen  190 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI  269 (544)
T ss_pred             CCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHh
Confidence            4321            11225689999999999999999999999999999999995 5678999999999999999999


Q ss_pred             HHhCCCcccCCCceeEEEEec
Q 018554          161 EAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       161 ~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..+|=.. ++|.  -|+|-.+
T Consensus       270 asMNlFD-LGGQ--yLRVGk~  287 (544)
T KOG0124|consen  270 ASMNLFD-LGGQ--YLRVGKC  287 (544)
T ss_pred             hhcchhh-cccc--eEecccc
Confidence            9998765 6664  4555443

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.87  E-value=7.4e-21  Score=185.85  Aligned_cols=79  Identities=19%  Similarity=0.340  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+||+.++++++|+++|+.||+|.+|+|++|+.++++||||||+|.+.++|.+||+.+|+.. +.|  +.|+|
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~e-lgG--r~LrV  278 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFD-LGG--QYLRV  278 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCe-eCC--eEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999999998765 344  44444


Q ss_pred             ec
Q 018554           92 KY   93 (354)
Q Consensus        92 ~~   93 (354)
                      .+
T Consensus       279 ~k  280 (612)
T TIGR01645       279 GK  280 (612)
T ss_pred             Ee
Confidence            43

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=1.2e-21  Score=167.46  Aligned_cols=141  Identities=23%  Similarity=0.475  Sum_probs=113.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ++++.+|||||||+.++||+-|..||.+.|.|.+|+|+.|-.                .+..|..-        +     
T Consensus         2 ~~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~----------------~v~wa~~p--------~-----   52 (321)
T KOG0148|consen    2 GSDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL----------------KVNWATAP--------G-----   52 (321)
T ss_pred             CCCCCceEEeeccChhhHHHHHHHHHHhccccccceeehhhh----------------ccccccCc--------c-----
Confidence            467889999999999999999999999999999999988710                00000000        0     


Q ss_pred             eeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554           90 QVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus        90 ~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                        ..++.. .+.---+||+.|...++.|+||+.|..||+|.+++|++| .++++|||+||-|..+++|+.||..|||.. 
T Consensus        53 --nQsk~t-~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqW-  128 (321)
T KOG0148|consen   53 --NQSKPT-SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQW-  128 (321)
T ss_pred             --cCCCCc-cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCee-
Confidence              000000 011245899999999999999999999999999999999 699999999999999999999999999987 


Q ss_pred             cCCCceeEEEEecCChH
Q 018554          169 MEGSSVPLVVKWADTEK  185 (354)
Q Consensus       169 ~~g~~~~l~v~~a~~~~  185 (354)
                      |.+  +.|+-.||..+.
T Consensus       129 lG~--R~IRTNWATRKp  143 (321)
T KOG0148|consen  129 LGR--RTIRTNWATRKP  143 (321)
T ss_pred             ecc--ceeeccccccCc
Confidence            444  789999997665

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.86  E-value=2.1e-21  Score=185.67  Aligned_cols=168  Identities=25%  Similarity=0.424  Sum_probs=141.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCC---CcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR---ASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg---~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ..++|||.||.++++.++|...|...|.|.+|.|.+.++..   .|.|||||+|.+.++|..|++.|++.. +.|  ..|
T Consensus       514 ~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtv-ldG--H~l  590 (725)
T KOG0110|consen  514 TETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTV-LDG--HKL  590 (725)
T ss_pred             cchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCce-ecC--ceE
Confidence            34449999999999999999999999999999887765422   356999999999999999999998765 777  556


Q ss_pred             eeeccc--------cccc--cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHH
Q 018554           90 QVKYAD--------GELE--RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALA  158 (354)
Q Consensus        90 ~v~~~~--------~~~~--~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~  158 (354)
                      .++++.        .+..  ....+|+|.|||...+..+|+++|..||.|.+|+|... ..+.+||||||+|-+..+|..
T Consensus       591 ~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~n  670 (725)
T KOG0110|consen  591 ELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKN  670 (725)
T ss_pred             EEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHH
Confidence            665554        1111  11458999999999999999999999999999999987 456679999999999999999


Q ss_pred             HHHHhCCCcccCCCceeEEEEecCChHH
Q 018554          159 ALEAINGKHKMEGSSVPLVVKWADTEKE  186 (354)
Q Consensus       159 Ai~~l~g~~~~~g~~~~l~v~~a~~~~~  186 (354)
                      |+++|..+++ -|  ++|++.||+....
T Consensus       671 A~~al~STHl-yG--RrLVLEwA~~d~~  695 (725)
T KOG0110|consen  671 AFDALGSTHL-YG--RRLVLEWAKSDNT  695 (725)
T ss_pred             HHHhhcccce-ec--hhhheehhccchH
Confidence            9999998885 44  6899999987654

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=9.1e-21  Score=177.05  Aligned_cols=166  Identities=28%  Similarity=0.451  Sum_probs=141.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      ...|||.||+.++|..+|.++|+.||.|.+|+|+.|.. | ++|| ||+|+++++|.+|++.+||.. +.+  +.+.|..
T Consensus        76 ~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~l-l~~--kki~vg~  149 (369)
T KOG0123|consen   76 PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGML-LNG--KKIYVGL  149 (369)
T ss_pred             CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcc-cCC--CeeEEee
Confidence            33399999999999999999999999999999999986 5 9999 999999999999999998855 444  5666655


Q ss_pred             ccccccc---------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 018554           94 ADGELER---------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN  164 (354)
Q Consensus        94 ~~~~~~~---------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  164 (354)
                      ...+.++         ...+++|.++..++++++|.++|..+|.|..+.++.+..+.+++|+||.|++.++|..|++.|+
T Consensus       150 ~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~  229 (369)
T KOG0123|consen  150 FERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLN  229 (369)
T ss_pred             ccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhcc
Confidence            4433332         2467899999999999999999999999999999999988899999999999999999999999


Q ss_pred             CCcccCCCceeEEEEecCChHHHH
Q 018554          165 GKHKMEGSSVPLVVKWADTEKERQ  188 (354)
Q Consensus       165 g~~~~~g~~~~l~v~~a~~~~~~~  188 (354)
                      +.. +++  ..+.|..+..+.++.
T Consensus       230 ~~~-~~~--~~~~V~~aqkk~e~~  250 (369)
T KOG0123|consen  230 GKI-FGD--KELYVGRAQKKSERE  250 (369)
T ss_pred             CCc-CCc--cceeecccccchhhH
Confidence            976 443  567777766644443

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.84  E-value=1.5e-21  Score=182.15  Aligned_cols=165  Identities=27%  Similarity=0.461  Sum_probs=141.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +..+.++||+-.|....+..||.+||+.+|+|.+|.+|.|+.+++++|.|||+|.|.+++..|| .|.|+.+ .|  .++
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrl-lg--~pv  250 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRL-LG--VPV  250 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcc-cC--cee
Confidence            4567889999999999999999999999999999999999999999999999999999999999 6767764 34  677


Q ss_pred             eeeccccccccc---------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCH
Q 018554           90 QVKYADGELERL---------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETK  153 (354)
Q Consensus        90 ~v~~~~~~~~~~---------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~  153 (354)
                      .|+....++...               -.+||||||-.++++++|+.+|+.||.|+.|.+.+|. +|.++||+||+|.+.
T Consensus       251 ~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~  330 (549)
T KOG0147|consen  251 IVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNK  330 (549)
T ss_pred             EecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecH
Confidence            776543332221               2239999999999999999999999999999999995 999999999999999


Q ss_pred             HHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          154 EQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       154 ~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++|.+|++.|||. .+-|.  .|+|..-
T Consensus       331 ~~ar~a~e~lngf-elAGr--~ikV~~v  355 (549)
T KOG0147|consen  331 EDARKALEQLNGF-ELAGR--LIKVSVV  355 (549)
T ss_pred             HHHHHHHHHhccc-eecCc--eEEEEEe
Confidence            9999999999994 46664  5555543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=2.7e-19  Score=152.86  Aligned_cols=117  Identities=45%  Similarity=0.724  Sum_probs=107.4

Q ss_pred             Cccceeecccccccc-ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 018554           86 SSPLQVKYADGELER-LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN  164 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~-~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  164 (354)
                      .++|+|+.++.+.+. +.++||||.|...-.|||++.+|..||.|+++.+++..++.+|||+||+|.+..+|..||..|+
T Consensus         2 nrpiqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLH   81 (371)
T KOG0146|consen    2 NRPIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALH   81 (371)
T ss_pred             CCCccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhc
Confidence            478889888877655 5789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCCCceeEEEEecCChHHHHHHHHHHHhhhccCC
Q 018554          165 GKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNL  202 (354)
Q Consensus       165 g~~~~~g~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~  202 (354)
                      |...+-|....|.|+|||++++|.-+++++...+...+
T Consensus        82 gSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~  119 (371)
T KOG0146|consen   82 GSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMF  119 (371)
T ss_pred             ccccCCCCccceEEEeccchHHHHHHHHHHHHHHhccc
Confidence            99999999999999999999999999998877666544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.79  E-value=2e-18  Score=139.90  Aligned_cols=145  Identities=18%  Similarity=0.348  Sum_probs=123.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ...+++|||||||.++-|.||.++|.+||.|.+|.|..-+   ..-+||||+|+|..+|+.||..-++-. +.+  ..|+
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYd-ydg--~rLR   76 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYD-YDG--CRLR   76 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccc-cCc--ceEE
Confidence            3568999999999999999999999999999999886543   245799999999999999998776655 444  8899


Q ss_pred             eecccccc---------------------------ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcc
Q 018554           91 VKYADGEL---------------------------ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSK  143 (354)
Q Consensus        91 v~~~~~~~---------------------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~  143 (354)
                      |.++..-.                           .+.+.+|.|.+||.+-+++||+++..+-|.|....+.+|      
T Consensus        77 VEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------  150 (241)
T KOG0105|consen   77 VEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------  150 (241)
T ss_pred             EEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------
Confidence            98875331                           112568999999999999999999999999999999986      


Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCCc
Q 018554          144 GCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus       144 g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                      |++.|+|...|+-+-|++.|+...
T Consensus       151 g~GvV~~~r~eDMkYAvr~ld~~~  174 (241)
T KOG0105|consen  151 GVGVVEYLRKEDMKYAVRKLDDQK  174 (241)
T ss_pred             cceeeeeeehhhHHHHHHhhcccc
Confidence            578999999999999999987654

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.78  E-value=4.4e-18  Score=154.45  Aligned_cols=161  Identities=19%  Similarity=0.368  Sum_probs=133.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~-~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ..+.+||.|||+++.+.||+++|.+ .|+|+.|.+..|.. |++||||.|||+++|.++||++.||. ..+.+  ++|.|
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk-~~~~G--R~l~v  118 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNK-YEVNG--RELVV  118 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhh-ccccC--ceEEE
Confidence            3455999999999999999999986 89999999999985 99999999999999999999999964 33555  66666


Q ss_pred             eccccccccc----------------------------------------------------------------------
Q 018554           92 KYADGELERL----------------------------------------------------------------------  101 (354)
Q Consensus        92 ~~~~~~~~~~----------------------------------------------------------------------  101 (354)
                      +-........                                                                      
T Consensus       119 KEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfg  198 (608)
T KOG4212|consen  119 KEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFG  198 (608)
T ss_pred             eccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhccc
Confidence            6321110000                                                                      


Q ss_pred             ----------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554          102 ----------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus       102 ----------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                                      ..++||+||.+.+..+.|++.|.--|.|+.|.+--|+.+.++|+|.|+|++.-+|.+||..|++
T Consensus       199 l~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  199 LSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             chhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhcc
Confidence                            3478999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CcccCCCceeEEEEe
Q 018554          166 KHKMEGSSVPLVVKW  180 (354)
Q Consensus       166 ~~~~~g~~~~l~v~~  180 (354)
                      .-.+   +++..+.+
T Consensus       279 ~g~~---~~~~~~Rl  290 (608)
T KOG4212|consen  279 QGLF---DRRMTVRL  290 (608)
T ss_pred             CCCc---cccceeec
Confidence            4322   24555555

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

Probab=99.76  E-value=4.6e-18  Score=138.83  Aligned_cols=85  Identities=28%  Similarity=0.372  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+||+++++|++|+++|++||.|.+|.|++|+.|++++|||||+|++.++|++||+.|++.. +.+  +.|+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~-i~G--r~l~  107 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKE-LNG--RHIR  107 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999999998765 555  7888


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |+++..+.
T Consensus       108 V~~a~~~~  115 (144)
T PLN03134        108 VNPANDRP  115 (144)
T ss_pred             EEeCCcCC
Confidence            88876543

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.75  E-value=4.8e-17  Score=136.99  Aligned_cols=159  Identities=21%  Similarity=0.428  Sum_probs=131.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554           12 EERVKLFVGQVPKHMTEAQLLA----MFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~----~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ....||||.||...+..++|++    +|++||+|.+|...+   |.+.||-|||.|.+.+.|..|+++|+|-.++ |  +
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFy-g--K   80 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFY-G--K   80 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCccc-C--c
Confidence            3455999999999999999999    999999999988766   4679999999999999999999999987643 3  6


Q ss_pred             cceeeccccccc---------------------------------------------------cccceEEEecCCCCCCH
Q 018554           88 PLQVKYADGELE---------------------------------------------------RLEHKLFIGMLPKNVSE  116 (354)
Q Consensus        88 ~l~v~~~~~~~~---------------------------------------------------~~~~~l~V~~l~~~~t~  116 (354)
                      ++++.|++.+..                                                   .....||+.+||.+++.
T Consensus        81 ~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~  160 (221)
T KOG4206|consen   81 PMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESES  160 (221)
T ss_pred             hhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhH
Confidence            777777643221                                                   11346899999999999


Q ss_pred             HHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          117 AEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       117 ~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      +.|..+|.+|.-.++|+++...    ++.|||+|.+...|..|...|.+..+-.  .-.+.|.+++
T Consensus       161 e~l~~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~--~~~m~i~~a~  220 (221)
T KOG4206|consen  161 EMLSDLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITK--KNTMQITFAK  220 (221)
T ss_pred             HHHHHHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceecc--CceEEecccC
Confidence            9999999999999999998753    5789999999999999999999866422  3467777664

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.72  E-value=7.6e-17  Score=134.59  Aligned_cols=156  Identities=25%  Similarity=0.317  Sum_probs=123.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEee-CCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIK-DKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~-d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      +...-+||||.+||.|+.-.||..+|..|---+.+.|.. ++..+-++-+|||+|.+..+|..|+++|||.++-......
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            345689999999999999999999999985555555543 3333345679999999999999999999998877776777


Q ss_pred             ceeeccccccccc-------------------------------------------------------------------
Q 018554           89 LQVKYADGELERL-------------------------------------------------------------------  101 (354)
Q Consensus        89 l~v~~~~~~~~~~-------------------------------------------------------------------  101 (354)
                      |++.+++....+.                                                                   
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            7777764322111                                                                   


Q ss_pred             --------------------cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHH
Q 018554          102 --------------------EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE  161 (354)
Q Consensus       102 --------------------~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~  161 (354)
                                          -.+|||.||..+||||+|+.+|+.|-....++|... .|  -.+||++|++.+.|..|+.
T Consensus       190 ~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g--~~vaf~~~~~~~~at~am~  266 (284)
T KOG1457|consen  190 APSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GG--MPVAFADFEEIEQATDAMN  266 (284)
T ss_pred             CCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CC--cceEeecHHHHHHHHHHHH
Confidence                                237999999999999999999999977666666532 22  4689999999999999999


Q ss_pred             HhCCCcc
Q 018554          162 AINGKHK  168 (354)
Q Consensus       162 ~l~g~~~  168 (354)
                      .|.|..+
T Consensus       267 ~lqg~~~  273 (284)
T KOG1457|consen  267 HLQGNLL  273 (284)
T ss_pred             Hhhccee
Confidence            9999763

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.72  E-value=1.3e-17  Score=140.68  Aligned_cols=77  Identities=25%  Similarity=0.375  Sum_probs=68.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .+...++||||||+|++.+|+|+++|++||+|+++.|+.|+.|||+|||+||+|.|.++|.+|++.  -..+|+|+...
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d--p~piIdGR~aN   84 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD--PNPIIDGRKAN   84 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC--CCCcccccccc
Confidence            455678999999999999999999999999999999999999999999999999999999999876  44677774333

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.71  E-value=4.2e-17  Score=152.59  Aligned_cols=160  Identities=22%  Similarity=0.415  Sum_probs=122.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +-.+||||||..+++|++|+.+|+.||.|+.|.+.+|..||+++||+||+|.+.++|++|++.||+ -.+.|  +.|+|.
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lng-felAG--r~ikV~  353 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNG-FELAG--RLIKVS  353 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhcc-ceecC--ceEEEE
Confidence            344499999999999999999999999999999999999999999999999999999999999998 44555  556555


Q ss_pred             ccccccc--------------c-c--------------------------------------------------------
Q 018554           93 YADGELE--------------R-L--------------------------------------------------------  101 (354)
Q Consensus        93 ~~~~~~~--------------~-~--------------------------------------------------------  101 (354)
                      .-..+..              . .                                                        
T Consensus       354 ~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~  433 (549)
T KOG0147|consen  354 VVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPA  433 (549)
T ss_pred             EeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcc
Confidence            3210000              0 0                                                        


Q ss_pred             ---------cceEEEecC--CCCCC--------HHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHH
Q 018554          102 ---------EHKLFIGML--PKNVS--------EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA  162 (354)
Q Consensus       102 ---------~~~l~V~~l--~~~~t--------~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~  162 (354)
                               +.++.+.|+  |.+.|        .|||.+.+++||.|..|.+..+.    -||.||+|.+.+.|..|+.+
T Consensus       434 ~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns----~g~VYvrc~s~~~A~~a~~a  509 (549)
T KOG0147|consen  434 DASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNS----AGCVYVRCPSAEAAGTAVKA  509 (549)
T ss_pred             ccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCC----CceEEEecCcHHHHHHHHHH
Confidence                     112233333  11111        35678888999999998887652    48999999999999999999


Q ss_pred             hCCCcccCCCceeEEEEecC
Q 018554          163 INGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       163 l~g~~~~~g~~~~l~v~~a~  182 (354)
                      |||.+ +.|  +.|+.+|-.
T Consensus       510 lhgrW-F~g--r~Ita~~~~  526 (549)
T KOG0147|consen  510 LHGRW-FAG--RMITAKYLP  526 (549)
T ss_pred             Hhhhh-hcc--ceeEEEEee
Confidence            99987 666  577777653

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

Probab=99.71  E-value=7.5e-17  Score=131.65  Aligned_cols=82  Identities=26%  Similarity=0.485  Sum_probs=74.5

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ....++|||+||++++|+++|+++|++||.|++++|+.| .++.++|||||+|++.++|++|++.||+.. ++|  +.|+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~-i~G--r~l~  107 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKE-LNG--RHIR  107 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEE
Confidence            334679999999999999999999999999999999998 488999999999999999999999999976 666  6899


Q ss_pred             EEecCC
Q 018554          178 VKWADT  183 (354)
Q Consensus       178 v~~a~~  183 (354)
                      |+|+..
T Consensus       108 V~~a~~  113 (144)
T PLN03134        108 VNPAND  113 (144)
T ss_pred             EEeCCc
Confidence            999864

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.71  E-value=2.5e-16  Score=145.55  Aligned_cols=161  Identities=17%  Similarity=0.271  Sum_probs=120.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +-....-|-+++|||++|++||.++|+.+ .|+++.+.+  .+|+..|-|||+|.+++++++|+++  .+..+..  +-|
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alkk--dR~~mg~--RYI   78 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKK--DRESMGH--RYI   78 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec--cCCCcCcceEEEeechHHHHHHHHh--hHHHhCC--ceE
Confidence            44566778899999999999999999999 567755554  4699999999999999999999987  3333332  444


Q ss_pred             eeecccccc------------ccccceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCCCCcceEEEEEeCCHHHH
Q 018554           90 QVKYADGEL------------ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQA  156 (354)
Q Consensus        90 ~v~~~~~~~------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~~~~~g~afV~f~~~~~A  156 (354)
                      .|-.+..+.            ......|-+++||+.||++||.++|+..-.|.+ |.++.+..+++.|-|||+|++.+.|
T Consensus        79 EVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~a  158 (510)
T KOG4211|consen   79 EVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESA  158 (510)
T ss_pred             EEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHH
Confidence            444332111            112457899999999999999999998866666 5566677888899999999999999


Q ss_pred             HHHHHHhCCCcccCCCceeEEEEec
Q 018554          157 LAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       157 ~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++|+..... . +.-  +=|+|-.+
T Consensus       159 e~Al~rhre-~-iGh--RYIEvF~S  179 (510)
T KOG4211|consen  159 EIALGRHRE-N-IGH--RYIEVFRS  179 (510)
T ss_pred             HHHHHHHHH-h-hcc--ceEEeehh
Confidence            999976433 2 333  44555433

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=5.5e-17  Score=137.99  Aligned_cols=144  Identities=24%  Similarity=0.421  Sum_probs=119.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .+||||+|++.+.+.||.++|..||.|.+|.++.        ||+||+|.|..+|+.||..+|++.+... .  +.+.++
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e-~--~vve~~   70 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGE-R--LVVEHA   70 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecce-e--eeeecc
Confidence            5799999999999999999999999999987644        6999999999999999999988775433 2  666666


Q ss_pred             ccc---------------c------ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCH
Q 018554           95 DGE---------------L------ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETK  153 (354)
Q Consensus        95 ~~~---------------~------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~  153 (354)
                      ...               .      ....+.|.|.++..++.+++|.++|..+|.+....+.       ++++||+|++.
T Consensus        71 r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~  143 (216)
T KOG0106|consen   71 RGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQ  143 (216)
T ss_pred             cccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhh
Confidence            521               0      1126789999999999999999999999998665553       67999999999


Q ss_pred             HHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          154 EQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       154 ~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ++|.+|++.|+++. +.+  +.|++.
T Consensus       144 ~da~ra~~~l~~~~-~~~--~~l~~~  166 (216)
T KOG0106|consen  144 EDAKRALEKLDGKK-LNG--RRISVE  166 (216)
T ss_pred             hhhhhcchhccchh-hcC--ceeeec
Confidence            99999999999987 454  466663

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.66  E-value=4e-16  Score=145.18  Aligned_cols=86  Identities=34%  Similarity=0.552  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||+++||++|+++|++||+|++|+|++|+.|++++|||||+|.+.++|++||+.||+.. +.+..+.|+
T Consensus       190 ~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~-~~g~~~~l~  268 (346)
T TIGR01659       190 SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI-PEGGSQPLT  268 (346)
T ss_pred             ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCc-cCCCceeEE
Confidence            3457889999999999999999999999999999999999999999999999999999999999998765 566567888


Q ss_pred             eeccccc
Q 018554           91 VKYADGE   97 (354)
Q Consensus        91 v~~~~~~   97 (354)
                      |++++..
T Consensus       269 V~~a~~~  275 (346)
T TIGR01659       269 VRLAEEH  275 (346)
T ss_pred             EEECCcc
Confidence            8887653

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).

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.66  E-value=1.8e-16  Score=133.77  Aligned_cols=79  Identities=20%  Similarity=0.323  Sum_probs=69.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .-+|||||+|+|++++|+|+++|++||+|++..|+.| .+++||||+||+|.|.++|.+|++.-  ..+|||  ++..|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp--~piIdG--R~aNcn   86 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP--NPIIDG--RKANCN   86 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC--CCcccc--cccccc
Confidence            3578999999999999999999999999999999999 58999999999999999999999854  467999  466777


Q ss_pred             ecCC
Q 018554          180 WADT  183 (354)
Q Consensus       180 ~a~~  183 (354)
                      +|--
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            7643

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.65  E-value=7.6e-15  Score=142.03  Aligned_cols=77  Identities=34%  Similarity=0.606  Sum_probs=67.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      -++|||||+|+++++|.||.++|++||+|++|.++.      +||||||++....+|.+|+.+|++..+   ..+.|++.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv---~~k~Iki~  490 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKV---ADKTIKIA  490 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccc---cceeeEEe
Confidence            468999999999999999999999999999998876      457999999999999999999976553   34788889


Q ss_pred             cccccc
Q 018554           93 YADGEL   98 (354)
Q Consensus        93 ~~~~~~   98 (354)
                      |+..+-
T Consensus       491 Wa~g~G  496 (894)
T KOG0132|consen  491 WAVGKG  496 (894)
T ss_pred             eeccCC
Confidence            986553

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.65  E-value=7e-15  Score=131.37  Aligned_cols=171  Identities=16%  Similarity=0.237  Sum_probs=131.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-ccCCCCCc-
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK-KTLPGASS-   87 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~-~~~~g~~~-   87 (354)
                      +...+-.|+|++|-..++|.||.+.++.||.|..+..+..+.      -|.|+|+|.+.|+.|+.-.-.. ..+.+..- 
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r------~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR------QALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccc------eeeeeeccccchhhheehhccCcccccCchhh
Confidence            445667799999999999999999999999999998877553      7999999999999998743222 22222111 


Q ss_pred             -----cceeeccccccccccceEEEecCC--CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHH
Q 018554           88 -----PLQVKYADGELERLEHKLFIGMLP--KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus        88 -----~l~v~~~~~~~~~~~~~l~V~~l~--~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                           .-++.....+.....+.|.+.-|.  +.+|.|.|..++...|.|.+|.|++. ++.   .|.|+|++.+.|++|.
T Consensus       101 ~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngV---QAmVEFdsv~~AqrAk  176 (494)
T KOG1456|consen  101 FNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGV---QAMVEFDSVEVAQRAK  176 (494)
T ss_pred             cccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cce---eeEEeechhHHHHHHH
Confidence                 111122222223334556655554  77999999999999999999999986 333   6999999999999999


Q ss_pred             HHhCCCcccCCCceeEEEEecCChHHHHHHH
Q 018554          161 EAINGKHKMEGSSVPLVVKWADTEKERQARR  191 (354)
Q Consensus       161 ~~l~g~~~~~g~~~~l~v~~a~~~~~~~~~~  191 (354)
                      ++|||..++.|+ +.|+|+||++.+.+..++
T Consensus       177 ~alNGADIYsGC-CTLKIeyAkP~rlnV~kn  206 (494)
T KOG1456|consen  177 AALNGADIYSGC-CTLKIEYAKPTRLNVQKN  206 (494)
T ss_pred             hhcccccccccc-eeEEEEecCcceeeeeec
Confidence            999999999987 899999999887665443

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=2.8e-15  Score=133.51  Aligned_cols=68  Identities=16%  Similarity=0.372  Sum_probs=63.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      +...-.+|||..+..|.+|+||+.+|+.||+|.+|.+-++..++.+|||+||+|.+..+-..||..+|
T Consensus       206 eAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  206 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             HHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            34567899999999999999999999999999999999999999999999999999999999998775

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

Probab=99.63  E-value=1.1e-15  Score=129.54  Aligned_cols=86  Identities=23%  Similarity=0.405  Sum_probs=78.7

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      +...+.++|-|.||+.+++|+||.++|.+||.|..|.|.+|+.||.+||||||.|.+.++|.+||+.|+|.-.   ....
T Consensus       184 R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gy---d~LI  260 (270)
T KOG0122|consen  184 RERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGY---DNLI  260 (270)
T ss_pred             ccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCccc---ceEE
Confidence            3455889999999999999999999999999999999999999999999999999999999999999988653   3478


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |+|.|++++
T Consensus       261 LrvEwskP~  269 (270)
T KOG0122|consen  261 LRVEWSKPS  269 (270)
T ss_pred             EEEEecCCC
Confidence            899998864

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.61  E-value=4.5e-15  Score=142.73  Aligned_cols=161  Identities=24%  Similarity=0.356  Sum_probs=124.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....+.|+|+|||..+..++|...|..||.|..|.+...   |.   -++|+|.+..+|.+|++.|....+   +..++
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~---G~---~aiv~fl~p~eAr~Afrklaysr~---k~~pl  451 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG---GT---GAIVEFLNPLEARKAFRKLAYSRF---KSAPL  451 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcc---cc---eeeeeecCccchHHHHHHhchhhh---ccCcc
Confidence            4456788999999999999999999999999998844321   21   389999999999999998865442   22333


Q ss_pred             eeecccccccc---------------------------------------------------ccceEEEecCCCCCCHHH
Q 018554           90 QVKYADGELER---------------------------------------------------LEHKLFIGMLPKNVSEAE  118 (354)
Q Consensus        90 ~v~~~~~~~~~---------------------------------------------------~~~~l~V~~l~~~~t~~~  118 (354)
                      .+.|+..+...                                                   ..++|||.||++++|.++
T Consensus       452 yle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~  531 (725)
T KOG0110|consen  452 YLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLED  531 (725)
T ss_pred             ccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhH
Confidence            33332111000                                                   033499999999999999


Q ss_pred             HHHhhccCCCeeEEEEeeCCCC----CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          119 VSALFSIYGTIKDLQILRGSQQ----TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       119 l~~~F~~~G~v~~i~i~~~~~~----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      |..+|...|.|.++.|...+..    .|.|||||+|.+.++|+.|++.|+|+. ++|+  .|.|+++.
T Consensus       532 l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtv-ldGH--~l~lk~S~  596 (725)
T KOG0110|consen  532 LEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTV-LDGH--KLELKISE  596 (725)
T ss_pred             HHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCce-ecCc--eEEEEecc
Confidence            9999999999999988776443    345999999999999999999999976 8886  45555554

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.61  E-value=2e-15  Score=136.39  Aligned_cols=173  Identities=18%  Similarity=0.227  Sum_probs=129.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ...++-|+++|||++++|+||.+++..||+|..+.+.+-++      -|||+|.|+++|...+....... -.-+..++.
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~-p~lr~~~~y   97 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVT-PVLRGQPIY   97 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccC-ccccCccee
Confidence            45788999999999999999999999999999998887554      79999999999988544332111 111223334


Q ss_pred             eecccccccc-----------------------------------------ccceEEEecCCCCCCHHHHHHhhccCCCe
Q 018554           91 VKYADGELER-----------------------------------------LEHKLFIGMLPKNVSEAEVSALFSIYGTI  129 (354)
Q Consensus        91 v~~~~~~~~~-----------------------------------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v  129 (354)
                      +.|+....-.                                         ..-+++|+++-+.++-|.|+++|++||.|
T Consensus        98 iq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~V  177 (492)
T KOG1190|consen   98 IQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFV  177 (492)
T ss_pred             ehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhccee
Confidence            4432110000                                         01256889999999999999999999999


Q ss_pred             eEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChHHHHHHHHHH
Q 018554          130 KDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQK  194 (354)
Q Consensus       130 ~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~~~~~~~~~~  194 (354)
                      .+|.-+...++   -.|+|.|.+.+.|..|..+|+|.-+++|+ |.|+|.|.+......+-...+
T Consensus       178 lKIiTF~Knn~---FQALvQy~d~~sAq~AK~aLdGqnIyngc-CtLrId~Sklt~LnvKynndk  238 (492)
T KOG1190|consen  178 LKIITFTKNNG---FQALVQYTDAVSAQAAKLALDGQNIYNGC-CTLRIDFSKLTDLNVKYNNDK  238 (492)
T ss_pred             EEEEEEecccc---hhhhhhccchhhHHHHHHhccCCcccCce-eEEEeehhhcccceeeccccc
Confidence            99877765432   25999999999999999999999999987 899999987654444333333

>PF00076 RRM_1: RNA recognition motif

Probab=99.61  E-value=2.5e-15  Score=107.25  Aligned_cols=63  Identities=30%  Similarity=0.648  Sum_probs=60.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554           17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        17 lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      |||+|||.++|+++|+++|++||.|..+.++.+ .+++.+|||||+|.+.++|++|++.+++..
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~   63 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKK   63 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCE
Confidence            799999999999999999999999999999998 568999999999999999999999998855

(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 ....

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

Probab=99.59  E-value=2.4e-15  Score=115.04  Aligned_cols=83  Identities=20%  Similarity=0.414  Sum_probs=75.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...++++||||||+..++||.|.++|+++|+|..|.+=.|+.++...|||||+|.+.++|..|++-+++.. ++.  ++|
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgtr-Ldd--r~i  108 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTR-LDD--RPI  108 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCc-ccc--cce
Confidence            45689999999999999999999999999999999999999999999999999999999999999998866 544  778


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      +++|.-
T Consensus       109 r~D~D~  114 (153)
T KOG0121|consen  109 RIDWDA  114 (153)
T ss_pred             eeeccc
Confidence            877654

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.59  E-value=4.3e-15  Score=145.44  Aligned_cols=108  Identities=24%  Similarity=0.269  Sum_probs=92.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEF--ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~--G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...++|||+||++++||++|+++|++|  |+|++|++++        +||||+|++.++|++|++.||+.. +.+  +.|
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~-i~G--r~I  299 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKE-LEG--SEI  299 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            346789999999999999999999999  9999998764        499999999999999999998876 555  888


Q ss_pred             eeecccccccc-----------------------------ccceEEEecCCCCCCHHHHHHhhccCCCee
Q 018554           90 QVKYADGELER-----------------------------LEHKLFIGMLPKNVSEAEVSALFSIYGTIK  130 (354)
Q Consensus        90 ~v~~~~~~~~~-----------------------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~  130 (354)
                      +|.|+++....                             ...++++++++++.+++.++++|..+|.|.
T Consensus       300 ~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       300 EVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             EEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhhccccCcccc
Confidence            99888653222                             256899999999999999999999998743

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.

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.58  E-value=3.3e-14  Score=128.62  Aligned_cols=144  Identities=33%  Similarity=0.522  Sum_probs=112.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .++|||+||+.++++++|.++|.+||.|..|.+..|+.+++++|||||+|.+.++|.+|++.+++.. +.+  +.+.|.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~-~~~--~~~~v~~  191 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKE-LEG--RPLRVQK  191 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCe-ECC--ceeEeec
Confidence            6999999999999999999999999999999999999999999999999999999999999998665 545  6666666


Q ss_pred             cc----ccccc---------------------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCC-cceEEE
Q 018554           94 AD----GELER---------------------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAF  147 (354)
Q Consensus        94 ~~----~~~~~---------------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~-~~g~af  147 (354)
                      ..    .....                     ....+++.+++..++.+++...|..+|.+..+.+....... .....+
T Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (306)
T COG0724         192 AQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSF  271 (306)
T ss_pred             cccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccc
Confidence            32    11111                     14578999999999999999999999999777666553322 223333


Q ss_pred             EEeCCHHHHHHHH
Q 018554          148 LKYETKEQALAAL  160 (354)
Q Consensus       148 V~f~~~~~A~~Ai  160 (354)
                      +.+.....+....
T Consensus       272 ~~~~~~~~~~~~~  284 (306)
T COG0724         272 VGNEASKDALESN  284 (306)
T ss_pred             cchhHHHhhhhhh
Confidence            4444444444433

>PF00076 RRM_1: RNA recognition motif

Probab=99.57  E-value=1.5e-14  Score=103.22  Aligned_cols=66  Identities=42%  Similarity=0.822  Sum_probs=62.4

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCC
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEG  171 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g  171 (354)
                      |||+|||.++|+++|+++|++||.|..+.+..+..+..+++|||+|++.++|++|++.|+|.. ++|
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~-~~~   66 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKK-ING   66 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEE-ETT
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCE-ECc
Confidence            799999999999999999999999999999998888889999999999999999999999966 665

(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 ....

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.56  E-value=1.5e-13  Score=122.00  Aligned_cols=161  Identities=13%  Similarity=0.302  Sum_probs=126.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVD--------EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~--------~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ..++.|||.|||.++|.+++.++|++||-|.        .|+|.++.. |+-+|=|.+.|-..++++.|++.|++..+ .
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~-r  209 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDEL-R  209 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccc-c
Confidence            3456699999999999999999999999876        378888876 99999999999999999999999988664 3


Q ss_pred             CCCccceeeccccc---------------------------------------cccccceEEEecCC----CCCC-----
Q 018554           84 GASSPLQVKYADGE---------------------------------------LERLEHKLFIGMLP----KNVS-----  115 (354)
Q Consensus        84 g~~~~l~v~~~~~~---------------------------------------~~~~~~~l~V~~l~----~~~t-----  115 (354)
                      |  +.|+|..|+-+                                       +.+..++|.+.|+=    ...+     
T Consensus       210 g--~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~  287 (382)
T KOG1548|consen  210 G--KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLN  287 (382)
T ss_pred             C--cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHH
Confidence            4  66777655211                                       11115678888872    1222     


Q ss_pred             --HHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          116 --EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       116 --~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                        +++|++-+++||.|.+|.|....   ..|.+-|.|.+.++|..||+.|+|+. ++|  +.|.....+
T Consensus       288 dlkedl~eec~K~G~v~~vvv~d~h---PdGvvtV~f~n~eeA~~ciq~m~GR~-fdg--Rql~A~i~D  350 (382)
T KOG1548|consen  288 DLKEDLTEECEKFGQVRKVVVYDRH---PDGVVTVSFRNNEEADQCIQTMDGRW-FDG--RQLTASIWD  350 (382)
T ss_pred             HHHHHHHHHHHHhCCcceEEEeccC---CCceeEEEeCChHHHHHHHHHhcCee-ecc--eEEEEEEeC
Confidence              45678889999999999988431   26889999999999999999999987 777  566655543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.56  E-value=7.2e-14  Score=126.39  Aligned_cols=158  Identities=20%  Similarity=0.318  Sum_probs=128.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccE-EEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGC-CFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~-aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      --+++|+++-.-+|-|.|..+|++||.|..|.-+..     +.|| |.|+|.|.++|..|..+|+|+.+..+ -+.|+++
T Consensus       150 vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~K-----nn~FQALvQy~d~~sAq~AK~aLdGqnIyng-cCtLrId  223 (492)
T KOG1190|consen  150 VLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTK-----NNGFQALVQYTDAVSAQAAKLALDGQNIYNG-CCTLRID  223 (492)
T ss_pred             eEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEec-----ccchhhhhhccchhhHHHHHHhccCCcccCc-eeEEEee
Confidence            346889999999999999999999999998866553     3456 99999999999999999999886554 5666666


Q ss_pred             ccc---------cccccc-------------------------------------------------------cceEEEe
Q 018554           93 YAD---------GELERL-------------------------------------------------------EHKLFIG  108 (354)
Q Consensus        93 ~~~---------~~~~~~-------------------------------------------------------~~~l~V~  108 (354)
                      |++         .++.|+                                                       .+.|.|.
T Consensus       224 ~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvs  303 (492)
T KOG1190|consen  224 FSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVS  303 (492)
T ss_pred             hhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEe
Confidence            542         111111                                                       2578888


Q ss_pred             cCC-CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          109 MLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       109 ~l~-~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      ||. +.+|.+.|..+|..||+|.+|+|++++    +.-|+|.|.|...|+-|++.|+|..+ .|  ++|+|.+.+..
T Consensus       304 nln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l-~g--k~lrvt~SKH~  373 (492)
T KOG1190|consen  304 NLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKL-YG--KKLRVTLSKHT  373 (492)
T ss_pred             cCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhccee-cC--ceEEEeeccCc
Confidence            885 679999999999999999999999875    34699999999999999999999874 44  68899887654

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=4.8e-16  Score=125.93  Aligned_cols=79  Identities=24%  Similarity=0.508  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      -.++.-|||||||.+.||.||..+|++||+|.+|.+++|+.||+++||||+.|+|..+...|+..|||..+ .+  +.|+
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki-~g--Rtir  108 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI-LG--RTIR  108 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCcee-cc--eeEE
Confidence            35677899999999999999999999999999999999999999999999999999999999999998774 33  6777


Q ss_pred             ee
Q 018554           91 VK   92 (354)
Q Consensus        91 v~   92 (354)
                      |.
T Consensus       109 VD  110 (219)
T KOG0126|consen  109 VD  110 (219)
T ss_pred             ee
Confidence            66

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.54  E-value=1.9e-13  Score=124.52  Aligned_cols=68  Identities=24%  Similarity=0.260  Sum_probs=62.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHN   78 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~   78 (354)
                      ......++||+||...+..+.|++.|.-.|+|+.|.+-.||. |.++|||.++|...-+|-.||..+++
T Consensus       211 ~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  211 SPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             CCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhcc
Confidence            345667899999999999999999999999999999999986 79999999999999999999998864

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

Probab=99.53  E-value=3.5e-14  Score=120.48  Aligned_cols=83  Identities=25%  Similarity=0.483  Sum_probs=75.8

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ..++++|-|.||+.+++|++|+++|..||.|..+.+.+| .+|.+||||||.|.++++|++||+.|||.- +  .++-|+
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~g-y--d~LILr  262 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYG-Y--DNLILR  262 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcc-c--ceEEEE
Confidence            335789999999999999999999999999999999999 599999999999999999999999999965 3  448899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+|++++
T Consensus       263 vEwskP~  269 (270)
T KOG0122|consen  263 VEWSKPS  269 (270)
T ss_pred             EEecCCC
Confidence            9999864

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=2.7e-14  Score=115.33  Aligned_cols=80  Identities=23%  Similarity=0.401  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..-.++||||||+.++++.||..+|..||+|.+|+|-+.+     -|||||||+|..+|++|+..|+++. +++  ..++
T Consensus         7 ~~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~-~cG--~r~r   78 (195)
T KOG0107|consen    7 RNGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKD-ICG--SRIR   78 (195)
T ss_pred             cCCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCcc-ccC--ceEE
Confidence            3458999999999999999999999999999999998854     4899999999999999999999988 555  6777


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |..+....
T Consensus        79 VE~S~G~~   86 (195)
T KOG0107|consen   79 VELSTGRP   86 (195)
T ss_pred             EEeecCCc
Confidence            77665443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.52  E-value=4.5e-14  Score=100.95  Aligned_cols=66  Identities=32%  Similarity=0.593  Sum_probs=59.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        17 lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      |||+|||+++++++|+++|+.||.|..+.+.+++. ++.+|+|||+|.+.++|.+|++.+++.. +.|
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~-~~g   66 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKE-IDG   66 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEE-ETT
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcE-ECC
Confidence            79999999999999999999999999999999988 8999999999999999999999986544 444

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.51  E-value=5.5e-14  Score=123.91  Aligned_cols=79  Identities=24%  Similarity=0.441  Sum_probs=71.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|+|.|||....|.||+..|++||.|.+|+|+++.-| ||||+||+|++.+||++|-++|||.. ++|  ++|+|..|
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~-VEG--RkIEVn~A  171 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTV-VEG--RKIEVNNA  171 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcce-eec--eEEEEecc
Confidence            678999999999999999999999999999999998655 49999999999999999999999987 777  68888887


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ..+
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            543

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.51  E-value=3.5e-13  Score=125.83  Aligned_cols=157  Identities=21%  Similarity=0.368  Sum_probs=115.5

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCC--Cccc---EEEEEeCCHHHHHHHHHHhcCC-
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR--ASRG---CCFVICPSRQEADKAVNACHNK-   79 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg--~~~G---~aFV~f~~~~~A~~Ai~~l~~~-   79 (354)
                      +..+...-+++||||+||++++|++|...|..||.+.--+-.+....+  -.+|   |+|+.|+++.++..-|.++... 
T Consensus       251 ~~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~  330 (520)
T KOG0129|consen  251 RGYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGE  330 (520)
T ss_pred             CCCCccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcc
Confidence            444556678999999999999999999999999986433322221111  2456   9999999999999888876421 


Q ss_pred             --ccCCC-----CCccceee---ccc-------cccccccceEEEecCCCCCCHHHHHHhhc-cCCCeeEEEEeeC-CCC
Q 018554           80 --KTLPG-----ASSPLQVK---YAD-------GELERLEHKLFIGMLPKNVSEAEVSALFS-IYGTIKDLQILRG-SQQ  140 (354)
Q Consensus        80 --~~~~g-----~~~~l~v~---~~~-------~~~~~~~~~l~V~~l~~~~t~~~l~~~F~-~~G~v~~i~i~~~-~~~  140 (354)
                        .++.-     +.+.++|.   .++       .......+|||||+|+--++.++|..+|+ .||.|..+-|-.| +-.
T Consensus       331 ~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~K  410 (520)
T KOG0129|consen  331 GNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLK  410 (520)
T ss_pred             cceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccC
Confidence              10100     11112221   111       11223378999999999999999999997 8999999999999 567


Q ss_pred             CcceEEEEEeCCHHHHHHHHHH
Q 018554          141 TSKGCAFLKYETKEQALAALEA  162 (354)
Q Consensus       141 ~~~g~afV~f~~~~~A~~Ai~~  162 (354)
                      -.+|-|-|+|++..+-.+||++
T Consensus       411 YPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  411 YPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCCcceeeecccHHHHHHHhh
Confidence            7899999999999999999975

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=1.1e-13  Score=131.28  Aligned_cols=172  Identities=20%  Similarity=0.374  Sum_probs=129.5

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||++||...+++.++++.+.||.+....++.|..+|-++||||.+|.|....+.|+..|||+.+. +  +
T Consensus       283 t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lg-d--~  359 (500)
T KOG0120|consen  283 TDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLG-D--K  359 (500)
T ss_pred             cCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhc-C--c
Confidence            345567789999999999999999999999999999999999999999999999999999999999999998853 3  3


Q ss_pred             cceeeccccccc--c-----------------------ccceEEEecC--CCCC-CH-------HHHHHhhccCCCeeEE
Q 018554           88 PLQVKYADGELE--R-----------------------LEHKLFIGML--PKNV-SE-------AEVSALFSIYGTIKDL  132 (354)
Q Consensus        88 ~l~v~~~~~~~~--~-----------------------~~~~l~V~~l--~~~~-t~-------~~l~~~F~~~G~v~~i  132 (354)
                      .|.|..+-....  .                       ....|...|+  +.++ ++       |+|+..+++||.|..|
T Consensus       360 ~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v  439 (500)
T KOG0120|consen  360 KLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSV  439 (500)
T ss_pred             eeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEE
Confidence            444433211000  0                       0112222221  0111 11       3467788899999999


Q ss_pred             EEeeC-CCC---CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChH
Q 018554          133 QILRG-SQQ---TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       133 ~i~~~-~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~  185 (354)
                      .|.++ ...   ...|..||+|.+.+++++|.++|+|.. +++  +.|..+|-+..+
T Consensus       440 ~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrK-F~n--RtVvtsYydeDk  493 (500)
T KOG0120|consen  440 EIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRK-FAN--RTVVASYYDEDK  493 (500)
T ss_pred             ecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCce-eCC--cEEEEEecCHHH
Confidence            99987 433   335899999999999999999999986 555  677888776553

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.50  E-value=9.5e-14  Score=121.41  Aligned_cols=76  Identities=14%  Similarity=0.166  Sum_probs=67.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .++|||+||++++||++|+++|+.||+|++|.|++|+.   .+|||||+|.+.++|++||. |++.. +.+  +.|+|.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~-l~g--r~V~Vt~   76 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGAT-IVD--QSVTITP   76 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCe-eCC--ceEEEEe
Confidence            68999999999999999999999999999999999864   57899999999999999995 87766 555  7788887


Q ss_pred             ccc
Q 018554           94 ADG   96 (354)
Q Consensus        94 ~~~   96 (354)
                      ++.
T Consensus        77 a~~   79 (260)
T PLN03120         77 AED   79 (260)
T ss_pred             ccC
Confidence            653

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.50  E-value=5.5e-14  Score=123.93  Aligned_cols=88  Identities=28%  Similarity=0.469  Sum_probs=75.1

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      .++.....++|+|.|||+..-|-||+..|++||+|.+|.||-+.  .-||||+||+|++.+||++|.++||+.. +.|  
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~-VEG--  163 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTV-VEG--  163 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcce-eec--
Confidence            34455667899999999999999999999999999999998864  3489999999999999999999999977 566  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|.|..+..+..
T Consensus       164 RkIEVn~ATarV~  176 (376)
T KOG0125|consen  164 RKIEVNNATARVH  176 (376)
T ss_pred             eEEEEeccchhhc
Confidence            7778877655443

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

Probab=99.49  E-value=8.9e-14  Score=121.15  Aligned_cols=82  Identities=20%  Similarity=0.385  Sum_probs=73.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+-+||||+-|+.+++|.+|++.|+.||+|+.|.|++|+.||+++|||||+|+++.+...|.+..++.. |++  +.|
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~-Idg--rri  173 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIK-IDG--RRI  173 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCce-ecC--cEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999998766 666  555


Q ss_pred             eeecc
Q 018554           90 QVKYA   94 (354)
Q Consensus        90 ~v~~~   94 (354)
                      -|.+-
T Consensus       174 ~VDvE  178 (335)
T KOG0113|consen  174 LVDVE  178 (335)
T ss_pred             EEEec
Confidence            55543

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.47  E-value=6.1e-14  Score=116.03  Aligned_cols=85  Identities=28%  Similarity=0.419  Sum_probs=76.9

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+.+...+|-|-||-..++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|.+..+|++|+++|++.. ++|  +
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~-ldg--R   83 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAV-LDG--R   83 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhccee-ecc--c
Confidence            4566778899999999999999999999999999999999999999999999999999999999999998865 666  7


Q ss_pred             cceeeccc
Q 018554           88 PLQVKYAD   95 (354)
Q Consensus        88 ~l~v~~~~   95 (354)
                      .|.|++++
T Consensus        84 elrVq~ar   91 (256)
T KOG4207|consen   84 ELRVQMAR   91 (256)
T ss_pred             eeeehhhh
Confidence            77777654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.47  E-value=2.4e-13  Score=118.87  Aligned_cols=75  Identities=15%  Similarity=0.299  Sum_probs=67.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||++.+|+++|+++|+.||+|++|+|+++..  .+|||||+|++.++|..|+. |||.. +.|  +.|+|.++
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~-l~g--r~V~Vt~a   77 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGAT-IVD--QSVTITPA   77 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCe-eCC--ceEEEEec
Confidence            46899999999999999999999999999999998853  47999999999999999995 99977 555  67888887


Q ss_pred             C
Q 018554          182 D  182 (354)
Q Consensus       182 ~  182 (354)
                      +
T Consensus        78 ~   78 (260)
T PLN03120         78 E   78 (260)
T ss_pred             c
Confidence            5

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.46  E-value=5e-13  Score=95.49  Aligned_cols=67  Identities=30%  Similarity=0.697  Sum_probs=60.2

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS  172 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  172 (354)
                      |||+|||+++++++|+++|+.||.|..+.+.+++++.++++|||+|.+.++|.+|++.+++.. ++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~-~~g~   67 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKE-IDGR   67 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEE-ETTE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcE-ECCE
Confidence            799999999999999999999999999999998778899999999999999999999988765 6663

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 ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.45  E-value=2.7e-13  Score=125.37  Aligned_cols=81  Identities=20%  Similarity=0.318  Sum_probs=69.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCH--HHHHHHHHHhcCCccCCCCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR--QEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~--~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      +......+||||||+++++++||+.+|..||.|.+|.|+++  ||  ||||||+|.+.  +++.+||+.|++..+ .|  
T Consensus         5 es~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEW-KG--   77 (759)
T PLN03213          5 SSGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVW-KG--   77 (759)
T ss_pred             ccCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCee-cC--
Confidence            34456689999999999999999999999999999999954  56  89999999987  789999999998774 44  


Q ss_pred             ccceeecccc
Q 018554           87 SPLQVKYADG   96 (354)
Q Consensus        87 ~~l~v~~~~~   96 (354)
                      +.|+|..+++
T Consensus        78 R~LKVNKAKP   87 (759)
T PLN03213         78 GRLRLEKAKE   87 (759)
T ss_pred             ceeEEeeccH
Confidence            7888887753

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.44  E-value=2.6e-13  Score=109.66  Aligned_cols=76  Identities=25%  Similarity=0.502  Sum_probs=66.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++||||||+..+++.||..+|..||.|..|.|-+..    .|||||+|++..+|+.|+..|+|+. |.|  ..|.|++.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~-~cG--~r~rVE~S   82 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKD-ICG--SRIRVELS   82 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCcc-ccC--ceEEEEee
Confidence            5899999999999999999999999999999998753    6899999999999999999999988 555  56777766


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ...
T Consensus        83 ~G~   85 (195)
T KOG0107|consen   83 TGR   85 (195)
T ss_pred             cCC
Confidence            443

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

Probab=99.44  E-value=2.4e-13  Score=104.17  Aligned_cols=82  Identities=24%  Similarity=0.475  Sum_probs=71.7

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      +.+++|||+||+..++||.|.++|+++|+|..|.+=.|+ +...-|||||+|.+.++|..|++-++|.. ++.  +.|++
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgtr-Ldd--r~ir~  110 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTR-LDD--RPIRI  110 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCc-ccc--cceee
Confidence            347899999999999999999999999999999988774 55667999999999999999999999987 555  68888


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .|.-.-
T Consensus       111 D~D~GF  116 (153)
T KOG0121|consen  111 DWDAGF  116 (153)
T ss_pred             eccccc
Confidence            886443

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

Probab=99.42  E-value=5.7e-13  Score=116.19  Aligned_cols=80  Identities=29%  Similarity=0.496  Sum_probs=71.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .-+||||+.|+++++|.+|+..|+.||.|+.|.|++| -+|+++|||||+|+++.+...|.+..+|.. |+|+.+.|.|+
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~-Idgrri~VDvE  178 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIK-IDGRRILVDVE  178 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCce-ecCcEEEEEec
Confidence            4689999999999999999999999999999999999 599999999999999999999999999976 88864444444


Q ss_pred             ec
Q 018554          180 WA  181 (354)
Q Consensus       180 ~a  181 (354)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            33

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.42  E-value=1e-11  Score=120.71  Aligned_cols=79  Identities=27%  Similarity=0.600  Sum_probs=70.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++|||||+|+.+++|+||+++|+.||+|++|.++..     |+||||++.++++|.+|+.+|++..+   ..+.|+|+||
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv---~~k~Iki~Wa  492 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKV---ADKTIKIAWA  492 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccc---cceeeEEeee
Confidence            779999999999999999999999999999999976     99999999999999999999997554   3478999999


Q ss_pred             CChHHHH
Q 018554          182 DTEKERQ  188 (354)
Q Consensus       182 ~~~~~~~  188 (354)
                      ..+..+.
T Consensus       493 ~g~G~ks  499 (894)
T KOG0132|consen  493 VGKGPKS  499 (894)
T ss_pred             ccCCcch
Confidence            7665443

>smart00362 RRM_2 RNA recognition motif

Probab=99.41  E-value=1.4e-12  Score=92.74  Aligned_cols=63  Identities=38%  Similarity=0.641  Sum_probs=59.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      +|||+|||.++++++|+++|++||.|.++.+.+++  +.++|+|||+|.+.++|++|++.+++..
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~   63 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTK   63 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcE
Confidence            59999999999999999999999999999999887  7789999999999999999999998755

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.40  E-value=1.2e-12  Score=112.77  Aligned_cols=74  Identities=14%  Similarity=0.162  Sum_probs=63.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ...+|||+||++++||++|+++|+.||+|++|+|++|.   +.+|||||+|+++++|+.|+ .|+|..+ .+  ..|.|.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l-~d--~~I~It   76 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATI-VD--QRVCIT   76 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCee-CC--ceEEEE
Confidence            45899999999999999999999999999999999994   45689999999999999999 6777774 33  456655


Q ss_pred             c
Q 018554           93 Y   93 (354)
Q Consensus        93 ~   93 (354)
                      .
T Consensus        77 ~   77 (243)
T PLN03121         77 R   77 (243)
T ss_pred             e
Confidence            4

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.40  E-value=5.7e-13  Score=125.87  Aligned_cols=82  Identities=26%  Similarity=0.466  Sum_probs=76.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      +.|||||||++++|++|.++|++.|.|.+++++.|+.||+.+||||++|.+.++|.+|++.|++.. +.+  +.|+|.|+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~-~~g--r~l~v~~~   95 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAE-FNG--RKLRVNYA   95 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcc-cCC--ceEEeecc
Confidence            999999999999999999999999999999999999999999999999999999999999999877 444  89999998


Q ss_pred             ccccc
Q 018554           95 DGELE   99 (354)
Q Consensus        95 ~~~~~   99 (354)
                      ..+..
T Consensus        96 ~~~~~  100 (435)
T KOG0108|consen   96 SNRKN  100 (435)
T ss_pred             cccch
Confidence            65544

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.40  E-value=1.6e-12  Score=95.92  Aligned_cols=109  Identities=21%  Similarity=0.328  Sum_probs=81.7

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ..+-..+..+-|||.|||+++|.|+..++|.+||.|..|+|-.++.   .+|-|||.|+|..+|++|++.|.+-.+ .  
T Consensus        10 ~~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~-~--   83 (124)
T KOG0114|consen   10 NIRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNV-D--   83 (124)
T ss_pred             CCCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhccccc-C--
Confidence            3344677889999999999999999999999999999999977654   679999999999999999999988664 3  


Q ss_pred             CccceeeccccccccccceEEEecCCCCCCHHHHHHhhccCC
Q 018554           86 SSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYG  127 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G  127 (354)
                      .+.+.|-+..+.....       -+...-.+++|..+=++||
T Consensus        84 ~ryl~vlyyq~~~~~~-------~~~~~k~~~~l~~~~~ky~  118 (124)
T KOG0114|consen   84 NRYLVVLYYQPEDAFK-------LMDSRKAREELSILKEKYG  118 (124)
T ss_pred             CceEEEEecCHHHHHH-------HHHhHHhhhHHHHHHHHhc
Confidence            3677776655433211       0122234555555555555

>PLN03213 repressor of silencing 3; Provisional

Probab=99.38  E-value=2.5e-12  Score=119.00  Aligned_cols=83  Identities=18%  Similarity=0.325  Sum_probs=72.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCH--HHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETK--EQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~--~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..+||||||.+.++++||+++|+.||.|.+|.|++. +|  ||||||+|.+.  .++.+||+.|||.. +.|  +.|+|.
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAE-WKG--R~LKVN   83 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCV-WKG--GRLRLE   83 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCe-ecC--ceeEEe
Confidence            568999999999999999999999999999999955 44  99999999987  78999999999987 555  689999


Q ss_pred             ecCChHHHHHH
Q 018554          180 WADTEKERQAR  190 (354)
Q Consensus       180 ~a~~~~~~~~~  190 (354)
                      .|++....+-+
T Consensus        84 KAKP~YLeRLk   94 (759)
T PLN03213         84 KAKEHYLARLK   94 (759)
T ss_pred             eccHHHHHHHH
Confidence            99887654433

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.38  E-value=4.7e-13  Score=110.82  Aligned_cols=78  Identities=29%  Similarity=0.490  Sum_probs=70.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...|-|-||.+.++.++|+.+|++||.|-+|.|.+|. +..++|||||.|.+..+|+.|+++|+|.. |+|  +.|.|.+
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~-ldg--RelrVq~   89 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAV-LDG--RELRVQM   89 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhccee-ecc--ceeeehh
Confidence            4579999999999999999999999999999999995 88999999999999999999999999976 888  5677766


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      |+
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            53

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.38  E-value=2.5e-13  Score=113.35  Aligned_cols=83  Identities=33%  Similarity=0.534  Sum_probs=76.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++||||+|..++||..|...|..||.|.+|.+..| .+++.|||+||+|+..|+|..||..+|+.. |.|  +.|+|.+
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesE-L~G--rtirVN~   86 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESE-LFG--RTIRVNL   86 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhh-hcc--eeEEEee
Confidence            578999999999999999999999999999999999 689999999999999999999999999988 555  6899999


Q ss_pred             cCChHHH
Q 018554          181 ADTEKER  187 (354)
Q Consensus       181 a~~~~~~  187 (354)
                      |++.+.+
T Consensus        87 AkP~kik   93 (298)
T KOG0111|consen   87 AKPEKIK   93 (298)
T ss_pred             cCCcccc
Confidence            9877543

>smart00360 RRM RNA recognition motif

Probab=99.38  E-value=2.4e-12  Score=91.06  Aligned_cols=62  Identities=35%  Similarity=0.644  Sum_probs=58.5

Q ss_pred             EcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554           19 VGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        19 Vg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      |+|||.++++++|+++|+.||.|.++.+..++.+++++|+|||+|.+.++|.+|++.+++..
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~   62 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKE   62 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCe
Confidence            68999999999999999999999999999998889999999999999999999999997654

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.38  E-value=1.2e-13  Score=112.01  Aligned_cols=103  Identities=26%  Similarity=0.464  Sum_probs=80.3

Q ss_pred             HHHHHhcCCccCCCCCccceeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEE
Q 018554           71 KAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLK  149 (354)
Q Consensus        71 ~Ai~~l~~~~~~~g~~~~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~  149 (354)
                      +-|+.||.+.+-.|  ..-+++|...-+  .+.-||||||++++||.||.-+|++||+|.+|.+++| .+|+|+||||+.
T Consensus         8 k~i~~lne~Elq~g--~~~~~SWH~~Yk--dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLc   83 (219)
T KOG0126|consen    8 KNIQKLNERELQLG--IADKKSWHQEYK--DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLC   83 (219)
T ss_pred             HHHHHhhHHhhccc--cccccchhhhcc--cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEE
Confidence            34556655543333  222445543322  2567999999999999999999999999999999999 599999999999


Q ss_pred             eCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          150 YETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       150 f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      |++..+..-|+..|||.. +.|  +.|+|..
T Consensus        84 YEDQRSTILAVDN~NGik-i~g--RtirVDH  111 (219)
T KOG0126|consen   84 YEDQRSTILAVDNLNGIK-ILG--RTIRVDH  111 (219)
T ss_pred             ecCccceEEEEeccCCce-ecc--eeEEeee
Confidence            999999999999999976 555  4566654

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.36  E-value=1.7e-13  Score=114.44  Aligned_cols=139  Identities=20%  Similarity=0.264  Sum_probs=117.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ..+..+||||+|+...++||-|.++|-+-|+|..|.|..++. ++.+ ||||.|+++.++..|++.+|+..+ .+  ..+
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l-~~--~e~   79 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDL-EE--DEE   79 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchh-cc--chh
Confidence            456789999999999999999999999999999999988876 5555 999999999999999999988664 33  344


Q ss_pred             eeeccccccccccceEEEec----CCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554           90 QVKYADGELERLEHKLFIGM----LPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus        90 ~v~~~~~~~~~~~~~l~V~~----l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      ++            +++.|+    |...++++.+.+.|+.-|.++.+++.++.+++.+.+.|+++-...+.-.++..-.+
T Consensus        80 q~------------~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~  147 (267)
T KOG4454|consen   80 QR------------TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQG  147 (267)
T ss_pred             hc------------ccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcc
Confidence            43            466677    88899999999999999999999999998899999999988776666666654433

>smart00362 RRM_2 RNA recognition motif

Probab=99.36  E-value=5.1e-12  Score=89.72  Aligned_cols=71  Identities=42%  Similarity=0.776  Sum_probs=63.5

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      +|||+||+.++++++|+++|..||.|.++.+.++. +.++++|||+|.+.++|++|++.+++.. ++|  +.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~-~~~--~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTK-LGG--RPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcE-ECC--EEEee
Confidence            58999999999999999999999999999999877 6778999999999999999999999866 555  45554

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.36  E-value=1.1e-11  Score=91.62  Aligned_cols=84  Identities=29%  Similarity=0.434  Sum_probs=70.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .+.|||.|||.++|.|++.++|.+||.|..|+|=-..  .-+|-|||.|++..+|.+|++.|+|..+ +  .+-|.|-+-
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~-~--~ryl~vlyy   92 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNV-D--NRYLVVLYY   92 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhccccc-C--CceEEEEec
Confidence            4679999999999999999999999999999986542  2289999999999999999999999874 4  477888887


Q ss_pred             CChHHHHHH
Q 018554          182 DTEKERQAR  190 (354)
Q Consensus       182 ~~~~~~~~~  190 (354)
                      ...+..+..
T Consensus        93 q~~~~~~~~  101 (124)
T KOG0114|consen   93 QPEDAFKLM  101 (124)
T ss_pred             CHHHHHHHH
Confidence            766555433

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.34  E-value=7.5e-13  Score=110.56  Aligned_cols=87  Identities=25%  Similarity=0.407  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++||||+|-.+++|..|...|-.||.|.+|.+..|..+++.|||+||+|...|+|..||..+|+.. +.|  +.|+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesE-L~G--rtir   83 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESE-LFG--RTIR   83 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhh-hcc--eeEE
Confidence            4567999999999999999999999999999999999999999999999999999999999999998877 555  8899


Q ss_pred             eecccccccc
Q 018554           91 VKYADGELER  100 (354)
Q Consensus        91 v~~~~~~~~~  100 (354)
                      |.++++.+-+
T Consensus        84 VN~AkP~kik   93 (298)
T KOG0111|consen   84 VNLAKPEKIK   93 (298)
T ss_pred             EeecCCcccc
Confidence            9998876543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.34  E-value=8.2e-12  Score=112.31  Aligned_cols=165  Identities=20%  Similarity=0.254  Sum_probs=117.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhh---c-CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccC-----
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKE---F-ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTL-----   82 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~---~-G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~-----   82 (354)
                      ++..-|-+++||+++++.|+.++|..   . |-++.|..++..+ ||..|-|||.|..+++|+.|+.+-  +..+     
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpd-grpTGdAFvlfa~ee~aq~aL~kh--rq~iGqRYI  235 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPD-GRPTGDAFVLFACEEDAQFALRKH--RQNIGQRYI  235 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCC-CCcccceEEEecCHHHHHHHHHHH--HHHHhHHHH
Confidence            44566788999999999999999952   2 2456666666544 899999999999999999998752  1111     


Q ss_pred             -----------------------CCCCcccee--eccccccccccceEEEecCCCCCCHHHHHHhhccCCC-eeE--EEE
Q 018554           83 -----------------------PGASSPLQV--KYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGT-IKD--LQI  134 (354)
Q Consensus        83 -----------------------~g~~~~l~v--~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~-v~~--i~i  134 (354)
                                             .+....+--  -.......+...+|-+++||++.+.|||.++|..|-. |+.  |.+
T Consensus       236 ElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHm  315 (508)
T KOG1365|consen  236 ELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHM  315 (508)
T ss_pred             HHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEE
Confidence                                   111111100  0000011122568999999999999999999998864 444  788


Q ss_pred             eeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       135 ~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      +.+..|+..|-|||+|.+.|+|..|..+.+.+. .  +.+-|+|--+.
T Consensus       316 v~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~-m--k~RYiEvfp~S  360 (508)
T KOG1365|consen  316 VLNGQGRPSGEAFIQMRNAERARAAAQKCHKKL-M--KSRYIEVFPCS  360 (508)
T ss_pred             EEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhh-c--ccceEEEeecc
Confidence            888899999999999999999999988777654 3  33445554443

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.33  E-value=2.1e-12  Score=99.82  Aligned_cols=81  Identities=23%  Similarity=0.377  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      +.+.--|||.++...++|++|.+.|..||+|++|.+-.|+.||-.+|||.|+|++.+.|.+|++++|+..++ +  ..+.
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll-~--q~v~  145 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELL-G--QNVS  145 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhh-C--Ccee
Confidence            444556999999999999999999999999999999999999999999999999999999999999987754 4  5666


Q ss_pred             eecc
Q 018554           91 VKYA   94 (354)
Q Consensus        91 v~~~   94 (354)
                      |.|+
T Consensus       146 VDw~  149 (170)
T KOG0130|consen  146 VDWC  149 (170)
T ss_pred             EEEE
Confidence            6665

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.33  E-value=4.8e-12  Score=116.02  Aligned_cols=81  Identities=28%  Similarity=0.495  Sum_probs=74.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .|-||||.||.++.|+||.-+|++.|+|-+++++.| .+|.+||||||+|.+.++|++||+.||+..+-.|+.+.+.|+.
T Consensus        83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             CceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            688999999999999999999999999999999999 6899999999999999999999999999988788666666665


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      ++
T Consensus       163 an  164 (506)
T KOG0117|consen  163 AN  164 (506)
T ss_pred             ec
Confidence            53

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.31  E-value=1.2e-11  Score=106.62  Aligned_cols=74  Identities=16%  Similarity=0.232  Sum_probs=64.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..+|||+||++.+|+++|+++|+.||+|++|+|++|  +..+++|||+|+++++|+.|+ .|+|..+ .+  ..|.|..+
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l-~d--~~I~It~~   78 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATI-VD--QRVCITRW   78 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCee-CC--ceEEEEeC
Confidence            368999999999999999999999999999999988  344689999999999999999 6999875 44  45777654

>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=99.30  E-value=2.3e-11  Score=86.79  Aligned_cols=73  Identities=41%  Similarity=0.719  Sum_probs=63.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +|+|+|||.++++++|+++|+.+|.|..+.+..+..+ +.+|+|||+|.+.++|..|++.+++.. +.+  +.+.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~-~~~--~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKE-LGG--RPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEe
Confidence            5899999999999999999999999999999998765 778999999999999999999998755 333  455443

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).

>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=99.28  E-value=3.7e-11  Score=85.68  Aligned_cols=74  Identities=43%  Similarity=0.802  Sum_probs=65.9

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      +|+|++|+..+++++|+++|..||.|..+.+..+.....+++|||+|.+.++|..|++.+++.. ++|  ..+.|++
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~-~~~--~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKE-LGG--RPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEeC
Confidence            4899999999999999999999999999999998766778999999999999999999999976 555  5666653

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).

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.27  E-value=8.2e-12  Score=96.59  Aligned_cols=80  Identities=26%  Similarity=0.472  Sum_probs=71.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .-.|||.++....||++|.+.|..||+|+.|.+-.| ++|-.+|||+|+|++.++|++|++++||..+++   ..|.|.|
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~---q~v~VDw  148 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG---QNVSVDW  148 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC---CceeEEE
Confidence            447999999999999999999999999999999988 699999999999999999999999999988654   3678888


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +-.+
T Consensus       149 ~Fv~  152 (170)
T KOG0130|consen  149 CFVK  152 (170)
T ss_pred             EEec
Confidence            7433

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.27  E-value=1.2e-11  Score=116.90  Aligned_cols=88  Identities=25%  Similarity=0.456  Sum_probs=78.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +.+||||++++++||+|.++|+..|.|.+++++.| .+|+.|||+|++|.+.++|.+|++.|||.. +.|  ++|+|.|+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~-~~g--r~l~v~~~   95 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAE-FNG--RKLRVNYA   95 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcc-cCC--ceEEeecc
Confidence            78999999999999999999999999999999999 589999999999999999999999999987 555  79999999


Q ss_pred             CChHHHHHHHHH
Q 018554          182 DTEKERQARRAQ  193 (354)
Q Consensus       182 ~~~~~~~~~~~~  193 (354)
                      ...+.+...+..
T Consensus        96 ~~~~~~~~~~~~  107 (435)
T KOG0108|consen   96 SNRKNAERSLAS  107 (435)
T ss_pred             cccchhHHHHhh
Confidence            877665544433

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.25  E-value=3.3e-10  Score=101.85  Aligned_cols=156  Identities=17%  Similarity=0.197  Sum_probs=125.0

Q ss_pred             CCeEEEcCC--CCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           14 RVKLFVGQV--PKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        14 ~~~lfVg~L--p~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...|.+.=|  =.-+|-+.|..+....|+|..|.|++.  +|   -.|.|||++.+.|++|.++|||..+..| -+.|++
T Consensus       120 N~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsG-CCTLKI  193 (494)
T KOG1456|consen  120 NKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSG-CCTLKI  193 (494)
T ss_pred             CeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhccccccccc-ceeEEE
Confidence            333444433  367899999999999999999999885  23   2599999999999999999999987666 578899


Q ss_pred             eccccccccc----------------------------------------------------------------------
Q 018554           92 KYADGELERL----------------------------------------------------------------------  101 (354)
Q Consensus        92 ~~~~~~~~~~----------------------------------------------------------------------  101 (354)
                      .|+++.+...                                                                      
T Consensus       194 eyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~  273 (494)
T KOG1456|consen  194 EYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYR  273 (494)
T ss_pred             EecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccc
Confidence            8886554321                                                                      


Q ss_pred             -------------cceEEEecCC-CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 018554          102 -------------EHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus       102 -------------~~~l~V~~l~-~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                                   .+.+.|-+|. ..++-+.|.++|=.||.|++|++++.+    .|-|.|++.|..+.++|+..||+..
T Consensus       274 ~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~  349 (494)
T KOG1456|consen  274 DGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIP  349 (494)
T ss_pred             cCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCc
Confidence                         3568888997 457788899999999999999999875    3579999999999999999999987


Q ss_pred             ccCCCceeEEEEecC
Q 018554          168 KMEGSSVPLVVKWAD  182 (354)
Q Consensus       168 ~~~g~~~~l~v~~a~  182 (354)
                      + .|.  +|.|.+.+
T Consensus       350 l-fG~--kl~v~~Sk  361 (494)
T KOG1456|consen  350 L-FGG--KLNVCVSK  361 (494)
T ss_pred             c-ccc--eEEEeecc
Confidence            5 453  56666543

>smart00360 RRM RNA recognition motif

Probab=99.24  E-value=3.9e-11  Score=84.79  Aligned_cols=69  Identities=45%  Similarity=0.803  Sum_probs=60.8

Q ss_pred             EecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          107 IGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       107 V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      |+||+..+++++|+++|+.||.|.++.+..+. ++.++++|||+|.+.++|.+|++.+++.. ++|  ..|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~-~~~--~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKE-LDG--RPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCe-eCC--cEEEe
Confidence            57899999999999999999999999999885 58889999999999999999999999866 555  44544

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.23  E-value=6.7e-12  Score=123.82  Aligned_cols=168  Identities=20%  Similarity=0.254  Sum_probs=139.3

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+...+++||+|||+..+++.+|+..|..+|.|.+|.|.+-+. ++..-|+||.|.+.+.+-.|...+.+..+..+   
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g---  441 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNG---  441 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccC---
Confidence            34667889999999999999999999999999999999877643 44445999999999999999888866554443   


Q ss_pred             cceeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 018554           88 PLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus        88 ~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                      .+++.+... +....+.+||++|..++....|...|..||.|..|.+-..     .-|++|.|++...|+.|++.+.|..
T Consensus       442 ~~r~glG~~-kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap  515 (975)
T KOG0112|consen  442 THRIGLGQP-KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAP  515 (975)
T ss_pred             ccccccccc-ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCc
Confidence            444444433 3444678999999999999999999999999999887754     4599999999999999999999987


Q ss_pred             ccCCCceeEEEEecCChHH
Q 018554          168 KMEGSSVPLVVKWADTEKE  186 (354)
Q Consensus       168 ~~~g~~~~l~v~~a~~~~~  186 (354)
                       +.+-.+++.|.||.....
T Consensus       516 -~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  516 -LGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             -CCCCCcccccccccCCCC
Confidence             777778899999987643

>smart00361 RRM_1 RNA recognition motif

Probab=99.22  E-value=4.3e-11  Score=85.38  Aligned_cols=56  Identities=20%  Similarity=0.372  Sum_probs=49.8

Q ss_pred             HHHHHHHHh----hcCCeeEEE-EeeCCCC--CCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           28 EAQLLAMFK----EFALVDEVN-IIKDKTT--RASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        28 e~~L~~~F~----~~G~v~~i~-i~~d~~t--g~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      +++|+++|+    +||.|.+|. |+.|+.+  ++++|||||+|.+.++|.+|++.||++. +.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~-~~g   64 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRY-FDG   64 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            678999998    999999996 7788777  8999999999999999999999999866 444

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=2.8e-11  Score=115.15  Aligned_cols=160  Identities=26%  Similarity=0.427  Sum_probs=123.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhc-----------C-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEF-----------A-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHN   78 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~-----------G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~   78 (354)
                      ....+.++|++|+..++++++..+|..-           | .|..+.+-.++      .|||++|.+.++|..|+... +
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~at~~~~~~-~  244 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEATEAMALD-G  244 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCchhhhhccc-c
Confidence            4567889999999999999999999764           4 36677665554      49999999999999987542 2


Q ss_pred             CccCCCCCccceee------------------------ccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEE
Q 018554           79 KKTLPGASSPLQVK------------------------YADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI  134 (354)
Q Consensus        79 ~~~~~g~~~~l~v~------------------------~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i  134 (354)
                       .++.|  .++++.                        +.........+++||++|+..+++++++++.+.||.+....+
T Consensus       245 -~~f~g--~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~l  321 (500)
T KOG0120|consen  245 -IIFEG--RPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRL  321 (500)
T ss_pred             -hhhCC--CCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhhee
Confidence             11222  222221                        112222333678999999999999999999999999999999


Q ss_pred             eeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCC
Q 018554          135 LRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       135 ~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~  183 (354)
                      +.|. ++.++||||.+|.+......|+..|||..+ .+  ..|+|..|-.
T Consensus       322 v~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~l-gd--~~lvvq~A~~  368 (500)
T KOG0120|consen  322 VKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQL-GD--KKLVVQRAIV  368 (500)
T ss_pred             ecccccccccceeeeeeeCCcchhhhhcccchhhh-cC--ceeEeehhhc
Confidence            9994 689999999999999999999999999884 44  4677766543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.21  E-value=3.4e-11  Score=107.33  Aligned_cols=76  Identities=36%  Similarity=0.601  Sum_probs=69.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...+|||++|...++|.||+++|.+||+|+.|.++..     ++||||+|.++++|+.|.+++-.+.+++|  .+|.|.|
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G--~Rl~i~W  299 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVING--FRLKIKW  299 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecc--eEEEEEe
Confidence            3678999999999999999999999999999999975     67999999999999999988877787888  6899999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      +.+
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            988

>PF13893 RRM_5: RNA recognition motif

Probab=99.20  E-value=8.9e-11  Score=79.86  Aligned_cols=56  Identities=36%  Similarity=0.740  Sum_probs=49.1

Q ss_pred             HHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          119 VSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       119 l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      |+++|++||+|+++.+.++.    +++|||+|.+.++|.+|++.|||.. +.|  +.|+|+||
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----RGFAFVEFASVEDAQKAIEQLNGRQ-FNG--RPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSE-ETT--EEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEEEC
Confidence            68999999999999998764    5899999999999999999999987 555  68999885

(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 ....

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.20  E-value=1.7e-11  Score=106.68  Aligned_cols=72  Identities=33%  Similarity=0.600  Sum_probs=65.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      .+|||||||.++++.+|+.+|++||+|.+++|+       |.|+||..++...|+.||+.|+|.. |+|  +.|+|+-++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-------KNYgFVHiEdktaaedairNLhgYt-Lhg--~nInVeaSk   72 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-------KNYGFVHIEDKTAAEDAIRNLHGYT-LHG--VNINVEASK   72 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-------cccceEEeecccccHHHHhhcccce-ecc--eEEEEEecc
Confidence            479999999999999999999999999999999       5599999999999999999999976 676  677887776


Q ss_pred             Ch
Q 018554          183 TE  184 (354)
Q Consensus       183 ~~  184 (354)
                      .+
T Consensus        73 sK   74 (346)
T KOG0109|consen   73 SK   74 (346)
T ss_pred             cc
Confidence            55

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.19  E-value=3e-11  Score=98.46  Aligned_cols=78  Identities=31%  Similarity=0.469  Sum_probs=70.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..+|||+||+..++++.|.++|-+.|.|.++.|.+|+ ++..+|||||+|.++|+|+-|++.||.- .+-|  ++|+|..
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~V-kLYg--rpIrv~k   85 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMV-KLYG--RPIRVNK   85 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHH-HhcC--ceeEEEe
Confidence            5789999999999999999999999999999999995 7778999999999999999999999964 4555  6888887


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            75

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.18  E-value=1.1e-10  Score=105.52  Aligned_cols=78  Identities=38%  Similarity=0.735  Sum_probs=71.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++.+|+++|+++|..||.|..+.+..|+ ++.++|+|||+|.+.++|..|++.+++.. +.|  +.|.|.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~-~~~--~~~~v~~  191 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKE-LEG--RPLRVQK  191 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCe-ECC--ceeEeec
Confidence            4899999999999999999999999999999999994 89999999999999999999999999876 555  6788888


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      +.
T Consensus       192 ~~  193 (306)
T COG0724         192 AQ  193 (306)
T ss_pred             cc
Confidence            54

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.17  E-value=4.9e-11  Score=97.28  Aligned_cols=79  Identities=24%  Similarity=0.501  Sum_probs=67.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .+++|||+|||.++.+.||.++|.+||.|.+|.+-....  .-.||||+|++..+|+.||..-+|.. ++|  ++|+|+|
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g--~ppfafVeFEd~RDAeDAiygRdGYd-ydg--~rLRVEf   79 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPG--PPPFAFVEFEDPRDAEDAIYGRDGYD-YDG--CRLRVEF   79 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCC--CCCeeEEEecCccchhhhhhcccccc-cCc--ceEEEEe
Confidence            368899999999999999999999999999998764321  14799999999999999999999977 777  6899998


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +..-
T Consensus        80 prgg   83 (241)
T KOG0105|consen   80 PRGG   83 (241)
T ss_pred             ccCC
Confidence            7543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.16  E-value=4e-09  Score=98.39  Aligned_cols=145  Identities=20%  Similarity=0.296  Sum_probs=107.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDE-VNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~-i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .....|-+++||+.|||+||.+||+-.-.|.+ |.+..|+. +++.|-|||+|++.+.|++|+..-+  ..+..  +-|.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~rhr--e~iGh--RYIE  175 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALGRHR--ENIGH--RYIE  175 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHHHHHHHHH--Hhhcc--ceEE
Confidence            46678999999999999999999998765655 45566654 7899999999999999999997521  11111  0010


Q ss_pred             eecc-----------------------------------cccc-----cc------------------------------
Q 018554           91 VKYA-----------------------------------DGEL-----ER------------------------------  100 (354)
Q Consensus        91 v~~~-----------------------------------~~~~-----~~------------------------------  100 (354)
                      |-.+                                   ..+.     .+                              
T Consensus       176 vF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~  255 (510)
T KOG4211|consen  176 VFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGR  255 (510)
T ss_pred             eehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccc
Confidence            0000                                   0000     00                              


Q ss_pred             ------------------------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHH
Q 018554          101 ------------------------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQA  156 (354)
Q Consensus       101 ------------------------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A  156 (354)
                                              ....++.++||+..++.++.++|+..-.+ .|.|.-..+++..|-|+|+|.+.++|
T Consensus       256 ~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~eda  334 (510)
T KOG4211|consen  256 DPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDA  334 (510)
T ss_pred             ccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhh
Confidence                                    02568999999999999999999876444 77777778899999999999999999


Q ss_pred             HHHHHH
Q 018554          157 LAALEA  162 (354)
Q Consensus       157 ~~Ai~~  162 (354)
                      ..|+.+
T Consensus       335 v~Amsk  340 (510)
T KOG4211|consen  335 VGAMGK  340 (510)
T ss_pred             Hhhhcc
Confidence            999853

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.15  E-value=3.8e-11  Score=102.72  Aligned_cols=162  Identities=18%  Similarity=0.339  Sum_probs=120.8

Q ss_pred             CCCCeEEEcCCCCCCCHHH-H--HHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           12 EERVKLFVGQVPKHMTEAQ-L--LAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~-L--~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .....+|++++-.++..+- |  ...|+.+-.....+++++.. +.-++++|+.|.+...-.++-..-+++. +.  ...
T Consensus        94 P~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kk-i~--~~~  169 (290)
T KOG0226|consen   94 PAVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKK-IG--KPP  169 (290)
T ss_pred             cccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhcccccccc-cc--Ccc
Confidence            4556678888877776665 4  67788887777888888875 6778999999987766665544333333 11  122


Q ss_pred             ceeec----cccc---cccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHH
Q 018554           89 LQVKY----ADGE---LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus        89 l~v~~----~~~~---~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                      ++..-    -++.   -.....+||+|.|..+++++.|...|.+|-.....++++| ++++++||+||-|.+..++..|+
T Consensus       170 VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAm  249 (290)
T KOG0226|consen  170 VRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAM  249 (290)
T ss_pred             eeeccccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHH
Confidence            33221    1221   1223568999999999999999999999999999999999 69999999999999999999999


Q ss_pred             HHhCCCcccCCCceeEEEEe
Q 018554          161 EAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       161 ~~l~g~~~~~g~~~~l~v~~  180 (354)
                      +++||+.+   .++.|.+..
T Consensus       250 rem~gkyV---gsrpiklRk  266 (290)
T KOG0226|consen  250 REMNGKYV---GSRPIKLRK  266 (290)
T ss_pred             Hhhccccc---ccchhHhhh
Confidence            99999875   345665543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.13  E-value=6.2e-11  Score=107.57  Aligned_cols=89  Identities=31%  Similarity=0.394  Sum_probs=75.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ...+||||+||.+++|++|+++|++||.|.++.++.|+.+.+.+||+||.|.+++++++++..  ..+.+.+  +.+.|+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~--~f~~~~g--k~vevk  171 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ--KFHDFNG--KKVEVK  171 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc--ceeeecC--ceeeEe
Confidence            356999999999999999999999999999999999999999999999999999999999865  3344555  777777


Q ss_pred             ccccccccccceE
Q 018554           93 YADGELERLEHKL  105 (354)
Q Consensus        93 ~~~~~~~~~~~~l  105 (354)
                      .+.++......+.
T Consensus       172 rA~pk~~~~~~~~  184 (311)
T KOG4205|consen  172 RAIPKEVMQSTKS  184 (311)
T ss_pred             eccchhhcccccc
Confidence            7777665554444

>PF13893 RRM_5: RNA recognition motif

Probab=99.12  E-value=1.9e-10  Score=78.26  Aligned_cols=56  Identities=38%  Similarity=0.681  Sum_probs=47.7

Q ss_pred             HHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           31 LLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        31 L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      |+++|++||+|.+|.+.+++     +++|||+|.+.++|++|++.||+.. +.+  +.|+|.|+
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-----RGFAFVEFASVEDAQKAIEQLNGRQ-FNG--RPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSE-ETT--EEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEEEC
Confidence            78999999999999997765     5799999999999999999998877 555  67888764

(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 ....

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.11  E-value=2.1e-12  Score=126.83  Aligned_cols=150  Identities=21%  Similarity=0.274  Sum_probs=126.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .+..++||.||+..+.++||...|..+|.+..+++.--+++++.||+|+|+|.+.+++.+||..... .++ +       
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~-~~~-g-------  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDS-CFF-G-------  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhh-hhh-h-------
Confidence            4567899999999999999999999999988888876677899999999999999999999976432 322 2       


Q ss_pred             eccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCC
Q 018554           92 KYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEG  171 (354)
Q Consensus        92 ~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g  171 (354)
                                ..+|+|.|++...|.++|+.+|+.+|.+.++.++..+.|+.+|.++|.|.++.++.+++...+...+   
T Consensus       736 ----------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~---  802 (881)
T KOG0128|consen  736 ----------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGK---  802 (881)
T ss_pred             ----------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhh---
Confidence                      3569999999999999999999999999999999889999999999999999999999877666443   


Q ss_pred             CceeEEEEecCC
Q 018554          172 SSVPLVVKWADT  183 (354)
Q Consensus       172 ~~~~l~v~~a~~  183 (354)
                      +...+.|...++
T Consensus       803 rE~~~~v~vsnp  814 (881)
T KOG0128|consen  803 RENNGEVQVSNP  814 (881)
T ss_pred             hhcCccccccCC
Confidence            223455555554

>smart00361 RRM_1 RNA recognition motif

Probab=99.09  E-value=4.4e-10  Score=80.13  Aligned_cols=60  Identities=20%  Similarity=0.467  Sum_probs=50.4

Q ss_pred             HHHHHHhhc----cCCCeeEEE-EeeC-CC--CCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          116 EAEVSALFS----IYGTIKDLQ-ILRG-SQ--QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       116 ~~~l~~~F~----~~G~v~~i~-i~~~-~~--~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      +++|+++|+    .||.|.+|. |+.+ .+  +.++|++||+|.+.++|.+|++.|||+. ++|  +.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~-~~g--r~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRY-FDG--RTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEe
Confidence            578888888    999999995 5555 34  7889999999999999999999999986 666  55654

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.08  E-value=1.7e-10  Score=102.91  Aligned_cols=83  Identities=18%  Similarity=0.315  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+...|||..|.+-++++||.-+|+.||+|.+|.|++|+.||.+.-||||+|++.+++++|.-.+++.. +..  +.|.
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvL-IDD--rRIH  312 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVL-IDD--RRIH  312 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhccee-ecc--ceEE
Confidence            4577899999999999999999999999999999999999999999999999999999999999997744 544  7888


Q ss_pred             eecccc
Q 018554           91 VKYADG   96 (354)
Q Consensus        91 v~~~~~   96 (354)
                      |.|++.
T Consensus       313 VDFSQS  318 (479)
T KOG0415|consen  313 VDFSQS  318 (479)
T ss_pred             eehhhh
Confidence            888754

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=99.06  E-value=1.7e-08  Score=90.12  Aligned_cols=81  Identities=21%  Similarity=0.369  Sum_probs=66.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCC--CeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYG--TIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G--~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++|||||-|++|++||.+.+...|  .+.+++++.++ +|.+||||+|...+..+..+.++.|-.+. +.|.. .+.+
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~-iHGQ~-P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKT-IHGQS-PTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccce-ecCCC-Ceee
Confidence            45799999999999999999998877  58888999885 79999999999999999999999888876 66653 4455


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .+-+..
T Consensus       158 ~~NK~~  163 (498)
T KOG4849|consen  158 SYNKTN  163 (498)
T ss_pred             ccchhh
Confidence            554443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.00  E-value=4.9e-10  Score=101.39  Aligned_cols=168  Identities=18%  Similarity=0.280  Sum_probs=129.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...+++|++++.+++.+.++..++...|.+..+.+........++|++.|.|...+.+..|+.... ...+.+.....-+
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~-~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESG-SKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhh-ccccccccccCcc
Confidence            468899999999999999999999999988888877777778899999999999999999997653 2222221111111


Q ss_pred             ecccc-----cc----ccccceEE-EecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHH
Q 018554           92 KYADG-----EL----ERLEHKLF-IGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus        92 ~~~~~-----~~----~~~~~~l~-V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                      .....     ..    .....++| |++|+.++++++|+.+|..+|.|..+++..+ .++..+|+++|.|.+...+..++
T Consensus       165 ~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~  244 (285)
T KOG4210|consen  165 NTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLAL  244 (285)
T ss_pred             cccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHh
Confidence            11111     11    11144555 9999999999999999999999999999987 58899999999999999999998


Q ss_pred             HHhCCCcccCCCceeEEEEecCCh
Q 018554          161 EAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       161 ~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      .. .... +.+  +.+.+...+..
T Consensus       245 ~~-~~~~-~~~--~~~~~~~~~~~  264 (285)
T KOG4210|consen  245 ND-QTRS-IGG--RPLRLEEDEPR  264 (285)
T ss_pred             hc-ccCc-ccC--cccccccCCCC
Confidence            76 4443 444  56777776654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.96  E-value=1.7e-09  Score=91.70  Aligned_cols=80  Identities=28%  Similarity=0.521  Sum_probs=69.5

Q ss_pred             cceEEEecCCCCCCHHHHHH----hhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSA----LFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~----~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ..+|||.||.+.+..++|++    +|++||+|.+|..++  +.+.||.|||.|++.+.|..|+++|+|..+++   +.++
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg---K~mr   83 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYG---KPMR   83 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccC---chhh
Confidence            34999999999999999988    999999999998884  45669999999999999999999999987543   5888


Q ss_pred             EEecCChHH
Q 018554          178 VKWADTEKE  186 (354)
Q Consensus       178 v~~a~~~~~  186 (354)
                      |.||..+..
T Consensus        84 iqyA~s~sd   92 (221)
T KOG4206|consen   84 IQYAKSDSD   92 (221)
T ss_pred             eecccCccc
Confidence            999876543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.96  E-value=2.5e-09  Score=89.21  Aligned_cols=82  Identities=26%  Similarity=0.383  Sum_probs=69.8

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhc-CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEF-ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~-G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ........-++|..||..+.+.++..+|.+| |.|..+++-|++.||.++|||||+|++++.|.-|-+.||+-. +.+  
T Consensus        43 ~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYL-l~e--  119 (214)
T KOG4208|consen   43 KPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYL-LME--  119 (214)
T ss_pred             CCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhh-hhh--
Confidence            4455667779999999999999999999998 788888888999999999999999999999999999998754 444  


Q ss_pred             ccceee
Q 018554           87 SPLQVK   92 (354)
Q Consensus        87 ~~l~v~   92 (354)
                      +.|.+.
T Consensus       120 ~lL~c~  125 (214)
T KOG4208|consen  120 HLLECH  125 (214)
T ss_pred             heeeeE
Confidence            344443

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.95  E-value=1.5e-09  Score=97.09  Aligned_cols=87  Identities=20%  Similarity=0.376  Sum_probs=76.7

Q ss_pred             ccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCcee
Q 018554           97 ELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP  175 (354)
Q Consensus        97 ~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~  175 (354)
                      +....++.|||-.|..-+|++||.-+|+.||.|..+.|++| ++|.+-.||||+|++.+++++|.-+|++.. |+.  ++
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvL-IDD--rR  310 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVL-IDD--RR  310 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhccee-ecc--ce
Confidence            33444789999999999999999999999999999999999 689999999999999999999999999865 554  78


Q ss_pred             EEEEecCChHH
Q 018554          176 LVVKWADTEKE  186 (354)
Q Consensus       176 l~v~~a~~~~~  186 (354)
                      |.|.|..+..+
T Consensus       311 IHVDFSQSVsk  321 (479)
T KOG0415|consen  311 IHVDFSQSVSK  321 (479)
T ss_pred             EEeehhhhhhh
Confidence            99999876544

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.93  E-value=2.6e-09  Score=95.44  Aligned_cols=82  Identities=24%  Similarity=0.482  Sum_probs=72.3

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ...++....+|||++|-..++|.||++.|.+||+|+.|.++..+      +||||+|.+.++|++|.+++-++.++.|  
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G--  292 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVING--  292 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecc--
Confidence            44567788999999998899999999999999999999998754      4999999999999999998877777776  


Q ss_pred             ccceeecccc
Q 018554           87 SPLQVKYADG   96 (354)
Q Consensus        87 ~~l~v~~~~~   96 (354)
                      ..|+|.|..+
T Consensus       293 ~Rl~i~Wg~~  302 (377)
T KOG0153|consen  293 FRLKIKWGRP  302 (377)
T ss_pred             eEEEEEeCCC
Confidence            8888888877

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.92  E-value=8.8e-09  Score=97.54  Aligned_cols=69  Identities=20%  Similarity=0.375  Sum_probs=59.7

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      ..+.+-..++|+|-|||..+++++|+++|+.||+|++|+.-+     ..+|.+||+|.|..+|+.|+++|++.+
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~  136 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRRE  136 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHH
Confidence            345567889999999999999999999999999999965544     356899999999999999999987554

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.88  E-value=1.9e-08  Score=75.54  Aligned_cols=81  Identities=21%  Similarity=0.244  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhh--cCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC-CCcccee
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKE--FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG-ASSPLQV   91 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~--~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g-~~~~l~v   91 (354)
                      +||.|+|||...|.++|.+++.+  .|...-+.+..|..++.+.|||||.|.+.+.|.+..+.++|+.+-.. ..+...+
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            68999999999999999999987  46778888999999999999999999999999999999999875322 2344555


Q ss_pred             eccc
Q 018554           92 KYAD   95 (354)
Q Consensus        92 ~~~~   95 (354)
                      .||+
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6554

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.85  E-value=6.5e-09  Score=98.17  Aligned_cols=82  Identities=21%  Similarity=0.332  Sum_probs=70.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...-.+.|||.+|+..+-..||+++|++||+|.-.+|+.+..+--.|+|+||++.+.++|.+||+.||... |.|  +.|
T Consensus       401 rs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTE-LHG--rmI  477 (940)
T KOG4661|consen  401 RSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTE-LHG--RMI  477 (940)
T ss_pred             ccccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhh-hcc--eee
Confidence            35567889999999999999999999999999999999987776788999999999999999999997655 555  556


Q ss_pred             eeecc
Q 018554           90 QVKYA   94 (354)
Q Consensus        90 ~v~~~   94 (354)
                      .|..+
T Consensus       478 SVEka  482 (940)
T KOG4661|consen  478 SVEKA  482 (940)
T ss_pred             eeeec
Confidence            66554

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.81  E-value=6.7e-09  Score=89.12  Aligned_cols=80  Identities=24%  Similarity=0.443  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      -+++..+||.|.|..+++++.|-..|.+|-.....++++|+.||+++||+||.|.|.+++..|+..++++-+ .  .++|
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyV-g--srpi  262 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYV-G--SRPI  262 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccc-c--cchh
Confidence            456788999999999999999999999999889999999999999999999999999999999999988764 2  3455


Q ss_pred             eee
Q 018554           90 QVK   92 (354)
Q Consensus        90 ~v~   92 (354)
                      ++.
T Consensus       263 klR  265 (290)
T KOG0226|consen  263 KLR  265 (290)
T ss_pred             Hhh
Confidence            444

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.79  E-value=1.7e-08  Score=84.31  Aligned_cols=80  Identities=26%  Similarity=0.419  Sum_probs=68.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccC-CCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIY-GTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~-G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|..++.-+.+.++..+|.+| |.|..+++-|+ ++|.|+|||||+|++++.|.-|.+.||+.. +.+  ..|.|.
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYL-l~e--~lL~c~  125 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYL-LME--HLLECH  125 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhh-hhh--heeeeE
Confidence            5678999999999999999999888 67888888787 699999999999999999999999999975 555  456666


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      +-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            65554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.78  E-value=9.3e-08  Score=86.57  Aligned_cols=150  Identities=17%  Similarity=0.215  Sum_probs=109.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...++.-|-.++|||.-++.+|..+|.-.-.+.-...+.....|+..|++.|.|.|.|.-+.|++.  .+..+..  +.+
T Consensus        56 ~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR--hkhh~g~--ryi  131 (508)
T KOG1365|consen   56 SADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR--HKHHMGT--RYI  131 (508)
T ss_pred             ccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh--hhhhccC--Cce
Confidence            344566677889999999999999998653333333333334477779999999999999999987  3343333  445


Q ss_pred             eeeccccccc-----------------cccceEEEecCCCCCCHHHHHHhhccC----CCeeEEEEeeCCCCCcceEEEE
Q 018554           90 QVKYADGELE-----------------RLEHKLFIGMLPKNVSEAEVSALFSIY----GTIKDLQILRGSQQTSKGCAFL  148 (354)
Q Consensus        90 ~v~~~~~~~~-----------------~~~~~l~V~~l~~~~t~~~l~~~F~~~----G~v~~i~i~~~~~~~~~g~afV  148 (354)
                      .|-.+..+.-                 ...-.|-+++||+++++.|+.++|...    |.++.|-+++..+|+..|-|||
T Consensus       132 evYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFv  211 (508)
T KOG1365|consen  132 EVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFV  211 (508)
T ss_pred             eeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEE
Confidence            4443322110                 112357889999999999999999632    3567788888788999999999


Q ss_pred             EeCCHHHHHHHHHHh
Q 018554          149 KYETKEQALAALEAI  163 (354)
Q Consensus       149 ~f~~~~~A~~Ai~~l  163 (354)
                      .|..+++|+.|+.+-
T Consensus       212 lfa~ee~aq~aL~kh  226 (508)
T KOG1365|consen  212 LFACEEDAQFALRKH  226 (508)
T ss_pred             EecCHHHHHHHHHHH
Confidence            999999999999753

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.77  E-value=1e-09  Score=100.11  Aligned_cols=152  Identities=24%  Similarity=0.409  Sum_probs=118.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFAL-VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~-v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .+||++||...++.+||..+|...-. ...-.+++       .||+||.+.|...|.+|++.++++..+.|  +.+.+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-------~gyafvd~pdq~wa~kaie~~sgk~elqG--kr~e~~~   72 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQG--KRQEVEH   72 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcC--ceeeccc
Confidence            57999999999999999999986411 11111222       36999999999999999999999888877  6777776


Q ss_pred             cccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc
Q 018554           94 ADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS  173 (354)
Q Consensus        94 ~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  173 (354)
                      ...++.+ ++++-|.|++..+.++.|..+..+||.|+.+..+...  ......-|+|.+.+.+..||..|+|..+ +.  
T Consensus        73 sv~kkqr-srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~--~etavvnvty~~~~~~~~ai~kl~g~Q~-en--  146 (584)
T KOG2193|consen   73 SVPKKQR-SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTD--SETAVVNVTYSAQQQHRQAIHKLNGPQL-EN--  146 (584)
T ss_pred             hhhHHHH-hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccc--hHHHHHHHHHHHHHHHHHHHHhhcchHh-hh--
Confidence            6665554 5679999999999999999999999999998775322  1234456899999999999999999774 43  


Q ss_pred             eeEEEEec
Q 018554          174 VPLVVKWA  181 (354)
Q Consensus       174 ~~l~v~~a  181 (354)
                      ..+.|.|-
T Consensus       147 ~~~k~~Yi  154 (584)
T KOG2193|consen  147 QHLKVGYI  154 (584)
T ss_pred             hhhhcccC
Confidence            34566654

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.75  E-value=3.2e-08  Score=86.57  Aligned_cols=81  Identities=22%  Similarity=0.399  Sum_probs=71.7

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      +..+.+|+|.||+..|+++||+++|+.||.++.+.+..++.|.+.|+|-|.|+..++|.+|++.+|+ ..++|..  +.+
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g-v~ldG~~--mk~  156 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG-VALDGRP--MKI  156 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC-cccCCce--eee
Confidence            3445789999999999999999999999999999999999999999999999999999999999999 5588854  555


Q ss_pred             EecC
Q 018554          179 KWAD  182 (354)
Q Consensus       179 ~~a~  182 (354)
                      ....
T Consensus       157 ~~i~  160 (243)
T KOG0533|consen  157 EIIS  160 (243)
T ss_pred             EEec
Confidence            5443

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

Probab=98.74  E-value=2.2e-08  Score=94.68  Aligned_cols=78  Identities=18%  Similarity=0.367  Sum_probs=69.4

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||.+|...+...||+++|++||.|+-.+|+.+ ++.-.++|+||++.+.++|.+||+.|+.+. |.|  +.|.|..
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTE-LHG--rmISVEk  481 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTE-LHG--RMISVEK  481 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhh-hcc--eeeeeee
Confidence            578999999999999999999999999999999988 555569999999999999999999999887 555  6777777


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      ++
T Consensus       482 aK  483 (940)
T KOG4661|consen  482 AK  483 (940)
T ss_pred             cc
Confidence            64

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.61  E-value=1.7e-07  Score=82.10  Aligned_cols=82  Identities=24%  Similarity=0.408  Sum_probs=71.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .+...++|+|.||+..++++||+++|++||.++.+.|-.|+. |++.|.|=|.|...++|+.|++.+++ ..+.+  +.+
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~g-v~ldG--~~m  154 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNG-VALDG--RPM  154 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcC-cccCC--cee
Confidence            445568899999999999999999999999999998888885 99999999999999999999999998 44666  556


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      ++....
T Consensus       155 k~~~i~  160 (243)
T KOG0533|consen  155 KIEIIS  160 (243)
T ss_pred             eeEEec
Confidence            665443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.59  E-value=8.7e-08  Score=90.47  Aligned_cols=65  Identities=23%  Similarity=0.329  Sum_probs=55.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHH
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA   75 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~   75 (354)
                      .....+|||+|||.++++++|+++|..||.|+...|......++..+||||+|.+.+++..||++
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A  349 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA  349 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc
Confidence            34455699999999999999999999999999988766442244448999999999999999988

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.58  E-value=2.7e-07  Score=89.43  Aligned_cols=74  Identities=18%  Similarity=0.321  Sum_probs=63.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCe-eEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTI-KDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v-~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      +.|-|.|+|.+++-+||.++|..|-.+ .+|.+.++..|...|-|.|.|++.++|.+|.+.|+++.+ ..  +.|.+.
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i-~n--r~V~l~  942 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKI-RN--RVVSLR  942 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcc-cc--eeEEEE
Confidence            378999999999999999999999754 567777778899999999999999999999999999885 33  445443

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.55  E-value=2.3e-07  Score=78.30  Aligned_cols=86  Identities=26%  Similarity=0.383  Sum_probs=67.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEee-C-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR-G-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~-~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .++|||.+||.++...||..+|..|---+...+.. + ....-+-+||++|.+.++|+.|+.+|||..+--.....|+++
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            68999999999999999999998886555544433 2 233445799999999999999999999976443445678888


Q ss_pred             ecCChHHH
Q 018554          180 WADTEKER  187 (354)
Q Consensus       180 ~a~~~~~~  187 (354)
                      +|+...++
T Consensus       114 lAKSNtK~  121 (284)
T KOG1457|consen  114 LAKSNTKR  121 (284)
T ss_pred             ehhcCccc
Confidence            88766444

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.50  E-value=1.5e-07  Score=82.64  Aligned_cols=82  Identities=20%  Similarity=0.346  Sum_probs=71.8

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.+.+||+|+...++.+++...|+.||.|..|.|..|+.++.++||+||+|.+.+.+++|+. |++.. +.+  .
T Consensus        95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~-i~~--~  170 (231)
T KOG4209|consen   95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSE-IPG--P  170 (231)
T ss_pred             hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcc-ccc--c
Confidence            4567789999999999999999999999999999999999999999999999999999999999998 77766 444  4


Q ss_pred             cceeec
Q 018554           88 PLQVKY   93 (354)
Q Consensus        88 ~l~v~~   93 (354)
                      .+.+.+
T Consensus       171 ~i~vt~  176 (231)
T KOG4209|consen  171 AIEVTL  176 (231)
T ss_pred             cceeee
Confidence            454443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.50  E-value=4.8e-08  Score=82.11  Aligned_cols=79  Identities=22%  Similarity=0.315  Sum_probs=68.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +++|||+|+...++||-|.++|.+-|.|.++.|..++.++.+ ||||.|+++.+..-|++.+||.. +.+....++....
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~-l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDD-LEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccch-hccchhhcccccC
Confidence            578999999999999999999999999999999998888877 99999999999999999999976 5554444544444


Q ss_pred             C
Q 018554          182 D  182 (354)
Q Consensus       182 ~  182 (354)
                      .
T Consensus        87 ~   87 (267)
T KOG4454|consen   87 N   87 (267)
T ss_pred             C
Confidence            4

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.48  E-value=3.6e-07  Score=88.55  Aligned_cols=162  Identities=11%  Similarity=0.052  Sum_probs=116.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.+.+-+.+.+.+.++.|+++||... .|..+.|..+...+--.|-++|+|....++.+|++.-  .....  .+.++
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn--~~~~~--~R~~q  382 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRN--PSDDV--NRPFQ  382 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcC--chhhh--hccee
Confidence            3567778888999999999999999753 3556667777664444799999999999999998762  11111  12333


Q ss_pred             eecccccc----------------------------------------ccccceEEEecCCCCCCHHHHHHhhccCCCee
Q 018554           91 VKYADGEL----------------------------------------ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIK  130 (354)
Q Consensus        91 v~~~~~~~----------------------------------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~  130 (354)
                      +..+-...                                        ......|||..||..+++.++.+.|..--.|+
T Consensus       383 ~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ve  462 (944)
T KOG4307|consen  383 TGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVE  462 (944)
T ss_pred             ecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhh
Confidence            32110000                                        00145899999999999999999998777777


Q ss_pred             E-EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          131 D-LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       131 ~-i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      + |.|-+..+++.++.|||.|..++++.+|...-+. + +-| .+.|+|.-
T Consensus       463 d~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k-~-y~G-~r~irv~s  510 (944)
T KOG4307|consen  463 DFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTK-F-YPG-HRIIRVDS  510 (944)
T ss_pred             heeEeccCCcccccchhhheeccccccchhhhcccc-c-ccC-ceEEEeec
Confidence            7 7777778888899999999999999888754333 3 333 35666654

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.44  E-value=4.5e-05  Score=68.64  Aligned_cols=73  Identities=16%  Similarity=0.313  Sum_probs=63.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFA--LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G--~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ......+|||||-|.+|++||.+.+...|  .+.+++.+.++.+|.+||||.|...+..++++.++.|-.+. +.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~-iHG  151 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKT-IHG  151 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccce-ecC
Confidence            44566799999999999999999998877  47889999999999999999999999999999999885444 555

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.42  E-value=1.8e-07  Score=80.09  Aligned_cols=72  Identities=32%  Similarity=0.585  Sum_probs=64.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      .++||++|++.+.+.+|.++|..||.|.++.+.       .+|+||+|++..+|..|+..||++. +.+.  .+.|.|+.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~-l~~e--~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKE-LCGE--RLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCce-ecce--eeeeeccc
Confidence            469999999999999999999999999999988       6799999999999999999999987 5553  38888876


Q ss_pred             Ch
Q 018554          183 TE  184 (354)
Q Consensus       183 ~~  184 (354)
                      ..
T Consensus        72 ~~   73 (216)
T KOG0106|consen   72 GK   73 (216)
T ss_pred             cc
Confidence            43

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.40  E-value=6.7e-07  Score=78.48  Aligned_cols=83  Identities=17%  Similarity=0.312  Sum_probs=71.5

Q ss_pred             cccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554           96 GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus        96 ~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      .+.+.....+||+|+...+|.+++..+|+.||.|..+.|..|+ .+.+|+|+||+|.+.+.+++|+. ||+.. +.+  .
T Consensus        95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~-i~~--~  170 (231)
T KOG4209|consen   95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSE-IPG--P  170 (231)
T ss_pred             hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcc-ccc--c
Confidence            3445557889999999999999999999999999999999985 56789999999999999999998 99987 555  5


Q ss_pred             eEEEEecC
Q 018554          175 PLVVKWAD  182 (354)
Q Consensus       175 ~l~v~~a~  182 (354)
                      .+.|.+..
T Consensus       171 ~i~vt~~r  178 (231)
T KOG4209|consen  171 AIEVTLKR  178 (231)
T ss_pred             cceeeeee
Confidence            77777654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.38  E-value=4e-06  Score=79.33  Aligned_cols=76  Identities=25%  Similarity=0.358  Sum_probs=62.4

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...|||+|||.++++++|+++|..||.|+...|.... .++..+|+||+|++.++++.||++-  ...+++  ++|.|+.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As--p~~ig~--~kl~Vee  363 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS--PLEIGG--RKLNVEE  363 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC--ccccCC--eeEEEEe
Confidence            3469999999999999999999999999998887643 4555599999999999999999874  344555  6777775


Q ss_pred             c
Q 018554          181 A  181 (354)
Q Consensus       181 a  181 (354)
                      .
T Consensus       364 k  364 (419)
T KOG0116|consen  364 K  364 (419)
T ss_pred             c
Confidence            3

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.36  E-value=1.3e-06  Score=78.51  Aligned_cols=78  Identities=23%  Similarity=0.385  Sum_probs=69.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeE--------EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKD--------LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS  173 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~--------i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  173 (354)
                      ...|||.|||.++|.+++.++|++||.|..        |++.++..|.-+|=|+|.|-.+++..-|++.|++.. +.|  
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~-~rg--  210 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDE-LRG--  210 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccc-ccC--
Confidence            456999999999999999999999998654        789999999999999999999999999999999987 445  


Q ss_pred             eeEEEEecC
Q 018554          174 VPLVVKWAD  182 (354)
Q Consensus       174 ~~l~v~~a~  182 (354)
                      +.|+|..|+
T Consensus       211 ~~~rVerAk  219 (382)
T KOG1548|consen  211 KKLRVERAK  219 (382)
T ss_pred             cEEEEehhh
Confidence            678888773

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.34  E-value=5.4e-06  Score=62.28  Aligned_cols=84  Identities=15%  Similarity=0.261  Sum_probs=67.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccC--CCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC-CCceeEEE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIY--GTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKME-GSSVPLVV  178 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~--G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~-g~~~~l~v  178 (354)
                      ++|-|+|+|...|.++|.+++...  |...-+-+.-| .+..+.|||||.|.+.+.|.+..+.++|+..-. .+.+...|
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            689999999999999999998543  55666777777 577789999999999999999999999987421 24567789


Q ss_pred             EecCChHH
Q 018554          179 KWADTEKE  186 (354)
Q Consensus       179 ~~a~~~~~  186 (354)
                      .||+-...
T Consensus        82 ~yAriQG~   89 (97)
T PF04059_consen   82 SYARIQGK   89 (97)
T ss_pred             ehhHhhCH
Confidence            98865543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.31  E-value=5.4e-07  Score=85.63  Aligned_cols=65  Identities=25%  Similarity=0.436  Sum_probs=58.3

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      ....+|+|-||+..|++++|+++|+.||+|+.|+..+.    .++.+||+|.|..+|++|+++||+.++
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~  137 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREI  137 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHh
Confidence            34689999999999999999999999999999765544    378999999999999999999999884

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.22  E-value=2e-06  Score=83.73  Aligned_cols=79  Identities=19%  Similarity=0.447  Sum_probs=68.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCC----CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ----TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      .++|||+||+..++++.|...|..||.|..++|+..++.    ..+.|+||-|-++.+|++|++.|+|..+   ....++
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv---~~~e~K  250 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV---MEYEMK  250 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee---eeeeee
Confidence            679999999999999999999999999999999987542    3458999999999999999999999775   336788


Q ss_pred             EEecCC
Q 018554          178 VKWADT  183 (354)
Q Consensus       178 v~~a~~  183 (354)
                      +-|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            888754

>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=98.14  E-value=1.4e-05  Score=57.37  Aligned_cols=70  Identities=20%  Similarity=0.356  Sum_probs=47.0

Q ss_pred             ceEEEecCCCCCCHHH----HHHhhccCC-CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          103 HKLFIGMLPKNVSEAE----VSALFSIYG-TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~----l~~~F~~~G-~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ..|+|.|||.+.+...    |+++++.+| .|..|.         .+.|.|.|.+.+.|.+|.+.|+|..+++   .+|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG---~kI~   70 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFG---NKIS   70 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSS---S--E
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhccccccc---ceEE
Confidence            4689999999888665    667888886 676653         4679999999999999999999988544   3789


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |++....
T Consensus        71 v~~~~~~   77 (90)
T PF11608_consen   71 VSFSPKN   77 (90)
T ss_dssp             EESS--S
T ss_pred             EEEcCCc
Confidence            9987443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_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=98.10  E-value=1.7e-05  Score=61.01  Aligned_cols=58  Identities=24%  Similarity=0.391  Sum_probs=39.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      +.|+|.++...++.++|++.|+.||.|..|.+.+.     ...|+|.|.+.++|++|++.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~   59 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKE   59 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHh
Confidence            46889999999999999999999999999999876     34799999999999999987743

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.03  E-value=7.6e-06  Score=79.84  Aligned_cols=82  Identities=23%  Similarity=0.423  Sum_probs=68.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC---CCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT---RASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~t---g~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      +.-.+.|||+||+..++|+.|...|..||+|..|+|+.-+.-   .+.+-|+||.|-+..+|+.|++.|++..+ .  ..
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv-~--~~  247 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV-M--EY  247 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee-e--ee
Confidence            456788999999999999999999999999999999976542   34567999999999999999999988654 2  35


Q ss_pred             cceeeccc
Q 018554           88 PLQVKYAD   95 (354)
Q Consensus        88 ~l~v~~~~   95 (354)
                      .+++.|.+
T Consensus       248 e~K~gWgk  255 (877)
T KOG0151|consen  248 EMKLGWGK  255 (877)
T ss_pred             eeeecccc
Confidence            66666653

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.03  E-value=2.4e-06  Score=77.86  Aligned_cols=146  Identities=14%  Similarity=0.131  Sum_probs=102.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC---CCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT---TRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~---tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ...|-|.||...+|.+++..+|.-.|+|.++.|+....   -......|||.|.|..++..|-. |.+..+++...+.+-
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            34899999999999999999999999999999987432   12345689999999988877643 323332322100000


Q ss_pred             e------------------------------------------------------eccccccccccceEEEecCCCCCCH
Q 018554           91 V------------------------------------------------------KYADGELERLEHKLFIGMLPKNVSE  116 (354)
Q Consensus        91 v------------------------------------------------------~~~~~~~~~~~~~l~V~~l~~~~t~  116 (354)
                      +                                                      .++..+.+...++++|.+|...+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l  165 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAIL  165 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcc
Confidence            0                                                      0001111122567999999999999


Q ss_pred             HHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 018554          117 AEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI  163 (354)
Q Consensus       117 ~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l  163 (354)
                      .++-+.|..+|+|....+-....   .-+|-|.|....+...|++..
T Consensus       166 ~e~~e~f~r~Gev~ya~~ask~~---s~~c~~sf~~qts~~halr~~  209 (479)
T KOG4676|consen  166 PESGESFERKGEVSYAHTASKSR---SSSCSHSFRKQTSSKHALRSH  209 (479)
T ss_pred             hhhhhhhhhcchhhhhhhhccCC---CcchhhhHhhhhhHHHHHHhc
Confidence            99999999999998876654322   346779999888888888753

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.02  E-value=8e-06  Score=74.02  Aligned_cols=87  Identities=21%  Similarity=0.300  Sum_probs=75.4

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD--------EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~--------~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      ..+.....+|||.+|+..+++++|.++|.++|.|.        .|+|-+|+.|++.+|-|.|.|+|...|+.||+-++++
T Consensus        60 ~~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agk  139 (351)
T KOG1995|consen   60 MADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGK  139 (351)
T ss_pred             cccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccc
Confidence            34467788999999999999999999999999876        5888899999999999999999999999999999888


Q ss_pred             ccCCCCCccceeeccccc
Q 018554           80 KTLPGASSPLQVKYADGE   97 (354)
Q Consensus        80 ~~~~g~~~~l~v~~~~~~   97 (354)
                      .+ .+  ..|+|..+...
T Consensus       140 df-~g--n~ikvs~a~~r  154 (351)
T KOG1995|consen  140 DF-CG--NTIKVSLAERR  154 (351)
T ss_pred             cc-cC--CCchhhhhhhc
Confidence            74 44  67777766543

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.91  E-value=2.8e-05  Score=59.78  Aligned_cols=58  Identities=17%  Similarity=0.222  Sum_probs=39.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcC
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHN   78 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~   78 (354)
                      +-|+|.++..+++.++|++.|+.||.|..|.+.+...      -|||.|.+.++|++|++++..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~   59 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKE   59 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHh
Confidence            4688999999999999999999999999998876443      799999999999999998753

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.83  E-value=4.7e-05  Score=50.72  Aligned_cols=53  Identities=21%  Similarity=0.394  Sum_probs=42.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHH
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV   73 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai   73 (354)
                      ++.|-|.|.+.+..+. +.+.|..||+|..+.+-.+.+      +.+|+|.+..+|++||
T Consensus         1 ~~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~~~------~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPESTN------WMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCCCc------EEEEEECCHHHHHhhC
Confidence            3678899998886655 555888999999988763333      8999999999999985

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.78  E-value=0.00016  Score=51.98  Aligned_cols=68  Identities=18%  Similarity=0.343  Sum_probs=44.6

Q ss_pred             CeEEEcCCCCCCCHHHHHH----HHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           15 VKLFVGQVPKHMTEAQLLA----MFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~----~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ..|+|.|||-+.+...|+.    +++.+| +|.+|          +.+.|+|.|.+.+.|++|.+.+++..++ |  ..|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVf-G--~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVF-G--NKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SS-S--S--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccc-c--ceE
Confidence            4699999999998876654    555676 67776          2357999999999999999999887754 3  567


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      .|++..
T Consensus        70 ~v~~~~   75 (90)
T PF11608_consen   70 SVSFSP   75 (90)
T ss_dssp             EEESS-
T ss_pred             EEEEcC
Confidence            777653

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.71  E-value=8e-05  Score=49.57  Aligned_cols=52  Identities=27%  Similarity=0.491  Sum_probs=42.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHH
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL  160 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai  160 (354)
                      +.|-|.+.+.+..+ +|..+|..||+|.++.+...     ..+.+|+|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            45778888877554 46669999999999888733     558999999999999985

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.71  E-value=3.2e-05  Score=70.29  Aligned_cols=86  Identities=21%  Similarity=0.348  Sum_probs=70.6

Q ss_pred             ccCCCCCCeEE-EcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            8 KKSSEERVKLF-VGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lf-Vg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      +.......++| |++|+.++++++|+..|..+|.|..+++..+..++.++||++|+|.+..++..++.. .... +.+  
T Consensus       178 ~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~-~~~--  253 (285)
T KOG4210|consen  178 RLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRS-IGG--  253 (285)
T ss_pred             ccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCc-ccC--
Confidence            44455566666 999999999999999999999999999999999999999999999999999999875 3333 444  


Q ss_pred             ccceeeccccc
Q 018554           87 SPLQVKYADGE   97 (354)
Q Consensus        87 ~~l~v~~~~~~   97 (354)
                      +++.+.+.+..
T Consensus       254 ~~~~~~~~~~~  264 (285)
T KOG4210|consen  254 RPLRLEEDEPR  264 (285)
T ss_pred             cccccccCCCC
Confidence            66666665544

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.67  E-value=9e-05  Score=70.80  Aligned_cols=74  Identities=19%  Similarity=0.186  Sum_probs=60.6

Q ss_pred             CCCCCCeEEEcCCCCCC--C----HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554           10 SSEERVKLFVGQVPKHM--T----EAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~--t----e~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ++.-...|+|-|+|.--  .    ..-|.++|+++|+|....+..|..+| ++||.|++|.+..+|++|++.|||+.+..
T Consensus        54 ~eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   54 AEGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             cCCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecc
Confidence            34567789999998532  2    23466789999999999988888755 99999999999999999999999988655


Q ss_pred             C
Q 018554           84 G   84 (354)
Q Consensus        84 g   84 (354)
                      .
T Consensus       133 n  133 (698)
T KOG2314|consen  133 N  133 (698)
T ss_pred             c
Confidence            4

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.62  E-value=0.00017  Score=64.82  Aligned_cols=81  Identities=22%  Similarity=0.471  Sum_probs=63.4

Q ss_pred             cceEEEecCCCCCCHHH----H--HHhhccCCCeeEEEEeeCC-CCCc-ce--EEEEEeCCHHHHHHHHHHhCCCcccCC
Q 018554          102 EHKLFIGMLPKNVSEAE----V--SALFSIYGTIKDLQILRGS-QQTS-KG--CAFLKYETKEQALAALEAINGKHKMEG  171 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~----l--~~~F~~~G~v~~i~i~~~~-~~~~-~g--~afV~f~~~~~A~~Ai~~l~g~~~~~g  171 (354)
                      .+-+||-+|+..+..|+    |  .++|.+||.|..|.|-+.. ...+ .+  -.+|+|.+.|+|.+||.+++|.. ++|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~-~DG  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL-LDG  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc-ccC
Confidence            34579999998888777    2  4899999999999887753 2111 12  24999999999999999999976 888


Q ss_pred             CceeEEEEecCChH
Q 018554          172 SSVPLVVKWADTEK  185 (354)
Q Consensus       172 ~~~~l~v~~a~~~~  185 (354)
                        +.|+..+..++.
T Consensus       193 --r~lkatYGTTKY  204 (480)
T COG5175         193 --RVLKATYGTTKY  204 (480)
T ss_pred             --ceEeeecCchHH
Confidence              688888887654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.61  E-value=0.00021  Score=67.88  Aligned_cols=68  Identities=26%  Similarity=0.382  Sum_probs=62.0

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHH
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA   75 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~-~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~   75 (354)
                      ...-+..+|||||+||.-++.++|..+|+. ||.|..+-|=.|..-+-.+|-|=|+|.+..+-.+||++
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            345678899999999999999999999994 99999999999966688999999999999999999986

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.57  E-value=5.7e-05  Score=68.60  Aligned_cols=79  Identities=29%  Similarity=0.396  Sum_probs=67.1

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeE--------EEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKD--------LQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS  172 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~--------i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  172 (354)
                      ..+|||-+|+..+++++|.++|.++|.|..        |.|.+| .++..|+-|.|.|+|...|+.||+-++++.+ .+ 
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf-~g-  143 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF-CG-  143 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc-cC-
Confidence            568999999999999999999999998754        566677 5889999999999999999999999999885 43 


Q ss_pred             ceeEEEEecCC
Q 018554          173 SVPLVVKWADT  183 (354)
Q Consensus       173 ~~~l~v~~a~~  183 (354)
                       -.|+|.+|..
T Consensus       144 -n~ikvs~a~~  153 (351)
T KOG1995|consen  144 -NTIKVSLAER  153 (351)
T ss_pred             -CCchhhhhhh
Confidence             4677776643

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.56  E-value=9.1e-05  Score=68.58  Aligned_cols=67  Identities=28%  Similarity=0.451  Sum_probs=56.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC---CC---C-C-------cceEEEEEeCCHHHHHHHHHHhCCC
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG---SQ---Q-T-------SKGCAFLKYETKEQALAALEAINGK  166 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~---~~---~-~-------~~g~afV~f~~~~~A~~Ai~~l~g~  166 (354)
                      ..++|.+-|||.+-.-|.|.++|..+|.|..|+|+..   ..   + .       .+-||+|+|+..+.|.+|.+.|+..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            3789999999999999999999999999999999875   11   1 1       2478999999999999999988654


Q ss_pred             c
Q 018554          167 H  167 (354)
Q Consensus       167 ~  167 (354)
                      .
T Consensus       310 ~  310 (484)
T KOG1855|consen  310 Q  310 (484)
T ss_pred             h
Confidence            3

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.48  E-value=9.1e-06  Score=81.00  Aligned_cols=149  Identities=25%  Similarity=0.208  Sum_probs=106.9

Q ss_pred             CCCeEEEcCCCCCCCHH-HHHHHHhhcCCeeEEEEeeCCCCCCccc-EEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           13 ERVKLFVGQVPKHMTEA-QLLAMFKEFALVDEVNIIKDKTTRASRG-CCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~-~L~~~F~~~G~v~~i~i~~d~~tg~~~G-~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....+.+.++.....+. .++..|..+|.|+.|++..... +.... +.++++....+++.|...- ++. +.+  +...
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~-k~h~q~~~~~~~s~~~~~esat~pa-~~~-~a~--~~~a  644 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGF-KAHEQPQQQKVQSKHGSAESATVPA-GGA-LAN--RSAA  644 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccc-cccccchhhhhhccccchhhccccc-ccc-cCC--cccc
Confidence            44556677776665555 6778888999999998866322 22333 8899999999999887653 222 222  3333


Q ss_pred             eecccccc-----------ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEe-eCCCCCcceEEEEEeCCHHHHHH
Q 018554           91 VKYADGEL-----------ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL-RGSQQTSKGCAFLKYETKEQALA  158 (354)
Q Consensus        91 v~~~~~~~-----------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~-~~~~~~~~g~afV~f~~~~~A~~  158 (354)
                      +..++.+.           .+..+++||.||+..+.++||+..|..+|.++.++|. ....+.-||+|++.|.+.+++.+
T Consensus       645 v~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~a  724 (881)
T KOG0128|consen  645 VGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGA  724 (881)
T ss_pred             CCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhh
Confidence            33332221           1235678999999999999999999999988887776 33567779999999999999999


Q ss_pred             HHHHhCCC
Q 018554          159 ALEAINGK  166 (354)
Q Consensus       159 Ai~~l~g~  166 (354)
                      ||...+..
T Consensus       725 aV~f~d~~  732 (881)
T KOG0128|consen  725 AVAFRDSC  732 (881)
T ss_pred             hhhhhhhh
Confidence            99766654

>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=97.39  E-value=0.00074  Score=51.15  Aligned_cols=78  Identities=27%  Similarity=0.339  Sum_probs=51.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEE-EeeC-------CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQ-ILRG-------SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS  173 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~-i~~~-------~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  173 (354)
                      ++-|.|=+.|.. ....|.++|++||+|.+.. +.++       ..........|+|+++.+|.+||.+ ||+. ++|. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i-~~g~-   81 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTI-FSGS-   81 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEE-ETTC-
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeE-EcCc-
Confidence            355788888888 5556778999999987764 1111       0011246889999999999999974 8865 6664 


Q ss_pred             eeEEEEecCC
Q 018554          174 VPLVVKWADT  183 (354)
Q Consensus       174 ~~l~v~~a~~  183 (354)
                      +.+-|++.+.
T Consensus        82 ~mvGV~~~~~   91 (100)
T PF05172_consen   82 LMVGVKPCDP   91 (100)
T ss_dssp             EEEEEEE-HH
T ss_pred             EEEEEEEcHH
Confidence            6678888753

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.36  E-value=0.00044  Score=60.10  Aligned_cols=89  Identities=16%  Similarity=0.178  Sum_probs=73.8

Q ss_pred             HHHHHHHHhcCCccCCCCCccceeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEE
Q 018554           68 EADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAF  147 (354)
Q Consensus        68 ~A~~Ai~~l~~~~~~~g~~~~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~af  147 (354)
                      -|..|...|++.. ..  .+.++|.|+-.      ..|||.||..-+.-|.|.+.|+.||.|+...+.-|..++..+-++
T Consensus         6 ~ae~ak~eLd~~~-~~--~~~lr~rfa~~------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~   76 (275)
T KOG0115|consen    6 LAEIAKRELDGRF-PK--GRSLRVRFAMH------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGI   76 (275)
T ss_pred             HHHHHHHhcCCCC-CC--CCceEEEeecc------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccch
Confidence            4556666775533 44  48899998865      359999999999999999999999999998888887777888999


Q ss_pred             EEeCCHHHHHHHHHHhCC
Q 018554          148 LKYETKEQALAALEAING  165 (354)
Q Consensus       148 V~f~~~~~A~~Ai~~l~g  165 (354)
                      |.|...-.|.+|++..+.
T Consensus        77 v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   77 VEFAKKPNARKAARRCRE   94 (275)
T ss_pred             hhhhcchhHHHHHHHhcc
Confidence            999999999999987743

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.35  E-value=0.00043  Score=66.31  Aligned_cols=76  Identities=20%  Similarity=0.339  Sum_probs=60.2

Q ss_pred             cceEEEecCCCC--CC----HHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCcee
Q 018554          102 EHKLFIGMLPKN--VS----EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP  175 (354)
Q Consensus       102 ~~~l~V~~l~~~--~t----~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~  175 (354)
                      ...|+|.|+|.-  ..    ...|..+|+++|+|..+.+..+..|..+||.|++|.+..+|+.|++.|||+.+...+  .
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH--t  135 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH--T  135 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccc--e
Confidence            467889998842  11    234678999999999999998877778999999999999999999999998843332  4


Q ss_pred             EEEE
Q 018554          176 LVVK  179 (354)
Q Consensus       176 l~v~  179 (354)
                      ..|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            4444

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.27  E-value=0.00029  Score=65.30  Aligned_cols=68  Identities=15%  Similarity=0.206  Sum_probs=57.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeC---CCC--CC--------cccEEEEEeCCHHHHHHHHHHhc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKD---KTT--RA--------SRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d---~~t--g~--------~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      .-..++|.+-|||.|-.-+.|.++|..+|.|..|+|..-   ...  +.        .+-||||+|...+.|.+|.+.++
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            348899999999999999999999999999999998765   111  11        25689999999999999999885


Q ss_pred             C
Q 018554           78 N   78 (354)
Q Consensus        78 ~   78 (354)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.26  E-value=0.00023  Score=61.73  Aligned_cols=71  Identities=13%  Similarity=0.189  Sum_probs=59.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC--------CCccc----EEEEEeCCHHHHHHHHHHhcCCc
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT--------RASRG----CCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~t--------g~~~G----~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      ..--||+++||+.++-.-|+++|+.||+|-.|.+-....+        |.+..    -|.|+|.+...|..+.+.||+..
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            5577999999999999999999999999999998876655        23322    27899999999999999999877


Q ss_pred             cCC
Q 018554           81 TLP   83 (354)
Q Consensus        81 ~~~   83 (354)
                      +..
T Consensus       153 Igg  155 (278)
T KOG3152|consen  153 IGG  155 (278)
T ss_pred             cCC
Confidence            433

>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=97.24  E-value=0.00066  Score=51.40  Aligned_cols=82  Identities=18%  Similarity=0.233  Sum_probs=50.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEE-EeeCCC------CCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVN-IIKDKT------TRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~-i~~d~~------tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ....+.|.|-+.|.. ....|.+.|++||.|.+.. +.++..      .-.......|+|++..+|.+||..  +..++.
T Consensus         3 ~~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~--NG~i~~   79 (100)
T PF05172_consen    3 QDSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK--NGTIFS   79 (100)
T ss_dssp             -GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT--TTEEET
T ss_pred             CcCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh--CCeEEc
Confidence            446678999999988 6778889999999988764 111100      011234899999999999999976  445455


Q ss_pred             CCCccceeecccc
Q 018554           84 GASSPLQVKYADG   96 (354)
Q Consensus        84 g~~~~l~v~~~~~   96 (354)
                      + ..-+-|.+.+.
T Consensus        80 g-~~mvGV~~~~~   91 (100)
T PF05172_consen   80 G-SLMVGVKPCDP   91 (100)
T ss_dssp             T-CEEEEEEE-HH
T ss_pred             C-cEEEEEEEcHH
Confidence            4 24455665543

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.02  E-value=0.0018  Score=56.32  Aligned_cols=64  Identities=17%  Similarity=0.249  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      ..|+|.||..-++-|.|..-|+.||+|+...++-|.. ++..+-++|+|...-.|.+|++.+...
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~~a~~a~rr~~~~   95 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKPNARKAARRCREG   95 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcchhHHHHHHHhccC
Confidence            6799999999999999999999999999887777754 788889999999999999999987433

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.00  E-value=0.0011  Score=61.45  Aligned_cols=79  Identities=27%  Similarity=0.393  Sum_probs=59.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      ++||++||...++..||+.+|...-.-..-.++-.     .||+||.+.+...|.+|++.++|+.-+.|  .++.|...-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-----~gyafvd~pdq~wa~kaie~~sgk~elqG--kr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-----SGYAFVDCPDQQWANKAIETLSGKVELQG--KRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-----cceeeccCCchhhhhhhHHhhchhhhhcC--ceeeccchh
Confidence            47999999999999999999965421111112211     58999999999999999999999877777  577887766


Q ss_pred             ChHHHH
Q 018554          183 TEKERQ  188 (354)
Q Consensus       183 ~~~~~~  188 (354)
                      .++.+.
T Consensus        75 ~kkqrs   80 (584)
T KOG2193|consen   75 PKKQRS   80 (584)
T ss_pred             hHHHHh
Confidence            665543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.00  E-value=0.0017  Score=58.47  Aligned_cols=105  Identities=10%  Similarity=0.296  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHH----H--HHHHhhcCCeeEEEEeeCCCC-CCcccEE--EEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554           15 VKLFVGQVPKHMTEAQ----L--LAMFKEFALVDEVNIIKDKTT-RASRGCC--FVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~----L--~~~F~~~G~v~~i~i~~d~~t-g~~~G~a--FV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .-+||-+|+..+..|+    |  .++|.+||+|..|.|-+.... ....+.+  ||+|.+.|+|.+||.+.++.. ++| 
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~-~DG-  192 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL-LDG-  192 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc-ccC-
Confidence            3489999998777766    3  479999999998877554311 1122333  999999999999999998755 666 


Q ss_pred             Cccceeecccccc---------ccccceEEEecCC---CCCCHHHHHHh
Q 018554           86 SSPLQVKYADGEL---------ERLEHKLFIGMLP---KNVSEAEVSAL  122 (354)
Q Consensus        86 ~~~l~v~~~~~~~---------~~~~~~l~V~~l~---~~~t~~~l~~~  122 (354)
                       +.|+..|-..+-         -....++|+..--   +..|.+||...
T Consensus       193 -r~lkatYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~  240 (480)
T COG5175         193 -RVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNS  240 (480)
T ss_pred             -ceEeeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhh
Confidence             777777654321         1113345543322   34667777543

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.98  E-value=0.056  Score=52.21  Aligned_cols=59  Identities=14%  Similarity=0.236  Sum_probs=49.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhc--cCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFS--IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~--~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      +.|.|.++.|+.++-+|+|+.+|.  .|-.+++|.+-.+.+      =||+|++..||++|.+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n------WyITfesd~DAQqAykylre  234 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN------WYITFESDTDAQQAYKYLRE  234 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc------eEEEeecchhHHHHHHHHHH
Confidence            357899999999999999999994  577888988876533      37999999999999987754

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.97  E-value=0.0046  Score=42.22  Aligned_cols=54  Identities=20%  Similarity=0.355  Sum_probs=45.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhc----CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHh
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEF----ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC   76 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~----G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l   76 (354)
                      ..+|+|.|+ -+++.+||+.+|..|    + ...|..+.|.       -|=|.|.|.+.|.+||.+|
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            468999999 458999999999998    4 4577778886       4889999999999999764

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.95  E-value=0.0044  Score=42.32  Aligned_cols=55  Identities=20%  Similarity=0.284  Sum_probs=44.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccC---CCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIY---GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI  163 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~---G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l  163 (354)
                      ..+|+|.+++ +++.+||+.+|..|   .....|..+.|.      -|-|.|.+.+.|.+|+.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            3579999994 57888899999888   135677777763      4789999999999999765

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.89  E-value=0.00045  Score=60.11  Aligned_cols=63  Identities=25%  Similarity=0.459  Sum_probs=50.3

Q ss_pred             HHHHHhhc-cCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          117 AEVSALFS-IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       117 ~~l~~~F~-~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      |||...|+ +||+|++++|..+....-+|-++|.|..+++|++|++.||+.. +.|  ++|.+.+..
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 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRW-YNG--RPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCcc-ccC--CcceeeecC
Confidence            44555554 9999999988876544457899999999999999999999987 676  577777653

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.81  E-value=0.0034  Score=55.61  Aligned_cols=67  Identities=22%  Similarity=0.348  Sum_probs=52.1

Q ss_pred             HHHHHHhhccCCCeeEEEEeeCCC-CCcc-eEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChH
Q 018554          116 EAEVSALFSIYGTIKDLQILRGSQ-QTSK-GCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       116 ~~~l~~~F~~~G~v~~i~i~~~~~-~~~~-g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~  185 (354)
                      ++++++.+++||.|..|.|+.+.. ...+ --.||+|+..++|.+|+..|||.. ++|  +.+...|-+..+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRy-FGG--r~v~A~Fyn~ek  368 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRY-FGG--RVVSACFYNLEK  368 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCce-ecc--eeeeheeccHHh
Confidence            557889999999999999988743 2222 348999999999999999999986 666  566666655443

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.80  E-value=0.0015  Score=63.11  Aligned_cols=84  Identities=15%  Similarity=0.254  Sum_probs=69.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhc-cCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFS-IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~-~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++.|||.||---.|.-.|+.++. .+|.|++..|-+-     |..|||.|.+.++|...+.+|||-..-.++.+.|.+
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI-----KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI-----KSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh-----hcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            3478899999999999999999997 5667777643322     568999999999999999999998877788889999


Q ss_pred             EecCChHHHH
Q 018554          179 KWADTEKERQ  188 (354)
Q Consensus       179 ~~a~~~~~~~  188 (354)
                      .|+.......
T Consensus       517 df~~~deld~  526 (718)
T KOG2416|consen  517 DFVRADELDK  526 (718)
T ss_pred             eecchhHHHH
Confidence            9987655443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.70  E-value=0.0089  Score=43.08  Aligned_cols=55  Identities=22%  Similarity=0.386  Sum_probs=41.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      .+-.+|+ +|+.+...||.++|+.||.| .|..+.|.       -|||...+.+.|..|++.+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            3445554 99999999999999999997 45555664       69999999999999998874

; 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.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.68  E-value=0.0015  Score=63.02  Aligned_cols=82  Identities=23%  Similarity=0.307  Sum_probs=67.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~-~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ....++.|+|.||=.-+|.-.|++++.+ .|.|++.+|  |+    -+..|||.|.+.++|...+.+|||..+-.+.-+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            4567888999999999999999999996 667887754  32    3348999999999999999999998887777777


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |.+.|...+
T Consensus       514 L~adf~~~d  522 (718)
T KOG2416|consen  514 LIADFVRAD  522 (718)
T ss_pred             eEeeecchh
Confidence            777776543

>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=96.54  E-value=0.045  Score=42.28  Aligned_cols=72  Identities=17%  Similarity=0.175  Sum_probs=52.9

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT   81 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~   81 (354)
                      ..+......+.+...|.-++.++|..+.+.+- .|+.++|++|..  .++--+.++|.+.++|+...+.+||+.+
T Consensus         7 ~~~~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen    7 LPDERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             CCCCCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            33444455555555566666677776666654 488899999864  3555699999999999999999999885

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.48  E-value=0.002  Score=55.99  Aligned_cols=71  Identities=13%  Similarity=0.273  Sum_probs=58.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-C--------CCcc----eEEEEEeCCHHHHHHHHHHhCCCc
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-Q--------QTSK----GCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~--------~~~~----g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                      ..-.||+++||..++...|+++|++||+|-.|.+-... .        +.++    .-++|+|.+...|.++.+.||++.
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            45789999999999999999999999999999886542 2        1222    348899999999999999999987


Q ss_pred             ccCCC
Q 018554          168 KMEGS  172 (354)
Q Consensus       168 ~~~g~  172 (354)
                       |.|+
T Consensus       153 -Iggk  156 (278)
T KOG3152|consen  153 -IGGK  156 (278)
T ss_pred             -cCCC
Confidence             5553

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.42  E-value=0.0052  Score=62.29  Aligned_cols=79  Identities=18%  Similarity=0.224  Sum_probs=67.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....+.+||++|..++....|...|..||.|..|.+-.    |.  -|++|.|++...+..|++.+.+.. +.+-.+.+
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----gq--~yayi~yes~~~aq~a~~~~rgap-~G~P~~r~  523 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----GQ--PYAYIQYESPPAAQAATHDMRGAP-LGGPPRRL  523 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----CC--cceeeecccCccchhhHHHHhcCc-CCCCCccc
Confidence            556788999999999999999999999999999876633    22  399999999999999999998877 55556778


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      .|.++.
T Consensus       524 rvdla~  529 (975)
T KOG0112|consen  524 RVDLAS  529 (975)
T ss_pred             cccccc
Confidence            998874

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.06  E-value=0.0038  Score=54.49  Aligned_cols=60  Identities=17%  Similarity=0.384  Sum_probs=44.7

Q ss_pred             HHHHHHHh-hcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           29 AQLLAMFK-EFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        29 ~~L~~~F~-~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +||...|+ +||+|++++|-.+.. -.-+|-++|.|..+++|++|++.||+.. +.+  ++|...
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw-~~G--~pi~ae  143 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRW-YNG--RPIHAE  143 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCcc-ccC--Ccceee
Confidence            45555556 799999987655432 3457899999999999999999998865 555  555443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.73  E-value=0.064  Score=42.78  Aligned_cols=76  Identities=21%  Similarity=0.308  Sum_probs=54.1

Q ss_pred             cCCCCCCeEEEcCCCCCCC-HHHHH---HHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            9 KSSEERVKLFVGQVPKHMT-EAQLL---AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~t-e~~L~---~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ..+..-.+|.|+=|.+++. .+||+   ..++.||+|.+|.+.-       +--|.|.|+|..+|.+|+.+++...  .|
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~--pg  151 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRA--PG  151 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCC--CC
Confidence            4566788999988776653 33444   4567799999987632       2269999999999999999997633  33


Q ss_pred             CCccceeeccc
Q 018554           85 ASSPLQVKYAD   95 (354)
Q Consensus        85 ~~~~l~v~~~~   95 (354)
                        ..++..|..
T Consensus       152 --tm~qCsWqq  160 (166)
T PF15023_consen  152 --TMFQCSWQQ  160 (166)
T ss_pred             --ceEEeeccc
Confidence              555555543

>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=95.73  E-value=0.11  Score=40.02  Aligned_cols=65  Identities=17%  Similarity=0.225  Sum_probs=50.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCC-CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYG-TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G-~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      ..+.+...++.++.++|..+.+.+- .|+.++|++|... ++-.++++|.+.++|.+..+..||+.+
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            3445555667777777876666664 4788999998654 477899999999999999999999873

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.61  E-value=0.05  Score=52.54  Aligned_cols=66  Identities=14%  Similarity=0.243  Sum_probs=53.2

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhh--cCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKE--FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~--~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      ..+-+...+.|-|.|+-||..+-+|+++.||+.  +-++.+|..--+.       -=||+|++..||..|.+.|.
T Consensus       166 gekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  166 GEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLR  233 (684)
T ss_pred             ccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHH
Confidence            344455667788999999999999999999986  6678888765543       25999999999999987663

>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=95.60  E-value=0.042  Score=46.41  Aligned_cols=82  Identities=23%  Similarity=0.278  Sum_probs=53.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhcc-CCCe---eEEEEeeC--CCC-CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc-
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSI-YGTI---KDLQILRG--SQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSS-  173 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~-~G~v---~~i~i~~~--~~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~-  173 (354)
                      ..+|.|++||.++|++++.+.++. ++..   ..+.-..+  ... ....-|+|.|.+.+++......++|..+.+.++ 
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            468999999999999999998876 6665   33332222  111 123569999999999999999999987666433 


Q ss_pred             -eeEEEEecCC
Q 018554          174 -VPLVVKWADT  183 (354)
Q Consensus       174 -~~l~v~~a~~  183 (354)
                       ....|++|--
T Consensus        87 ~~~~~VE~Apy   97 (176)
T PF03467_consen   87 EYPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEEE-SS
T ss_pred             CcceeEEEcch
Confidence             3556777743

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.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.58  E-value=0.05  Score=43.86  Aligned_cols=55  Identities=22%  Similarity=0.456  Sum_probs=41.6

Q ss_pred             HHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCC
Q 018554          118 EVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       118 ~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~  183 (354)
                      +|.+.|..||+|.-++++.+       .-+|+|.+-++|.+|+. ++|.. +.|  +.|+|++..+
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~-v~g--~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQ-VNG--RTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSE-ETT--EEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcE-ECC--EEEEEEeCCc
Confidence            57788899999999988854       67999999999999995 79987 565  5666665443

; PDB: 1UFW_A 2DNR_A.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.54  E-value=0.036  Score=49.32  Aligned_cols=64  Identities=17%  Similarity=0.135  Sum_probs=48.8

Q ss_pred             HHHHHHHHhhcCCeeEEEEeeCCCCCCcc-cEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           28 EAQLLAMFKEFALVDEVNIIKDKTTRASR-GCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        28 e~~L~~~F~~~G~v~~i~i~~d~~tg~~~-G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      |+++++.+++||.|..|.|..+...-..+ --.||+|+..++|.+|+-.|||+- +.|  +.++..|-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRy-FGG--r~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRY-FGG--RVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCce-ecc--eeeeheec
Confidence            45788899999999999998876533322 247999999999999999998855 555  55555443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.46  E-value=0.021  Score=52.76  Aligned_cols=79  Identities=11%  Similarity=0.242  Sum_probs=59.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC----CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS----QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~----~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..|.|.||..+.|.|+++.+|.-.|+|.++.++...    -....-.|||.|.+...+..|-. |.++.+++-  ..|.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdr--aliv~   84 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDR--ALIVR   84 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeee--eEEEE
Confidence            368999999999999999999999999999998742    23345689999999988887764 555554542  33444


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      -+++..
T Consensus        85 p~~~~~   90 (479)
T KOG4676|consen   85 PYGDEV   90 (479)
T ss_pred             ecCCCC
Confidence            455433

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.07  E-value=0.086  Score=49.77  Aligned_cols=70  Identities=20%  Similarity=0.305  Sum_probs=59.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTL   82 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~   82 (354)
                      +...+.|+|-.+|..++--||..|+..+- .|.+|+|+||...  ++=-..|+|.+.++|+...+.+||+.+.
T Consensus        71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   71 ASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            33489999999999999999999999875 5999999997542  3335999999999999999999998753

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.78  E-value=0.027  Score=51.28  Aligned_cols=78  Identities=15%  Similarity=0.364  Sum_probs=55.2

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEeeCCCC-CCccc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           15 VKLFVGQVPKHMTEAQLL---AMFKEFALVDEVNIIKDKTT-RASRG--CCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~---~~F~~~G~v~~i~i~~d~~t-g~~~G--~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .-+||-+|+.++..+++.   ++|.+||.|..|.+.++... ...-+  -++|+|...++|..||...++.. +.+  +.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~-~dg--~~  154 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFV-DDG--RA  154 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHH-hhh--hh
Confidence            557888898776666554   48999999999988887631 11111  28999999999999999987744 444  44


Q ss_pred             ceeeccc
Q 018554           89 LQVKYAD   95 (354)
Q Consensus        89 l~v~~~~   95 (354)
                      ++..+..
T Consensus       155 lka~~gt  161 (327)
T KOG2068|consen  155 LKASLGT  161 (327)
T ss_pred             hHHhhCC
Confidence            5555443

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.76  E-value=0.03  Score=47.31  Aligned_cols=75  Identities=8%  Similarity=0.091  Sum_probs=47.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCe---eEEEEee-CCCCCCc-ccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKE-FALV---DEVNIIK-DKTTRAS-RGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~-~G~v---~~i~i~~-d~~tg~~-~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .....+|.|++||+++||+++.+.++. ++..   ..+.-.. +...+.+ -.-|||.|.+.+++....+.+++..+.+.
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            445679999999999999999997776 6654   2333112 2222222 24599999999999999999988766554


Q ss_pred             C
Q 018554           85 A   85 (354)
Q Consensus        85 ~   85 (354)
                      +
T Consensus        84 k   84 (176)
T PF03467_consen   84 K   84 (176)
T ss_dssp             T
T ss_pred             C
Confidence            3

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.

>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=94.68  E-value=0.021  Score=42.03  Aligned_cols=65  Identities=9%  Similarity=0.128  Sum_probs=41.3

Q ss_pred             EEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccccc--------cccccceEEEecCCCCCCHHHHHHhh
Q 018554           59 CFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGE--------LERLEHKLFIGMLPKNVSEAEVSALF  123 (354)
Q Consensus        59 aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~~~--------~~~~~~~l~V~~l~~~~t~~~l~~~F  123 (354)
                      |.|+|.+.+.|++.++.-.....+.+....++++.....        .....++|.|.|||..+++|+|++.+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            689999999999998763222223332233333322111        11226789999999999999998754

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.64  E-value=0.2  Score=39.99  Aligned_cols=73  Identities=19%  Similarity=0.375  Sum_probs=53.7

Q ss_pred             ccccceEEEecCCCCCC-HHH---HHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554           99 ERLEHKLFIGMLPKNVS-EAE---VSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t-~~~---l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      +..-.+|.|+=|..++. .+|   |...++.||.|++|...-      +.-|.|.|+|..+|.+|+.++...  ..|  .
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s~--~pg--t  152 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQSR--APG--T  152 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcCC--CCC--c
Confidence            33456788877765543 334   445668999999998873      567999999999999999998764  333  4


Q ss_pred             eEEEEec
Q 018554          175 PLVVKWA  181 (354)
Q Consensus       175 ~l~v~~a  181 (354)
                      .+.++|-
T Consensus       153 m~qCsWq  159 (166)
T PF15023_consen  153 MFQCSWQ  159 (166)
T ss_pred             eEEeecc
Confidence            6788874

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.45  E-value=0.016  Score=52.65  Aligned_cols=79  Identities=19%  Similarity=0.386  Sum_probs=59.0

Q ss_pred             ceEEEecCCCCCCHHHHH---HhhccCCCeeEEEEeeCCC--C--CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCcee
Q 018554          103 HKLFIGMLPKNVSEAEVS---ALFSIYGTIKDLQILRGSQ--Q--TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP  175 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~---~~F~~~G~v~~i~i~~~~~--~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~  175 (354)
                      +.+||-+|+..+.++++.   +.|.+||.|..|.+.++..  .  ....-++|+|+..++|..||..++|.. ++|+  .
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~-~dg~--~  154 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFV-DDGR--A  154 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHH-hhhh--h
Confidence            457999999887766553   6889999999999988752  1  112348999999999999999999954 7774  3


Q ss_pred             EEEEecCCh
Q 018554          176 LVVKWADTE  184 (354)
Q Consensus       176 l~v~~a~~~  184 (354)
                      |+..++.++
T Consensus       155 lka~~gttk  163 (327)
T KOG2068|consen  155 LKASLGTTK  163 (327)
T ss_pred             hHHhhCCCc
Confidence            555665544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.32  E-value=0.26  Score=35.71  Aligned_cols=55  Identities=22%  Similarity=0.471  Sum_probs=40.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      +..||. +|.++...||.++|+.||.|. |..+.|      .-|||....++.|..|+..++-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhcc
Confidence            455665 999999999999999999864 444433      3699999999999999988764

; 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.

>KOG2893 consensus Zn finger protein [General function prediction only]

Probab=94.28  E-value=3.3  Score=36.00  Aligned_cols=8  Identities=0%  Similarity=0.302  Sum_probs=3.5

Q ss_pred             CCCCCHHH
Q 018554          111 PKNVSEAE  118 (354)
Q Consensus       111 ~~~~t~~~  118 (354)
                      ..+.++|.
T Consensus        17 nrefddek   24 (341)
T KOG2893|consen   17 NREFDDEK   24 (341)
T ss_pred             ccccchhh
Confidence            33444444

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.08  E-value=0.15  Score=48.20  Aligned_cols=66  Identities=20%  Similarity=0.323  Sum_probs=57.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCC-CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYG-TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G-~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      ...|+|-.+|..++-.||..++..|- .|.+|+|+||.... +-.++|+|.+.++|....+.+||+.+
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn-rymvLIkFr~q~da~~Fy~efNGk~F  140 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN-RYMVLIKFRDQADADTFYEEFNGKQF  140 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc-eEEEEEEeccchhHHHHHHHcCCCcC
Confidence            56799999999999999999997765 69999999975544 66799999999999999999999874

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.00  E-value=0.22  Score=44.71  Aligned_cols=75  Identities=23%  Similarity=0.269  Sum_probs=53.5

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      |-|-+++.. ....|..+|++||+|.+...-  ++   -.+-+|+|.++.+|++||.. ||+. |+|. +-|-|+-+..+
T Consensus       200 VTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~--~n---gNwMhirYssr~~A~KALsk-ng~i-i~g~-vmiGVkpCtDk  270 (350)
T KOG4285|consen  200 VTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP--SN---GNWMHIRYSSRTHAQKALSK-NGTI-IDGD-VMIGVKPCTDK  270 (350)
T ss_pred             EEEeccCcc-chhHHHHHHHhhCeeeeeecC--CC---CceEEEEecchhHHHHhhhh-cCee-eccc-eEEeeeecCCH
Confidence            444455544 344577899999999886655  23   34889999999999999975 7754 6654 77788876665


Q ss_pred             HHHH
Q 018554          185 KERQ  188 (354)
Q Consensus       185 ~~~~  188 (354)
                      ...+
T Consensus       271 svi~  274 (350)
T KOG4285|consen  271 SVIN  274 (350)
T ss_pred             HHhc
Confidence            5443

>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=93.98  E-value=0.19  Score=34.90  Aligned_cols=50  Identities=16%  Similarity=0.313  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccC
Q 018554           24 KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTL   82 (354)
Q Consensus        24 ~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~   82 (354)
                      ..++-+||+..+..|+-   .+|..|+.     || ||.|.|.++|++|.+..+++.++
T Consensus        10 ~~~~v~d~K~~Lr~y~~---~~I~~d~t-----Gf-YIvF~~~~Ea~rC~~~~~~~~~f   59 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW---DRIRDDRT-----GF-YIVFNDSKEAERCFRAEDGTLFF   59 (66)
T ss_pred             CCccHHHHHHHHhcCCc---ceEEecCC-----EE-EEEECChHHHHHHHHhcCCCEEE
Confidence            46788999999999964   24555653     34 89999999999999998876643

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.94  E-value=0.038  Score=55.86  Aligned_cols=74  Identities=19%  Similarity=0.245  Sum_probs=61.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .+..+-|..-..+...|..+|.+||+|.+++..+|-+      .|.|+|.+.+.|..|+++++|+.+.. .+-+.+|.++
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~-~g~Ps~V~~a  371 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSV-TGAPSRVSFA  371 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccc-cCCceeEEec
Confidence            3445566677889999999999999999999999876      79999999999999999999987543 2456777766


Q ss_pred             c
Q 018554           95 D   95 (354)
Q Consensus        95 ~   95 (354)
                      +
T Consensus       372 k  372 (1007)
T KOG4574|consen  372 K  372 (1007)
T ss_pred             c
Confidence            4

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.85  E-value=0.035  Score=56.11  Aligned_cols=75  Identities=27%  Similarity=0.372  Sum_probs=62.6

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCC
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~  183 (354)
                      +.++.|....++..-|..+|++||.|.++..+++     -..|.|.|.+.+.|..|+++|.|+.+.. ...+.+|.+|+.
T Consensus       300 ~~~~~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  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSV-TGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccc-cCCceeEEeccc
Confidence            4566677777888899999999999999999988     4479999999999999999999998543 235788888864


Q ss_pred             h
Q 018554          184 E  184 (354)
Q Consensus       184 ~  184 (354)
                      -
T Consensus       374 ~  374 (1007)
T KOG4574|consen  374 L  374 (1007)
T ss_pred             c
Confidence            3

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.31  E-value=0.35  Score=43.43  Aligned_cols=63  Identities=19%  Similarity=0.168  Sum_probs=47.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ....|-|-+++.. .-..|.++|++||+|.+...-.      +--+-+|.|.+.-+|+|||..  +..+|.+
T Consensus       196 ~D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALsk--ng~ii~g  258 (350)
T KOG4285|consen  196 ADTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALSK--NGTIIDG  258 (350)
T ss_pred             ccceEEEeccCcc-chhHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhhh--cCeeecc
Confidence            3677888899876 3456778999999988765432      223899999999999999987  4454544

>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=93.30  E-value=4.4  Score=36.55  Aligned_cols=152  Identities=14%  Similarity=0.225  Sum_probs=94.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC-------CCCcccEEEEEeCCHHHHHHHHH----HhcC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT-------TRASRGCCFVICPSRQEADKAVN----ACHN   78 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~-------tg~~~G~aFV~f~~~~~A~~Ai~----~l~~   78 (354)
                      +.=..|.|.+.||..+++--++..-|.+||.|++|.++.+..       ..+......+.|-+.+.|-...+    .|..
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            344567899999999999999999999999999999998761       11334578899999888765533    2211


Q ss_pred             C-ccCCCCCccceeecccc---------ccc------------------cccceEEEecCCCCCCHHHH-HHhh---ccC
Q 018554           79 K-KTLPGASSPLQVKYADG---------ELE------------------RLEHKLFIGMLPKNVSEAEV-SALF---SIY  126 (354)
Q Consensus        79 ~-~~~~g~~~~l~v~~~~~---------~~~------------------~~~~~l~V~~l~~~~t~~~l-~~~F---~~~  126 (354)
                      - ..+  +...|.+.+..-         +.+                  ...+.|.|. +...+.++++ .+.+   ..=
T Consensus        91 fK~~L--~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL~~~  167 (309)
T PF10567_consen   91 FKTKL--KSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFLKNS  167 (309)
T ss_pred             HHHhc--CCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhhccC
Confidence            0 111  123344433220         000                  014455554 3344544443 2222   222


Q ss_pred             C----CeeEEEEeeCC---CCCcceEEEEEeCCHHHHHHHHHHhC
Q 018554          127 G----TIKDLQILRGS---QQTSKGCAFLKYETKEQALAALEAIN  164 (354)
Q Consensus       127 G----~v~~i~i~~~~---~~~~~g~afV~f~~~~~A~~Ai~~l~  164 (354)
                      +    .+++|.++...   +.-.+.||.++|-+..-|.+.++-|.
T Consensus       168 ~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  168 NNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             CCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            2    37888888642   33446899999999999999887665

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.

>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=92.49  E-value=0.32  Score=41.27  Aligned_cols=61  Identities=25%  Similarity=0.325  Sum_probs=43.0

Q ss_pred             CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhC--CCcccCCCceeEEEEecCC
Q 018554          115 SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN--GKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       115 t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~~g~~~~l~v~~a~~  183 (354)
                      ..+.|+++|..++.+..+.+++.     -+-..|.|.+.++|.+|...|+  +.. +.|  ..++|-|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~-~~g--~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTS-FNG--KRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSE-ETT--EE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccc-cCC--CceEEEEccc
Confidence            45789999999999988888864     3468899999999999999998  766 454  4678887743

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.

>KOG2236 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.45  E-value=7.5  Score=37.33  Aligned_cols=13  Identities=31%  Similarity=0.930  Sum_probs=9.4

Q ss_pred             HHHhhccCCCeeE
Q 018554          119 VSALFSIYGTIKD  131 (354)
Q Consensus       119 l~~~F~~~G~v~~  131 (354)
                      |-.+|+-||.|..
T Consensus       247 lG~I~EiFGpV~~  259 (483)
T KOG2236|consen  247 LGQIFEIFGPVKN  259 (483)
T ss_pred             chhhhhhhcccCC
Confidence            5567778887765

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=91.67  E-value=0.36  Score=38.97  Aligned_cols=53  Identities=23%  Similarity=0.343  Sum_probs=38.9

Q ss_pred             HHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           30 QLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        30 ~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      +|.+.|..||+|.-|+++.+        .-+|+|.+-++|-+|+.. ++.+ +.|  +.++++..
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~-dg~~-v~g--~~l~i~LK  104 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSL-DGIQ-VNG--RTLKIRLK  104 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHG-CCSE-ETT--EEEEEEE-
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHcc-CCcE-ECC--EEEEEEeC
Confidence            77788889999888877665        479999999999999854 5655 455  55665543

; PDB: 1UFW_A 2DNR_A.

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

Probab=91.33  E-value=0.021  Score=56.30  Aligned_cols=65  Identities=12%  Similarity=0.090  Sum_probs=54.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ...+..++||+||...+..+-++.+...+|.|.++....         |+|..|.....+..|+..++... +.+
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~-~~~  100 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELN-IDD  100 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccC-CCc
Confidence            345678999999999999999999999999988775443         99999999999999998875433 444

>KOG2893 consensus Zn finger protein [General function prediction only]

Probab=90.25  E-value=4.2  Score=35.42  Aligned_cols=11  Identities=45%  Similarity=0.896  Sum_probs=4.8

Q ss_pred             CCCCCCCCCCC
Q 018554          219 GYAPPYNGYGY  229 (354)
Q Consensus       219 ~~~p~~~~~~~  229 (354)
                      |+.|+...||.
T Consensus       132 g~~pp~~~~gm  142 (341)
T KOG2893|consen  132 GPPPPSMAYGM  142 (341)
T ss_pred             CCCCcccccCC
Confidence            44444444443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=89.34  E-value=0.21  Score=47.57  Aligned_cols=60  Identities=18%  Similarity=0.351  Sum_probs=46.9

Q ss_pred             CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCC
Q 018554          115 SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       115 t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~  183 (354)
                      |.++|..+|.+||+|+.|.|-..     ---|.|+|.+..+|-+|.. ..+.. |++  +.|+|-|-+.
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~av-lnn--r~iKl~whnp  445 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAV-LNN--RFIKLFWHNP  445 (526)
T ss_pred             hHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccce-ecC--ceeEEEEecC
Confidence            46789999999999999998765     2368999999999987774 45544 665  6778888665

>KOG2236 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.70  E-value=8  Score=37.15  Aligned_cols=7  Identities=0%  Similarity=0.041  Sum_probs=4.2

Q ss_pred             EEEeCCH
Q 018554          147 FLKYETK  153 (354)
Q Consensus       147 fV~f~~~  153 (354)
                      .++|.+-
T Consensus       318 e~dfSDD  324 (483)
T KOG2236|consen  318 EQDFSDD  324 (483)
T ss_pred             hhccchH
Confidence            3677663

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.33  E-value=2  Score=42.19  Aligned_cols=79  Identities=20%  Similarity=0.282  Sum_probs=61.3

Q ss_pred             ccceEEEecCCCC-CCHHHHHHhhccC----CCeeEEEEeeCCCCC----------------------------------
Q 018554          101 LEHKLFIGMLPKN-VSEAEVSALFSIY----GTIKDLQILRGSQQT----------------------------------  141 (354)
Q Consensus       101 ~~~~l~V~~l~~~-~t~~~l~~~F~~~----G~v~~i~i~~~~~~~----------------------------------  141 (354)
                      .+++|-|-||.|+ +.-+||.-+|..|    |.|.+|.|.....|+                                  
T Consensus       173 ~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~~  252 (650)
T KOG2318|consen  173 ETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEED  252 (650)
T ss_pred             ccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhhh
Confidence            3678999999986 7788999999877    589999997643331                                  


Q ss_pred             --------------cceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          142 --------------SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       142 --------------~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                                    ..-||.|+|.+.+.|....+..+|.. ++.....|.++|
T Consensus       253 ~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~E-fEsS~~~~DLRF  304 (650)
T KOG2318|consen  253 VDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIE-FESSANKLDLRF  304 (650)
T ss_pred             HHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcce-eccccceeeeee
Confidence                          11479999999999999999999977 554545555555

>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=88.07  E-value=1.7  Score=30.12  Aligned_cols=50  Identities=14%  Similarity=0.219  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccc
Q 018554          112 KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKM  169 (354)
Q Consensus       112 ~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  169 (354)
                      ..++-++++..+..|+-   .+|..|++    | -||.|.+.++|+++.+..+++.++
T Consensus        10 ~~~~v~d~K~~Lr~y~~---~~I~~d~t----G-fYIvF~~~~Ea~rC~~~~~~~~~f   59 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW---DRIRDDRT----G-FYIVFNDSKEAERCFRAEDGTLFF   59 (66)
T ss_pred             CCccHHHHHHHHhcCCc---ceEEecCC----E-EEEEECChHHHHHHHHhcCCCEEE
Confidence            35788999999999852   34445543    3 389999999999999999998753

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]

Probab=86.68  E-value=8.4  Score=37.00  Aligned_cols=12  Identities=25%  Similarity=0.313  Sum_probs=6.4

Q ss_pred             CCCcCCCCCCCC
Q 018554          234 SYGLMQYRLPPM  245 (354)
Q Consensus       234 ~~g~~~~~~~p~  245 (354)
                      +.+|++|.+.++
T Consensus       547 ~~~Y~P~~PQ~~  558 (654)
T COG5180         547 MGMYMPFQPQPM  558 (654)
T ss_pred             cccccCCCCCcc
Confidence            344566665444

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=86.05  E-value=2.6  Score=30.80  Aligned_cols=58  Identities=16%  Similarity=0.197  Sum_probs=44.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhh-cC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHh
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKE-FA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC   76 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~-~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l   76 (354)
                      .-|+--++.+.+..++++.++. || .|.+|+.+.-+. +  .-=|||.+...++|.+....+
T Consensus        22 n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~-~--~KKA~V~L~~g~~A~~va~ki   81 (84)
T PRK14548         22 NKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPK-G--EKKAYVKLAEEYDAEEIASRL   81 (84)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCC-C--cEEEEEEeCCCCcHHHHHHhh
Confidence            4556678899999999999998 78 588888777542 1  113999999998888876554

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=85.53  E-value=1.6  Score=37.11  Aligned_cols=59  Identities=20%  Similarity=0.256  Sum_probs=40.5

Q ss_pred             CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc--CCccCCCCCccceeecc
Q 018554           27 TEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH--NKKTLPGASSPLQVKYA   94 (354)
Q Consensus        27 te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~--~~~~~~g~~~~l~v~~~   94 (354)
                      ..+.|+++|..++.+....+.+.-      +-..|.|.+.++|.+|...|+  +.. +.+  ..+++.++
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~-~~g--~~l~~yf~   68 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTS-FNG--KRLRVYFG   68 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSE-ETT--EE-EEE--
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccc-cCC--CceEEEEc
Confidence            568999999999998887777653      368999999999999999987  444 333  44666555

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.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=84.89  E-value=0.43  Score=45.50  Aligned_cols=76  Identities=18%  Similarity=0.254  Sum_probs=53.8

Q ss_pred             CCCCeEEEcCCCCCC-CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPKHM-TEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~-te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .+.+.|=+.-++... +.++|...|.+||+|++|.|-....      .|.|+|.+..+|-+|-. .++.. +.+  +.|+
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~-s~~av-lnn--r~iK  439 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYA-SHGAV-LNN--RFIK  439 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhc-cccce-ecC--ceeE
Confidence            344555555555543 6779999999999999998855422      68999999999966643 33433 544  7888


Q ss_pred             eeccccc
Q 018554           91 VKYADGE   97 (354)
Q Consensus        91 v~~~~~~   97 (354)
                      +.|.+..
T Consensus       440 l~whnps  446 (526)
T KOG2135|consen  440 LFWHNPS  446 (526)
T ss_pred             EEEecCC
Confidence            8887653

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=83.74  E-value=3.5  Score=36.87  Aligned_cols=53  Identities=11%  Similarity=0.240  Sum_probs=39.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHH
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ   67 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~   67 (354)
                      .......|+|+||+.|+--.||+..+.+-+.+ -..|-+.    -.+|-||+.|.|..
T Consensus       326 ~a~~~~di~~~nl~rd~rv~dlk~~lr~~~~~-pm~iswk----g~~~k~flh~~~~~  378 (396)
T KOG4410|consen  326 EAGAKTDIKLTNLSRDIRVKDLKSELRKRECT-PMSISWK----GHFGKCFLHFGNRK  378 (396)
T ss_pred             cCccccceeeccCccccchHHHHHHHHhcCCC-ceeEeee----cCCcceeEecCCcc
Confidence            34455679999999999999999999988753 2333332    35678999997754

>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=83.69  E-value=4.9  Score=28.43  Aligned_cols=59  Identities=25%  Similarity=0.408  Sum_probs=34.0

Q ss_pred             CCCCHHHHHHhhccC-C----CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          112 KNVSEAEVSALFSIY-G----TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       112 ~~~t~~~l~~~F~~~-G----~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..++..+|..++..- |    .|-+|+|..+       |+||+-.. +.|.++++.|++.. +.|  +.|+|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~-~~g--k~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKK-IKG--KKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT---SSS------EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCC-CCC--eeEEEEEC
Confidence            456777888777544 3    4778888854       88998876 57889999999876 666  56666653

; PDB: 2G0C_A 3MOJ_B.

>TIGR03636 L23_arch archaeal ribosomal protein L23

Probab=83.53  E-value=4.1  Score=29.22  Aligned_cols=58  Identities=14%  Similarity=0.175  Sum_probs=44.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhh-cC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHh
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKE-FA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC   76 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~-~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l   76 (354)
                      .-|+-.++.+.+..+|++.++. |+ .|.+|+.+.-+.   ..==|||.+...++|.+.-..+
T Consensus        15 n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~---~~KKA~VtL~~g~~a~~va~k~   74 (77)
T TIGR03636        15 NKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPR---GEKKAYVKLAEEYAAEEIASRL   74 (77)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCC---CceEEEEEECCCCcHHHHHHhh
Confidence            4667778999999999999998 77 588888766542   1113999999888887765543

This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.

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

Probab=82.32  E-value=0.76  Score=45.69  Aligned_cols=64  Identities=13%  Similarity=0.194  Sum_probs=55.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS  173 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  173 (354)
                      ...++||+++...+..+-++.+...+|-|..++...        |+|..|.....+.+|+..++... +++..
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~-~~~~k  102 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELN-IDDQK  102 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccC-CCcch
Confidence            367899999999999999999999999998887764        89999999999999999887754 55543

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.50  E-value=4.2  Score=38.18  Aligned_cols=58  Identities=17%  Similarity=0.249  Sum_probs=47.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHH
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFAL-VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA   75 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~-v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~   75 (354)
                      .+=.+.|=|.++|.....+||...|+.|+. --+|+.+.|.       .+|..|.+...|..||..
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            334567889999999999999999999975 4456666665       699999999999999865

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	354
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		7e-36
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		1e-09
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		9e-36
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-09
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-32
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		4e-09
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-18
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-16
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-16
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		3e-16
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		5e-16
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		1e-15
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		3e-09
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		8e-15
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		5e-08
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		9e-15
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		4e-09
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-14
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-13
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-13
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-12
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-07
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-07
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		4e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-07
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		5e-07
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		7e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		4e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-06
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		5e-06
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		1e-05
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		2e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		4e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		4e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		4e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		8e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		2e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-04
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		2e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		5e-04
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		6e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-04

>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 =  147 bits (372), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 72/172 (41%), Positives = 112/172 (65%), Gaps = 4/172 (2%)
Query: 15  VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR--ASRGCCFVICPSRQEADKA 72
           +K+FVGQVP+  +E  L  +F+++  V E+N+++D++     S+GCCFV   +R+ A +A
Sbjct: 16  IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Query: 73  VNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIK 130
            NA HN K LPG   P+Q+K AD E      + KLFIGM+ K  +E ++  +FS +G I+
Sbjct: 76  QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 135
Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
           + +ILRG    S+GCAF+ + T+  A  A++A++    MEG S P+VVK+AD
Sbjct: 136 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 187

>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 = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 52/88 (59%), Gaps = 9/88 (10%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 160
           K+F+G +P+  SE ++  LF  YG + ++ +LR   Q    SKGC F+ + T++   AAL
Sbjct: 17  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK---AAL 73
Query: 161 EAINGKHKME---GSSVPLVVKWADTEK 185
           EA N  H M+   G   P+ +K AD+EK
Sbjct: 74  EAQNALHNMKVLPGMHHPIQMKPADSEK 101

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score =  147 bits (371), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 72/172 (41%), Positives = 112/172 (65%), Gaps = 4/172 (2%)
Query: 15  VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR--ASRGCCFVICPSRQEADKA 72
           +K+FVGQVP+  +E  L  +F+++  V E+N+++D++     S+GCCFV   +R+ A +A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 73  VNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIK 130
            NA HN K LPG   P+Q+K AD E      + KLFIGM+ K  +E ++  +FS +G I+
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123
Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
           + +ILRG    S+GCAF+ + T+  A  A++A++    MEG S P+VVK+AD
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 52/88 (59%), Gaps = 9/88 (10%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 160
           K+F+G +P+  SE ++  LF  YG + ++ +LR   Q    SKGC F+ + T++   AAL
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK---AAL 61
Query: 161 EAINGKHKME---GSSVPLVVKWADTEK 185
           EA N  H M+   G   P+ +K AD+EK
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEK 89

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score =  136 bits (343), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/172 (40%), Positives = 105/172 (61%), Gaps = 4/172 (2%)
Query: 15  VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR--ASRGCCFVICPSRQEADKA 72
           +K FVGQVP+  +E  L  +F+++  V E+N+++D++     S+GCCFV   +R+ A +A
Sbjct: 4   IKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 73  VNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGTIK 130
            NA HN K LPG   P+Q K AD E      + KLFIG + K  +E ++   FS +G I+
Sbjct: 64  QNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIE 123
Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
           + +ILRG    S+GCAF+ + T+  A  A++A +     EG S P VVK+AD
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 160
           K F+G +P+  SE ++  LF  YG + ++ +LR   Q    SKGC F+ + T++ AL A 
Sbjct: 5   KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 161 EAINGKHKMEGSSVPLVVKWADTEK 185
            A++    + G   P+  K AD+EK
Sbjct: 65  NALHNXKVLPGXHHPIQXKPADSEK 89

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 89.4 bits (220), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/83 (51%), Positives = 57/83 (68%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLF+GML K  SE +V  LF  +G I++  ILRG    SKGCAF+KY +  +A AA+ A+
Sbjct: 17  KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 164 NGKHKMEGSSVPLVVKWADTEKE 186
           +G   M G+S  LVVK+ADT+KE
Sbjct: 77  HGSQTMPGASSSLVVKFADTDKE 99

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 84.0 bits (206), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 54/171 (31%), Positives = 97/171 (56%), Gaps = 8/171 (4%)
Query: 14  RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           R  L V  +P++MT+ +L ++F     V+   +I+DK    S G  FV   + ++A++A+
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 74  NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
           N  +    L   S  ++V YA    E + +  L+I  LP+ +++ +V  +FS +G I + 
Sbjct: 62  NTLNG---LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 133 QILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           ++L   Q T  S+G AF++++ + +A  A+ + NG HK  GSS P+ VK+A
Sbjct: 119 RVL-VDQTTGLSRGVAFIRFDKRSEAEEAITSFNG-HKPPGSSEPITVKFA 167

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 82.8 bits (203), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/85 (48%), Positives = 58/85 (68%)
Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           + KLF+GML K  SE +V  LF  +G I +  +LRG   +SKGCAF+K+ +  +A AA+ 
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 162 AINGKHKMEGSSVPLVVKWADTEKE 186
           A++G   M G+S  LVVK+ADT+KE
Sbjct: 75  ALHGSQTMPGASSSLVVKFADTDKE 99

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/85 (45%), Positives = 58/85 (68%)
Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           + KLF+GML K  ++ +V  +F  +GTI +  +LRG   TSKGCAF+K++T  +A AA+ 
Sbjct: 12  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAIN 71
Query: 162 AINGKHKMEGSSVPLVVKWADTEKE 186
            ++    + G+S  LVVK+ADTEKE
Sbjct: 72  TLHSSRTLPGASSSLVVKFADTEKE 96

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 82.0 bits (201), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 53/171 (30%), Positives = 96/171 (56%), Gaps = 8/171 (4%)
Query: 14  RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           R  L V  +P++MT+ +L ++F     V+   +I+DK    S G  FV   + ++A++A+
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 74  NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
           N  +    L   S  ++V YA    E + +  L+I  LP+ +++ +V  +FS +G I + 
Sbjct: 62  NTLNG---LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 133 QILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           ++L   Q T  S+G AF++++ + +A  A+ + NG HK  GSS P+ V +A
Sbjct: 119 RVL-VDQTTGLSRGVAFIRFDKRSEAEEAITSFNG-HKPPGSSEPITVXFA 167

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 57/85 (67%), Gaps = 2/85 (2%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR--ASRGCCFVICPSRQEADKA 72
          +K+FVGQVP+  +E  L  +F+++  V E+N+++D++     S+GCCFV   +R+ A +A
Sbjct: 4  IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 73 VNACHNKKTLPGASSPLQVKYADGE 97
           NA HN K LPG   P+Q+K AD E
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPADSE 88

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---SKGCAFLKYETKEQALAAL 160
           K+F+G +P+  SE ++  LF  YG + ++ +LR   Q    SKGC F+ + T++ AL A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 161 EAINGKHKMEGSSVPLVVKWADTE 184
            A++    + G   P+ +K AD+E
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSE 88

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 77.8 bits (190), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 54/83 (65%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          +KLFVGQ+P+ + E  L  +F+EF  + E+ ++KD+ T   +GC F+   +R  A KA +
Sbjct: 16 IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 75 ACHNKKTLPGASSPLQVKYADGE 97
          A H +KTLPG + P+QVK A  E
Sbjct: 76 ALHEQKTLPGMNRPIQVKPAASE 98

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 162
           KLF+G +P+ + E ++  LF  +G I +L +L+       KGCAFL Y  ++ AL A  A
Sbjct: 17  KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 163 INGKHKMEGSSVPLVVKWADTE 184
           ++ +  + G + P+ VK A +E
Sbjct: 77  LHEQKTLPGMNRPIQVKPAASE 98

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 77.8 bits (190), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 35/81 (43%), Positives = 55/81 (67%)
Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          +KLF+GQ+P+++ E  L  +F+EF  + E+ ++KD+ T   +GC F+    R+ A KA +
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 75 ACHNKKTLPGASSPLQVKYAD 95
          A H +KTLPG + P+QVK AD
Sbjct: 74 ALHEQKTLPGMNRPIQVKPAD 94

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA 162
           KLFIG +P+N+ E ++  LF  +G I +L +L+       KGCAFL Y  +E AL A  A
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 163 INGKHKMEGSSVPLVVKWAD 182
           ++ +  + G + P+ VK AD
Sbjct: 75  LHEQKTLPGMNRPIQVKPAD 94

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 92/171 (53%), Gaps = 6/171 (3%)
Query: 14  RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           +  L V  +P++MT+ +  ++F     ++   +++DK T  S G  FV      +ADKA+
Sbjct: 4   KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 74  NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
           N  +  K     +  ++V YA      + +  L++  LPK +S+ E+  LFS YG I   
Sbjct: 64  NTLNGLKL---QTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITS 120
Query: 133 QILRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
           +IL       S+G  F++++ + +A  A++ +NG+  + G++ P+ VK+A+
Sbjct: 121 RILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPL-GAAEPITVKFAN 170

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 86/167 (51%), Gaps = 6/167 (3%)
Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L V  +P+ MT+ +L A+F+    ++   I++D  T  S G  FV   S  ++ +A+   
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 77  HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
           +    +   +  L+V YA    E + +  L++  LP+ +++ ++  +F  YG+I    IL
Sbjct: 66  NG---ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 136 RGSQQTS-KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           R       +G AF++Y  +E+A  A+ A+N     EG S PL V+ A
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP-EGGSQPLSVRLA 168

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 72.8 bits (177), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/170 (27%), Positives = 91/170 (53%), Gaps = 6/170 (3%)
Query: 14  RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           +  L V  +P++MT+ +  ++F     ++   +++DK T  S G  FV     ++A+KA+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 74  NACHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
           N  +    L   +  ++V YA      + +  L++  LPK +++ E+  LFS YG I   
Sbjct: 62  NTLNG---LRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS 118
Query: 133 QILRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           +IL       S+G  F++++ + +A  A++ +NG  K  G++ P+ VK+A
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG-QKPSGATEPITVKFA 167

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/168 (27%), Positives = 85/168 (50%), Gaps = 6/168 (3%)
Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L V  +P+  T+ +L A+F+    ++   I +D  T  S G  FV   S  ++ +A+   
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 77  HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
           +    +   +  L+V YA    E + +  L++  LP+ +++ ++  +F  YG+I    IL
Sbjct: 77  NG---ITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 133
Query: 136 RGSQQTS-KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
           R       +G AF++Y  +E+A  A+ A+N     EG S PL V+ A+
Sbjct: 134 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP-EGGSQPLSVRLAE 180

>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 = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 70/150 (46%), Gaps = 3/150 (2%)
Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L+VG +   +TEA L   F     +  + + +D  TR S G  +V      +A++A++  
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 77  HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
            N   + G    +     D  L +     +FI  L K++    +   FS +G I   +++
Sbjct: 78  -NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV 136
Query: 136 RGSQQTSKGCAFLKYETKEQALAALEAING 165
              +  SKG  F+ +ET+E A  A+E +NG
Sbjct: 137 -CDENGSKGYGFVHFETQEAAERAIEKMNG 165

>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 = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 70/141 (49%), Gaps = 6/141 (4%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E D A+NA
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 76  CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             +K           V   D +         K+F+G + ++  E  +   F  YG I+ +
Sbjct: 76  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 135
Query: 133 QIL--RGSQQTSKGCAFLKYE 151
           +I+  RGS +  +G AF+ ++
Sbjct: 136 EIMTDRGSGK-KRGFAFVTFD 155

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 70/141 (49%), Gaps = 6/141 (4%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E D A+NA
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 76  CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             +K           V   D +         K+F+G + ++  E  +   F  YG I+ +
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 133 QIL--RGSQQTSKGCAFLKYE 151
           +I+  RGS +  +G AF+ ++
Sbjct: 135 EIMTDRGSGK-KRGFAFVTFD 154

>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 = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 70/141 (49%), Gaps = 6/141 (4%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E D A+NA
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 76  CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             +K           V   D +         K+F+G + ++  E  +   F  YG I+ +
Sbjct: 74  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 133
Query: 133 QIL--RGSQQTSKGCAFLKYE 151
           +I+  RGS +  +G AF+ ++
Sbjct: 134 EIMTDRGSGK-KRGFAFVTFD 153

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 70/141 (49%), Gaps = 6/141 (4%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E D A+NA
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 76  CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             +K           V   D +         K+F+G + ++  E  +   F  YG I+ +
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134
Query: 133 QIL--RGSQQTSKGCAFLKYE 151
           +I+  RGS +  +G AF+ ++
Sbjct: 135 EIMTDRGSGK-KRGFAFVTFD 154

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +PK M++ ++  +F ++  +    I+ D+ T  SRG  F+    R EA++A+   
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 77 HNKKTLPGASSPLQVKYAD 95
          + +K L GA+ P+ VK+A+
Sbjct: 64 NGQKPL-GAAEPITVKFAN 81

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 51/82 (62%), Gaps = 2/82 (2%)
Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAAL 160
           +  L++  LPK +S+ E+  LFS YG I   +IL   +   S+G  F++++ + +A  A+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 161 EAINGKHKMEGSSVPLVVKWAD 182
           + +NG+  + G++ P+ VK+A+
Sbjct: 61  KGLNGQKPL-GAAEPITVKFAN 81

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 70/141 (49%), Gaps = 6/141 (4%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E D A+NA
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 76  CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             +K           V   D +         K+F+G + ++  E  +   F  YG I+ +
Sbjct: 73  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 132
Query: 133 QIL--RGSQQTSKGCAFLKYE 151
           +I+  RGS +  +G AF+ ++
Sbjct: 133 EIMTDRGSGK-KRGFAFVTFD 152

>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 = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 70/150 (46%), Gaps = 3/150 (2%)
Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L+VG +   +TEA L   F     +  + + +D  TR S G  +V      +A++A++  
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 77  HNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL 135
            N   + G    +     D  L +     +FI  L K++    +   FS +G I   +++
Sbjct: 73  -NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV 131
Query: 136 RGSQQTSKGCAFLKYETKEQALAALEAING 165
              +  SKG  F+ +ET+E A  A+E +NG
Sbjct: 132 -CDENGSKGYGFVHFETQEAAERAIEKMNG 160

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 70/141 (49%), Gaps = 6/141 (4%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E D A+NA
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 76  CHNKKTLPGASSPLQVKYADGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
             +K           V   D +         K+F+G + ++  E  +   F  YG I+ +
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127
Query: 133 QIL--RGSQQTSKGCAFLKYE 151
           +I+  RGS +  +G AF+ ++
Sbjct: 128 EIMTDRGSGK-KRGFAFVTFD 147

>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 = 51.6 bits (122), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/80 (36%), Positives = 49/80 (61%), Gaps = 3/80 (3%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L+V  +P+ +T+ QL  +F ++  + + NI++DK T   RG  FV    R+EA +A++A 
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 77 HNKKTLP-GASSPLQVKYAD 95
          +N   +P G S PL V+ A+
Sbjct: 76 NN--VIPEGGSQPLSVRLAE 93

>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 = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAI 163
           L++  LP+ +++ ++  +F  YG+I    ILR       +G AF++Y  +E+A  A+ A+
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 164 NGKHKMEGSSVPLVVKWAD 182
           N     EG S PL V+ A+
Sbjct: 76  NNVIP-EGGSQPLSVRLAE 93

>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 = 40/143 (27%), Positives = 63/143 (44%), Gaps = 11/143 (7%)
Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           K+F+G +    TE  L   F ++  V ++ I+KD  T  SRG  F+        D+ V  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 76  CH---NKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL 132
            H    K   P  + P   +   G       K+F+G +  +V   E    FS +GTI D 
Sbjct: 65  QHILDGKVIDPKRAIPRDEQDKTG-------KIFVGGIGPDVRPKEFEEFFSQWGTIIDA 117
Query: 133 QI-LRGSQQTSKGCAFLKYETKE 154
           Q+ L      S+G  F+ Y++ +
Sbjct: 118 QLMLDKDTGQSRGFGFVTYDSAD 140

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 163
           LF+  + +   E E+   F  YG IK++ + L      SKG A ++YET +QALAA EA+
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 164 NGKHKMEGSSVPLVVKW 180
           NG   M G ++   V W
Sbjct: 135 NGAEIM-GQTIQ--VDW 148

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 163
           LF+  + +   E E+   F  YG IK++ + L      SKG A ++YET +QALAA EA+
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 164 NGKHKM 169
           NG   M
Sbjct: 89  NGAEIM 94

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 40/64 (62%)
Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           +HKLFI  LP + ++ E+  +   +GT+KDL+++       KG A+++YE + QA  A+ 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 162 AING 165
            ++G
Sbjct: 77  KMDG 80

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 75/181 (41%), Gaps = 40/181 (22%)
Query: 16  KLFVGQVPKHMTEAQLLAMF-------------------------KEFALVDEVNIIKDK 50
           +L+VG +P  +TE  ++  F                         K FA ++  ++ +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 51  TTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL----EHKLF 106
              A  G  F      Q     +   H+ + LPG S    V Y  G +  +     HKLF
Sbjct: 66  QAMAFDGIIF------QGQSLKIRRPHDYQPLPGMSENPSV-YVPGVVSTVVPDSAHKLF 118
Query: 107 IGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALAALEA 162
           IG LP  +++ +V  L + +G +K   +++ S    SKG AF +Y      +QA+A L  
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 163 I 163
           +
Sbjct: 179 M 179

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 33/57 (57%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
          K+FVG +P H T+A L   F+ F  ++E  +I D+ T  SRG  FV    R  A++A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 33/59 (55%)
Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          K+FVG +P +  E +L   FK+F +V EV +I D   +  RG  F+     Q  D+AVN
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 160
           E KLF+G L  + +E  +  +FS YG I ++ +++  + Q S+G  F+ +E  + A  A+
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 161 EAINGK 166
            A+NGK
Sbjct: 72  MAMNGK 77

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 42/177 (23%), Positives = 70/177 (39%), Gaps = 52/177 (29%)
Query: 16  KLFVGQVPKHMTEAQLLAMF-------------------------KEFALVDEVNIIKDK 50
           +L+VG +P  +TE  ++  F                         K FA ++  ++ +  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 51  TTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGML 110
              A  G  F      Q     +   H+ + LPGA                 HKLFIG L
Sbjct: 68  QAMAFDGIIF------QGQSLKIRRPHDYQPLPGA-----------------HKLFIGGL 104
Query: 111 PKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALAALEAI 163
           P  +++ +V  L + +G +K   +++ S    SKG AF +Y      +QA+A L  +
Sbjct: 105 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 161

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          ++V  +P  +T   L  +F ++  V +V I+KDK TR S+G  F++   +  A     A 
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 77 HNKK 80
          +NK+
Sbjct: 79 NNKQ 82

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/148 (25%), Positives = 68/148 (45%), Gaps = 14/148 (9%)
Query: 14  RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           R +LFVG +P  +TE ++  +F+++    EV I KDK      G  F+   +R  A+ A 
Sbjct: 22  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAK 75
Query: 74  NACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQ 133
               N   +P     L+V++A          L +  LP+ VS   +   FS++G ++   
Sbjct: 76  VELDN---MPLRGKQLRVRFACHSA-----SLTVRNLPQYVSNELLEEAFSVFGQVERAV 127
Query: 134 ILRGSQQTSKGCAFLKYETKEQALAALE 161
           ++   +    G   +++  K  A  AL+
Sbjct: 128 VIVDDRGRPSGKGIVEFSGKPAARKALD 155

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 9/72 (12%)
Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKE 154
           +GEL     +LF+   P +V E+E++ +F  +G +K+++IL        G AF+++E  E
Sbjct: 26  EGELSNT--RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAE 76
Query: 155 QALAALEAINGK 166
            A  A+E ++GK
Sbjct: 77  SAAKAIEEVHGK 88

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLFIG L +  +E  + A+F  +G I ++ +++     S+G AF+ +E    A  A + +
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 164 NGK 166
           NGK
Sbjct: 69  NGK 71

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/177 (23%), Positives = 70/177 (39%), Gaps = 52/177 (29%)
Query: 16  KLFVGQVPKHMTEAQLLAMF-------------------------KEFALVDEVNIIKDK 50
           +L+VG +P  +TE  ++  F                         K FA ++  ++ +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 51  TTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGML 110
              A  G  F      Q     +   H+ + LPGA                 HKLFIG L
Sbjct: 66  QAMAFDGIIF------QGQSLKIRRPHDYQPLPGA-----------------HKLFIGGL 102
Query: 111 PKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKY---ETKEQALAALEAI 163
           P  +++ +V  L + +G +K   +++ S    SKG AF +Y      +QA+A L  +
Sbjct: 103 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 159

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L+I  LP ++ E E+  +   +G +   +ILR S  TS+G  F + E+ E+  A +   N
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 165 GK 166
           GK
Sbjct: 88  GK 89

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIK--DLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           K+ IG L +NV++  +  +FS YG IK  D+ + R     SKG A++++E  ++A  AL+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 162 AING 165
            ++G
Sbjct: 66  HMDG 69

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQALAALEAI 163
           LF+  + +  +E ++   F+ YG IK++ + L       KG   ++YET ++A AA+E +
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 164 NGKHKMEGSSVPLVVKW 180
           NG+  M     P+ V W
Sbjct: 85  NGQDLM---GQPISVDW 98

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 7/63 (11%)
Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +LF+   P +V E+E++ +F  +G +K+++IL        G AF+++E  E A  A+E +
Sbjct: 6   RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEV 58
Query: 164 NGK 166
           +GK
Sbjct: 59  HGK 61

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 45/172 (26%), Positives = 76/172 (44%), Gaps = 25/172 (14%)
Query: 14  RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           R +LFVG +P  +TE     +F+ +    EV I +D      RG  F+   SR  A+ A 
Sbjct: 22  RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIA- 74
Query: 74  NACHNKKTLPGA---SSPLQVKYADGELERLEH--KLFIGMLPKNVSEAEVSALFSIYGT 128
                K  L G    S PL++++A        H   L +  L   VS   +   FS +G 
Sbjct: 75  -----KAELDGTILKSRPLRIRFAT-------HGAALTVKNLSPVVSNELLEQAFSQFGP 122
Query: 129 IKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI-NGKHKMEGSSVPLVVK 179
           ++   ++   +  + G  F+++  K  A  ALE   +G   +  +  P++V+
Sbjct: 123 VEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE 174

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	354
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-72
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-26
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-50
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-48
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-37
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-36
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-36
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-27
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-36
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-28
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-31
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-28
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-28
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-28
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-27
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-26
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-27
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-26
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-26
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-20
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-17
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-18
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-17
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-17
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	8e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-15
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	8e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-14
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	9e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	9e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-11
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-08
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-12
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-13
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	7e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-11
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-13
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	8e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-11
2div_A	99	TRNA selenocysteine associated protein; structural	1e-12
2div_A	99	TRNA selenocysteine associated protein; structural	4e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-12
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-11
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	8e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	9e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-11
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-11
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-07
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-04
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-11
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-07
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-05
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-10
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-10
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	6e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-09
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-10
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	8e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	8e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	9e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	9e-06
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	4e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	8e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	8e-04

>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 =  222 bits (568), Expect = 1e-72
 Identities = 72/174 (41%), Positives = 113/174 (64%), Gaps = 4/174 (2%)

Query: 13  ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRA--SRGCCFVICPSRQEAD 70
           + +K+FVGQVP+  +E  L  +F+++  V E+N+++D++     S+GCCFV   +R+ A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 71  KAVNACHNKKTLPGASSPLQVKYADGELERL--EHKLFIGMLPKNVSEAEVSALFSIYGT 128
           +A NA HN K LPG   P+Q+K AD E      + KLFIGM+ K  +E ++  +FS +G 
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121

Query: 129 IKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
           I++ +ILRG    S+GCAF+ + T+  A  A++A++    MEG S P+VVK+AD
Sbjct: 122 IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175

>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 =  102 bits (256), Expect = 3e-26
 Identities = 35/92 (38%), Positives = 51/92 (55%), Gaps = 1/92 (1%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
           +  EK ++ E  KLF+G + K  TE  +  MF  F  ++E  I++      SRGC FV  
Sbjct: 85  ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGL-SRGCAFVTF 143

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYAD 95
            +R  A  A+ A H  +T+ G SSP+ VK+AD
Sbjct: 144 TTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175

>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 = 93.4 bits (233), Expect = 5e-23
 Identities = 29/92 (31%), Positives = 50/92 (54%), Gaps = 3/92 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR---GSQQTSKGCAFLKYETKEQALAAL 160
           K+F+G +P+  SE ++  LF  YG + ++ +LR    +   SKGC F+ + T++ AL A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            A++    + G   P+ +K AD+EK       
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNNAVEDR 96

>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 =  163 bits (416), Expect = 5e-50
 Identities = 50/168 (29%), Positives = 86/168 (51%), Gaps = 6/168 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            L V  +P+ MT+ +L A+F+    ++   I++D  T  S G  FV   S  ++ +A+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 76  CHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
             N  T+      L+V YA    E + +  L++  LP+ +++ ++  +F  YG+I    I
Sbjct: 65  -LNGITVRN--KRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121

Query: 135 LRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           LR       +G AF++Y  +E+A  A+ A+N     EG S PL V+ A
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI-PEGGSQPLSVRLA 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 = 81.5 bits (202), Expect = 1e-18
 Identities = 29/87 (33%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
              S +   L+V  +P+ +T+ QL  +F ++  + + NI++DK T   RG  FV    R+
Sbjct: 83  GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYA 94
           EA +A++A +N     G S PL V+ A
Sbjct: 143 EAQEAISALNN-VIPEGGSQPLSVRLA 168

>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 =  158 bits (402), Expect = 7e-48
 Identities = 46/168 (27%), Positives = 90/168 (53%), Gaps = 6/168 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            L V  +P++MT+ +  ++F     ++   +++DK T  S G  FV     ++A+KA+N 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 76  CHNKKTLPGASSPLQVKYADGELERL-EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI 134
            +  +        ++V YA      + +  L++  LPK +++ E+  LFS YG I   +I
Sbjct: 64  LNGLRLQTK---TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120

Query: 135 LRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           L       S+G  F++++ + +A  A++ +NG+ K  G++ P+ VK+A
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ-KPSGATEPITVKFA 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 = 78.4 bits (194), Expect = 1e-17
 Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
             +S     L+V  +PK MT+ +L  +F ++  +    I+ D+ T  SRG  F+    R 
Sbjct: 82  SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYA 94
           EA++A+   +  +   GA+ P+ VK+A
Sbjct: 142 EAEEAIKGLNG-QKPSGATEPITVKFA 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 = 69.9 bits (172), Expect = 1e-14
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR-GSQQTSKGCAFLKYETKEQALAAL 160
           +  L +  LP+N+++ E  +LF   G I+  +++R      S G  F+ Y   + A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQ 188
             +NG  +++     + V +A       
Sbjct: 62  NTLNG-LRLQTK--TIKVSYARPSSASI 86

>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 =  129 bits (327), Expect = 1e-37
 Identities = 41/90 (45%), Positives = 58/90 (64%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           + KLF+GML K  SE +V  LF  +G I +  +LRG   +SKGCAF+K+ +  +A AA+ 
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARR 191
           A++G   M G+S  LVVK+ADT+KE     
Sbjct: 75  ALHGSQTMPGASSSLVVKFADTDKESGPSS 104

>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 =  102 bits (256), Expect = 3e-27
 Identities = 38/97 (39%), Positives = 57/97 (58%), Gaps = 2/97 (2%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
           S  E +   +R KLFVG + K  +E  +L +F+ F ++DE  +++      S+GC FV  
Sbjct: 6   SGSESRGGRDR-KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKF 63

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
            S  EA  A++A H  +T+PGASS L VK+AD + E 
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>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 = 1e-36
 Identities = 48/225 (21%), Positives = 87/225 (38%), Gaps = 18/225 (8%)

Query: 5   KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICP 64
           K  +K+  +R +LFVG +P  +TE     +F+ +    EV I +D      RG  F+   
Sbjct: 13  KPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLE 66

Query: 65  SRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFS 124
           SR  A+ A     +   L     PL++++A          L +  L   VS   +   FS
Sbjct: 67  SRTLAEIAKAEL-DGTILKS--RPLRIRFATHG-----AALTVKNLSPVVSNELLEQAFS 118

Query: 125 IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK-HKMEGSSVPLVVKWADT 183
            +G ++   ++   +  + G  F+++  K  A  ALE        +  +  P++V+  + 
Sbjct: 119 QFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQ 178

Query: 184 EKERQARRAQKAQSQANNLPNADSQHPSLF--GALPMGYAPPYNG 226
             +      +K   +         Q P     G     YA  +  
Sbjct: 179 FDDEDG-LPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKA 222

>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 =  131 bits (332), Expect = 3e-36
 Identities = 41/189 (21%), Positives = 71/189 (37%), Gaps = 11/189 (5%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            L V  +P  +T+ Q   + + F  ++   ++  + T  S+G  F     +  A +A + 
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 76  CHNKKTLPGASSPLQVKYADGELERLE----HKLFIGMLPKNVSEAE-VSALFSIYGTIK 130
              K  L      L V + D             L +  LP   ++ + +    S   +  
Sbjct: 157 LLGKP-LGP--RTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT 213

Query: 131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
             Q+  G     KG A L+YET E A  A +  +G   + GS   L V +       ++ 
Sbjct: 214 FCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGL-SLGGS--HLRVSFCAPGPPGRSM 270

Query: 191 RAQKAQSQA 199
            A    +QA
Sbjct: 271 LAALIAAQA 279

>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 =  106 bits (268), Expect = 6e-27
 Identities = 38/192 (19%), Positives = 80/192 (41%), Gaps = 21/192 (10%)

Query: 5   KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICP 64
           +  ++    R K+ +  +P  +T  ++  +  ++    E+           +G  FV   
Sbjct: 13  EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLL 65

Query: 65  SRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFS 124
           + ++A+ A+NA H  + L      L V+         +  L +  LP ++++ +   L  
Sbjct: 66  NGEQAEAAINAFHQSR-LRE--RELSVQLQ-----PTDALLCVANLPPSLTQQQFEELVR 117

Query: 125 IYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD 182
            +G+++   ++  S++T  SKG  F +Y  K+ A  A   + GK  +      L V W D
Sbjct: 118 PFGSLERCFLVY-SERTGQSKGYGFAEYMKKDSAARAKSDLLGK-PLGPR--TLYVHWTD 173

Query: 183 TEKERQARRAQK 194
             +   A    +
Sbjct: 174 AGQLTPALLHSR 185

>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 =  125 bits (315), Expect = 7e-36
 Identities = 36/89 (40%), Positives = 57/89 (64%)

Query: 12  EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
            + +KLF+GQ+P+++ E  L  +F+EF  + E+ ++KD+ T   +GC F+    R+ A K
Sbjct: 11  HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALK 70

Query: 72  AVNACHNKKTLPGASSPLQVKYADGELER 100
           A +A H +KTLPG + P+QVK AD E   
Sbjct: 71  AQSALHEQKTLPGMNRPIQVKPADSESRG 99

>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 =  105 bits (265), Expect = 1e-28
 Identities = 34/98 (34%), Positives = 54/98 (55%), Gaps = 1/98 (1%)

Query: 94  ADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYET 152
           + G  +    KLFIG +P+N+ E ++  LF  +G I +L +L+       KGCAFL Y  
Sbjct: 5   SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64

Query: 153 KEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           +E AL A  A++ +  + G + P+ VK AD+E    + 
Sbjct: 65  RESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSG 102

>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 =  117 bits (296), Expect = 1e-31
 Identities = 49/200 (24%), Positives = 93/200 (46%), Gaps = 11/200 (5%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L+VG +   +TEA L   F     +  + + +D  TR S G  +V      +A++A++  
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 77  HNKKTLPGASSPLQVKYA--DGELERLEH-KLFIGMLPKNVSEAEVSALFSIYGTIKDLQ 133
            N   + G   P+++ ++  D  L +     +FI  L K++    +   FS +G I   +
Sbjct: 78  -NFDVIKG--KPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCK 134

Query: 134 ILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
           ++   +  SKG  F+ +ET+E A  A+E +NG   M  +   + V    + KER+A    
Sbjct: 135 VVC-DENGSKGYGFVHFETQEAAERAIEKMNG---MLLNDRKVFVGRFKSRKEREAELGA 190

Query: 194 KA-QSQANNLPNADSQHPSL 212
           +A +    ++P+       +
Sbjct: 191 RAKEFYPYDVPDYAGSSGRI 210

>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 (273), Expect = 1e-28
 Identities = 44/203 (21%), Positives = 92/203 (45%), Gaps = 12/203 (5%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
           M++S+  K+  + R KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  F
Sbjct: 1   MSKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59

Query: 61  VICPSRQEADKAVNA-CH---NKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSE 116
           V   + +E D A+NA  H    +   P  +   +     G    +  K+F+G + ++  E
Sbjct: 60  VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTV-KKIFVGGIKEDTEE 118

Query: 117 AEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP 175
             +   F  YG I+ ++I+        +G AF+ ++  +     +      H + G +  
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI--QKYHTVNGHNC- 175

Query: 176 LVVKWADTEKERQARRAQKAQSQ 198
             V+ A   K+  A  +   + +
Sbjct: 176 -EVRKA-LSKQEMASASSSQRGR 196

>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 =  106 bits (268), Expect = 4e-28
 Identities = 36/169 (21%), Positives = 76/169 (44%), Gaps = 11/169 (6%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           L+VG + K +TE  L   F+    +  + I+ DK  + +    FV      +A+ A+   
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIALQTL 61

Query: 77  HNKKTLPGASSPLQVKYA--DGELER-LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQ 133
            N K +    + +++ +A    +        LF+G L  NV +  +   F  + +     
Sbjct: 62  -NGKQIEN--NIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 134 ILRGSQ-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           ++   Q  +S+G  F+ + +++ A  A++++ G    + +  PL + WA
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG---QDLNGRPLRINWA 164

>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 = 57.5 bits (140), Expect = 3e-10
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 3/84 (3%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++G L K ++E  +   F + G I +++I+      +   AF++Y     A  AL+ +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 165 GKHKMEGSSVPLVVKWADTEKERQ 188
           GK ++E +   + + WA   ++  
Sbjct: 63  GK-QIENN--IVKINWAFQSQQSS 83

>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 = 50.6 bits (122), Expect = 8e-08
 Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 3/91 (3%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
            + ++ SS++   LFVG +  ++ +  L   FK+F      +++ D  T +SRG  FV  
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
            S+ +A  A+++    + L G   PL++ +A
Sbjct: 137 TSQDDAQNAMDSM-QGQDLNG--RPLRINWA 164

>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 =  105 bits (265), Expect = 9e-28
 Identities = 40/173 (23%), Positives = 75/173 (43%), Gaps = 14/173 (8%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEV-----NIIKDKTTRASRGCCFVICPSRQEAD 70
           +L+VG +P  +TE  ++  F     +  +     N +        +   F+   S  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 71  KAVNACHNKKTLPGASSPLQVKYA-DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTI 129
           +A+    +     G    L+++   D +     HKLFIG LP  +++ +V  L + +G +
Sbjct: 66  QAMAF--DGIIFQG--QSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPL 121

Query: 130 KDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           K   +++ S    SKG AF +Y        A+  +NG  ++      L+V+ A
Sbjct: 122 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG-MQLGDK--KLLVQRA 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 = 63.8 bits (156), Expect = 2e-12
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 6   KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS 65
            + +      KLF+G +P ++ + Q+  +   F  +   N++KD  T  S+G  F     
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 66  RQEADKAVNACHNKKTLPGASSPLQVKYA 94
               D+A+    N   L      L V+ A
Sbjct: 146 INVTDQAIAGL-NGMQL--GDKKLLVQRA 171

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  105 bits (265), Expect = 3e-27
 Identities = 33/191 (17%), Positives = 77/191 (40%), Gaps = 19/191 (9%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
           + + + +     +++VG +   + E  +   F  F  +  +++  D  T   +G  FV  
Sbjct: 18  AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLE------------HKLFIGMLP 111
              + A  A+    N   L G    ++V       +               +++++  + 
Sbjct: 78  EVPEAAQLALEQ-MNSVMLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVH 134

Query: 112 KNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAINGKHKME 170
           +++S+ ++ ++F  +G IK   + R       KG  F++YE  + +  A+ ++N    + 
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL-FDLG 193

Query: 171 GSSVPLVVKWA 181
           G    L V  A
Sbjct: 194 GQ--YLRVGKA 202

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 67.3 bits (165), Expect = 2e-13
 Identities = 24/103 (23%), Positives = 43/103 (41%), Gaps = 4/103 (3%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQAL 157
             +  ++++G +   + E  +   F+ +G IK + +   S     KG AF++YE  E A 
Sbjct: 25  LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84

Query: 158 AALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN 200
            ALE +N    + G    + V       + Q    Q A+    
Sbjct: 85  LALEQMNS-VMLGGR--NIKVGRPSNIGQAQPIIDQLAEEARA 124

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 56.9 bits (138), Expect = 8e-10
 Identities = 15/93 (16%), Positives = 39/93 (41%), Gaps = 3/93 (3%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
               +  + +    +++V  V + +++  + ++F+ F  +    + +D TT   +G  F+
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

Query: 62  ICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
                Q +  AV++ +           L+V  A
Sbjct: 173 EYEKAQSSQDAVSSMNLFDL---GGQYLRVGKA 202

>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 =  107 bits (269), Expect = 4e-27
 Identities = 34/190 (17%), Positives = 73/190 (38%), Gaps = 20/190 (10%)

Query: 5   KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEF-ALVDEVNIIKDKTTRASRGCCFVIC 63
            +   S      L++   P   T+  +  + ++   +   + +   +    SR   ++  
Sbjct: 108 NEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT-SRRFAYIDV 166

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYAD-GELERLEH-------KLFIGMLPKNVS 115
            S+++A   V   +  K + G    L  K ++  E  +          ++ I  L   + 
Sbjct: 167 TSKEDARYCVEKLNGLK-IEG--YTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELL 223

Query: 116 -EAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEAINGKHKMEGS 172
            E  +   F  +G+I+ + I  G ++   +  CAF+ +E K+ A  AL+  N    +   
Sbjct: 224 DENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSL-LGNR 281

Query: 173 SVPLVVKWAD 182
              + V  AD
Sbjct: 282 --EISVSLAD 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 =  103 bits (260), Expect = 8e-26
 Identities = 34/206 (16%), Positives = 77/206 (37%), Gaps = 21/206 (10%)

Query: 1   MAESKKEKKSSEERVK---LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRG 57
              SKK  ++     +   + V  +PK   + ++   FK    +  V++      + +  
Sbjct: 25  GLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFR 82

Query: 58  CCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEA 117
              +       A  A+      K +    + + V +        E  L++   P + ++ 
Sbjct: 83  FARIEFARYDGALAAIT--KTHKVVGQ--NEIIVSHLT------ECTLWMTNFPPSYTQR 132

Query: 118 EVSALFSIYGTIK-DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL 176
            +  L      +   +++      TS+  A++   +KE A   +E +NG  K+EG    L
Sbjct: 133 NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL-KIEGY--TL 189

Query: 177 VVKWADTEKERQARRAQKAQSQANNL 202
           V K ++     +++R   A  +   +
Sbjct: 190 VTKVSN--PLEKSKRTDSATLEGREI 213

>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 = 64.2 bits (157), Expect = 7e-12
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 83  PGASSPLQVKYADGELERLEH-KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT 141
           P A+     K  +      E   + +  LPK+ ++ +V   F   G I  + +    ++ 
Sbjct: 21  PAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK- 79

Query: 142 SKGCAFLKYETKEQALAALEAINGK 166
           +   A +++   + ALAA+   +  
Sbjct: 80  NFRFARIEFARYDGALAAITKTHKV 104

>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 =  104 bits (261), Expect = 7e-27
 Identities = 44/197 (22%), Positives = 79/197 (40%), Gaps = 27/197 (13%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEV-----NIIKDKTTRASRGCCFVICPSRQEAD 70
           +L+VG +P  +TE  ++  F     +  +     N +        +   F+   S  E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 71  KA--------------VNACHNKKTLPGASSPLQVKYADGELERLE---HKLFIGMLPKN 113
           +A              +   H+ + LPG S    V         +    HKLFIG LP  
Sbjct: 66  QAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 114 VSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAINGKHKMEGS 172
           +++ +V  L + +G +K   +++ S    SKG AF +Y        A+  +NG  ++   
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG-MQLGDK 184

Query: 173 SVPLVVKWADTEKERQA 189
              L+V+ A +   + A
Sbjct: 185 --KLLVQRA-SVGAKNA 198

>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 = 63.1 bits (154), Expect = 5e-12
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 3/93 (3%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
                     +   KLF+G +P ++ + Q+  +   F  +   N++KD  T  S+G  F 
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161

Query: 62  ICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
                   D+A+   +  +        L V+ A
Sbjct: 162 EYVDINVTDQAIAGLNGMQL---GDKKLLVQRA 191

>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 =  101 bits (255), Expect = 3e-26
 Identities = 43/167 (25%), Positives = 74/167 (44%), Gaps = 13/167 (7%)

Query: 12  EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
           +E  K+F+G +    TE  L   F ++  V ++ I+KD  T  SRG  F+        D+
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 72  AVNACHNKKTLPGASSPLQVKYA--DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTI 129
            V   H    L G    +  K A    E ++   K+F+G +  +V   E    FS +GTI
Sbjct: 61  VVKTQH---ILDG--KVIDPKRAIPRDEQDK-TGKIFVGGIGPDVRPKEFEEFFSQWGTI 114

Query: 130 KDLQIL--RGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV 174
            D Q++  + + Q S+G  F+ Y++ +      +  N     +   +
Sbjct: 115 IDAQLMLDKDTGQ-SRGFGFVTYDSADAVDRVCQ--NKFIDFKDRKI 158

>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 = 65.6 bits (161), Expect = 4e-13
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
           +   ++  K+FVG +   +   +    F ++  + +  ++ DK T  SRG  FV   S  
Sbjct: 81  RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD 140

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYA 94
             D+     +           +++K A
Sbjct: 141 AVDRVCQ--NKFIDFKD--RKIEIKRA 163

>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 =  100 bits (252), Expect = 9e-26
 Identities = 32/178 (17%), Positives = 77/178 (43%), Gaps = 15/178 (8%)

Query: 7   EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
           E   S     LF+G +  + + A+L     E    +++ ++  +T   +R   +V   S 
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT-NRKFGYVDFESA 64

Query: 67  QEADKAVNACHNKKTLPGASSPLQVKYADGELERLE---HKLFIGMLPKNVSEAEVSALF 123
           ++ +KA+        + G  + ++++   G   +       L    L  N++E E+  +F
Sbjct: 65  EDLEKALEL--TGLKVFG--NEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVF 120

Query: 124 SIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
                I+   ++    + SKG A+++++++  A   LE   G  +++G    + + + 
Sbjct: 121 EDALEIR---LVSQDGK-SKGIAYIEFKSEADAEKNLEEKQGA-EIDGR--SVSLYYT 171

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 66.1 bits (162), Expect = 4e-13
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            LFIG L  N S AE+    S      DL ++     T++   ++ +E+ E    ALE +
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
            G  K+ G    + ++       ++ R A+ 
Sbjct: 74  TG-LKVFG--NEIKLEKPKGRDSKKVRAART 101

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 51.8 bits (125), Expect = 3e-08
 Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 8/90 (8%)

Query: 5   KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICP 64
            ++ K       L    +  ++TE +L  +F++      + I        S+G  ++   
Sbjct: 90  GRDSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFK 144

Query: 65  SRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           S  +A+K +        + G    + + Y 
Sbjct: 145 SEADAEKNLEEK-QGAEIDG--RSVSLYYT 171

>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 = 82.5 bits (204), Expect = 8e-20
 Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 6/102 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGT-IKDLQILRGSQQT--SKGCAFLKYETKEQALAA 159
            +LFIG +PK     E+    +     + D+ +   +     ++G AF++YE+   A  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 160 LEA-INGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN 200
               + G+ ++ G    + V WA+ E +      +     ++
Sbjct: 69  RRKLMPGRIQLWGH--QIAVDWAEPEIDVDEDVMETVSGPSS 108

>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 = 74.4 bits (183), Expect = 8e-17
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 3/93 (3%)

Query: 10  SSEERVKLFVGQVPKHMTEAQLLAMFKEF-ALVDEVNIIKD-KTTRASRGCCFVICPSRQ 67
            S    +LF+G +PK     ++L    +    V +V +         +RG  FV   S +
Sbjct: 4   GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYADGELER 100
            A  A       +        + V +A+ E++ 
Sbjct: 64  AAAMARRKLMPGRIQLW-GHQIAVDWAEPEIDV 95

>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 = 82.2 bits (202), Expect = 4e-18
 Identities = 32/225 (14%), Positives = 64/225 (28%), Gaps = 17/225 (7%)

Query: 103 HKLFIGMLPKNVSEAEV----SALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           H ++I  L + + + E+     A+FS +G I D+ + R  +   +G AF+ ++    A  
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATN 67

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPM 218
           AL ++ G    +    P+ +++A T+ +  A+       +         +          
Sbjct: 68  ALRSMQGFPFYDK---PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124

Query: 219 GYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMGPR 278
                         G    M       +      G  P +     +           G  
Sbjct: 125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIP--------PPGLA 176

Query: 279 NYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSP 323
              +PP                             L N P   + 
Sbjct: 177 PGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNE 221

>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 = 51.0 bits (121), Expect = 2e-07
 Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 6/79 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           H LF+  LP+  +E  +S LF+ +   K+++++ G        AF++++ + QA AA +A
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDA 263

Query: 163 INGKHKMEGSSVPLVVKWA 181
           + G  K+   +  + + +A
Sbjct: 264 LQG-FKI-TQNNAMKISFA 280

>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 = 49.1 bits (116), Expect = 7e-07
 Identities = 15/92 (16%), Positives = 39/92 (42%), Gaps = 10/92 (10%)

Query: 17  LFVGQVPKHMTEAQLL----AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
           +++  + + + + +L     A+F +F  + ++ + +       RG  FVI      A  A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK---MRGQAFVIFKEVSSATNA 68

Query: 73  VNACHNKKTLPGASSPLQVKYADGELERLEHK 104
           + +       P    P++++YA  + + +   
Sbjct: 69  LRSMQGF---PFYDKPMRIQYAKTDSDIIAKM 97

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.9 bits (105), Expect = 2e-05
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 18  FVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH 77
           F+  +P+   E  L  +F +F         + +         FV   +  +A  A +A  
Sbjct: 211 FLTNLPEETNELMLSMLFNQFP-----GFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQ 265

Query: 78  NKKTLPGASSPLQVKYA 94
             K      + +++ +A
Sbjct: 266 GFKITQN--NAMKISFA 280

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 76.3 bits (188), Expect = 1e-17
 Identities = 17/98 (17%), Positives = 43/98 (43%), Gaps = 2/98 (2%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           +     ++I   P + +  ++       G + ++Q+ R   +  KG  F+ +++ E A  
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQ 196
            +E    K+K   + + ++ K     K+ + R+  K +
Sbjct: 68  FVETPGQKYK--ETDLLILFKDDYFAKKNEERKQNKVE 103

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 16/101 (15%), Positives = 33/101 (32%), Gaps = 4/101 (3%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
               K   + R  +++   P   T   +    ++   V  + + +    +A +G  FV+ 
Sbjct: 2   RWILKNDVKNR-SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVF 59

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHK 104
            S + A K V      +        +  K      +  E K
Sbjct: 60  DSIESAKKFVET--PGQKYKETDLLILFKDDYFAKKNEERK 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 = 76.1 bits (188), Expect = 2e-17
 Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 6/99 (6%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
           +++  K+  ++   L++  +P  M E +L  M K F  V    I++D +   SRG  F  
Sbjct: 14  QAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT-SRGVGFAR 72

Query: 63  CPSRQEADKAVNA-----CHNKKTLPGASSPLQVKYADG 96
             S ++ +  +             +   + PL  K++  
Sbjct: 73  MESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGP 111

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 26/108 (24%), Positives = 49/108 (45%), Gaps = 9/108 (8%)

Query: 85  ASSPLQVKYADGELERLEH----KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ 140
            SS L+      ++ + +      L+I  LP ++ E E+  +   +G +   +ILR S  
Sbjct: 4   GSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG 63

Query: 141 TSKGCAFLKYETKEQALAALEAING-----KHKMEGSSVPLVVKWADT 183
           TS+G  F + E+ E+  A +   NG        +   + PL+ K++  
Sbjct: 64  TSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGP 111

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 77.8 bits (191), Expect = 5e-17
 Identities = 28/207 (13%), Positives = 59/207 (28%), Gaps = 51/207 (24%)

Query: 17  LFVGQV-PKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L V  +    M   ++  +F  +  V++V  +K K      G   V        D+A+  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61

Query: 76  CHNKKTLPGASSPLQVKYA--------------------------------------DGE 97
            +N          + V  +                                         
Sbjct: 62  LNNN---FMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118

Query: 98  LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQI-LRGSQQTSKGCAFLKYETKEQA 156
           ++   + L     P  V+E     +    G  +   + +   +        L++++K  A
Sbjct: 119 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDA 178

Query: 157 LAALEAINGKHKMEGS--SVPLVVKWA 181
           L  L  +N  ++M+      P  +K  
Sbjct: 179 LETLGFLNH-YQMKNPNGPYPYTLKLC 204

>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 = 76.9 bits (189), Expect = 7e-17
 Identities = 36/199 (18%), Positives = 66/199 (33%), Gaps = 44/199 (22%)

Query: 17  LFVGQV-PKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L V  + P+ +T   L  +F  +  V  V I+ +K     +    V      +A  A++ 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 76  CHNKK-------------------TLPGASSPLQVKYADGELERLE-------------- 102
            +  K                           L   Y +  L R +              
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             L +  +P +VSE ++  LFS  G +          Q  +  A ++  + E+A+ AL  
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---QKDRKMALIQMGSVEEAVQALID 177

Query: 163 INGKHKMEGSSVPLVVKWA 181
           ++     E     L V ++
Sbjct: 178 LHNHDLGENH--HLRVSFS 194

>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 = 59.1 bits (143), Expect = 1e-10
 Identities = 26/123 (21%), Positives = 48/123 (39%), Gaps = 9/123 (7%)

Query: 105 LFIGML-PKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           L +  L P+ V+   +  LF +YG ++ ++IL       K  A ++     QA  A+  +
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQLAMSHL 61

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQH-PSLFGALPMGYAP 222
           NG  K+ G   P+ +  +  +  +  R  Q+ Q    +  N+                 P
Sbjct: 62  NGH-KLHGK--PIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118

Query: 223 PYN 225
           P  
Sbjct: 119 PSA 121

>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 = 73.8 bits (182), Expect = 8e-17
 Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 7/87 (8%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           +KL+IG L   V+  ++  LF         Q+L        G AF+ Y  +  A+ A+E 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIET 63

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQA 189
           ++GK ++ G    + V ++ ++K R +
Sbjct: 64  LSGKVELHGK--IMEVDYSVSKKLRSS 88

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 8/92 (8%)

Query: 9   KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
             S    KL++G +   +T   L  +F +  L     ++         G  FV  P +  
Sbjct: 3   SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNW 56

Query: 69  ADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           A +A+     K  L G    ++V Y+  +  R
Sbjct: 57  AIRAIETLSGKVELHG--KIMEVDYSVSKKLR 86

>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 = 73.8 bits (182), Expect = 8e-17
 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
             +L++G L  N S A ++  F  +G+I+ +  ++G        A+++YE+ + A AA  
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACA 71

Query: 162 AINGKHKMEGSSVPLVVKWADTEKER 187
            + G   + G    L V +A +    
Sbjct: 72  KMRGF-PLGGPDRRLRVDFAKSGPSS 96

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +L+VG +  + + A L   F  F  +  ++ +K           ++   S   A  A   
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 76 CHNKKTLPGASSPLQVKYADGE 97
                L G    L+V +A   
Sbjct: 73 MRG-FPLGGPDRRLRVDFAKSG 93

>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 = 72.7 bits (179), Expect = 3e-16
 Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 4/89 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
           K+ +  +P   ++ E+  LFS +G +K +++ +    T   +G  F+ + TK+ A  A  
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQAR 190
           A+     + G    LV++WAD+E   Q+ 
Sbjct: 77  ALCHSTHLYGR--RLVLEWADSEVTVQSG 103

>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 = 72.0 bits (177), Expect = 5e-16
 Identities = 27/100 (27%), Positives = 46/100 (46%), Gaps = 3/100 (3%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT-TRASRGCCF 60
           + S  +    +   K+ V  +P    + ++  +F  F  +  V + K  T T A RG  F
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           V   ++Q+A KA NA  +   L G    L +++AD E+  
Sbjct: 63  VDFITKQDAKKAFNALCHSTHLYG--RRLVLEWADSEVTV 100

>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 = 70.8 bits (174), Expect = 7e-16
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L++G L   ++E ++   F  +G I+ + +++      + CAF+++ T++ A  A E  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 164 NGKHKMEGSSVPLVVKWA 181
             K  + G    L VKW 
Sbjct: 69  FNKLIVNGR--RLNVKWG 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 = 63.8 bits (156), Expect = 3e-13
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L+VG +   +TE  L   F +F  +  + +++ +       C F+   +RQ A+ A   
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAEK 67

Query: 76 CHNKKTLPGASSPLQVKYA 94
            NK  + G    L VK+ 
Sbjct: 68 SFNKLIVNG--RRLNVKWG 84

>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 = 70.1 bits (172), Expect = 3e-15
 Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 3/94 (3%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S        E   +F+  +     E  L  + ++F  +  V ++    T  S+GC F   
Sbjct: 5  SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 64 PSRQEADKAVNACHNKKTLPGASS---PLQVKYA 94
           +++ A K + A   +    G       L+V  A
Sbjct: 65 MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 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 = 63.1 bits (154), Expect = 8e-13
 Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 6/92 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            +FI  L  +  E  +  +   +G +K ++++    ++  SKGCAF ++ T+E A   L 
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH-SKGCAFAQFMTQEAAQKCLA 75

Query: 162 AINGKHKMEGSSV---PLVVKWADTEKERQAR 190
           A + + +  G  +    L V  A T  E  + 
Sbjct: 76  AASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>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 = 69.2 bits (170), Expect = 5e-15
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 8/88 (9%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
            +LF+G LP +++E E+  LF  YG   ++ I +      KG  F++ ET+  A  A   
Sbjct: 16  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-----DKGFGFIRLETRTLAEIAKVE 70

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQAR 190
           ++    + G    L V++A       + 
Sbjct: 71  LDNM-PLRGK--QLRVRFACHSASLTSG 95

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S   +K+  +R +LFVG +P  +TE ++  +F+++    EV I KDK      G  F+  
Sbjct: 5  SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRL 58

Query: 64 PSRQEADKAVNACHNK 79
           +R  A+ A     N 
Sbjct: 59 ETRTLAEIAKVELDNM 74

>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 = 71.0 bits (174), Expect = 5e-15
 Identities = 30/93 (32%), Positives = 53/93 (56%), Gaps = 6/93 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            LF+  + +   E E+   F  YG IK++ +    ++T  SKG A ++YET +QALAA E
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL-DRRTGFSKGYALVEYETHKQALAAKE 132

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
           A+NG  ++ G    + V W   +  ++ ++++K
Sbjct: 133 ALNGA-EIMGQ--TIQVDWCFVKGPKRVKKSEK 162

>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 = 59.1 bits (143), Expect = 8e-11
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 3/93 (3%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
            E +   + S E   LFV  + +   E ++   F ++  +  +++  D+ T  S+G   V
Sbjct: 60  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119

Query: 62  ICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
              + ++A  A  A  N   + G    +QV + 
Sbjct: 120 EYETHKQALAAKEAL-NGAEIMG--QTIQVDWC 149

>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 = 69.2 bits (170), Expect = 5e-15
 Identities = 28/101 (27%), Positives = 53/101 (52%), Gaps = 12/101 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            LF+  L   V+E  +   FS +G ++ ++ L       K  AF+ ++ ++ A+ A+E +
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEM 65

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPN 204
           NGK  +EG    + + +A    +++  R  KAQ QA + P+
Sbjct: 66  NGK-DLEGE--NIEIVFAKPPDQKRKER--KAQRQAASGPS 101

>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 = 48.8 bits (117), Expect = 8e-08
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 11/94 (11%)

Query: 7   EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
                 +   LFV  +   +TE  L   F +F  ++ V  +KD          F+    R
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDER 55

Query: 67  QEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
             A KA+    N K L G    +++ +A    ++
Sbjct: 56  DGAVKAMEE-MNGKDLEG--ENIEIVFAKPPDQK 86

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 69.2 bits (170), Expect = 7e-15
 Identities = 28/104 (26%), Positives = 48/104 (46%), Gaps = 8/104 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            +FI  L K++    +   FS +G I   +++   +  SKG  F+ +ET+E A  A+E +
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-DENGSKGYGFVHFETQEAAERAIEKM 65

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN----NLP 203
           NG   +      + V    + KER+A    +A+   N    N  
Sbjct: 66  NGM-LLNDR--KVFVGRFKSRKEREAELGARAKEFTNVYIKNFG 106

>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 = 57.6 bits (140), Expect = 8e-11
 Identities = 20/114 (17%), Positives = 39/114 (34%), Gaps = 14/114 (12%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            +F+  + K +    L   F  F  +    ++ D+    S+G  FV   +++ A++A+  
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 64

Query: 76  CHNKKTLPGASSPLQVKYADGELERLEHK---------LFIGMLPKNVSEAEVS 120
             N   L      + V       ER             ++I       + A  S
Sbjct: 65  M-NGMLLND--RKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAAAS 115

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 67.9 bits (166), Expect = 1e-14
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KL I  +P ++    + +L   YG ++  + +     +      + Y +K+QA  AL+ +
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQARQALDKL 74

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQ 188
           NG  ++E     L V +   E   Q
Sbjct: 75  NG-FQLENF--TLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
            +   KL +  +P H+    L ++  ++ +V+    +   +  A     +    S+ +A
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYS---SKDQA 67

Query: 70 DKAVNACHNKKTLPGASSPLQVKYADGE 97
           +A++   N   L      L+V Y   E
Sbjct: 68 RQALDKL-NGFQLEN--FTLKVAYIPDE 92

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 68.6 bits (168), Expect = 1e-14
 Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 3/91 (3%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
            KL +  L   VS+A++  LF+ +GT+K   +       S G A + +E +  AL A++ 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
             G   ++G   P+ ++   ++ + +     
Sbjct: 96  YKGV-PLDGR--PMDIQLVASQIDLEHHHHH 123

>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 = 63.2 bits (154), Expect = 1e-12
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 4/101 (3%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
                 +  E   KL V  +   +++A +  +F EF  + +  +  D++ R S G   V 
Sbjct: 24  SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVH 82

Query: 63  CPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEH 103
              R +A KA+         P    P+ ++    +++   H
Sbjct: 83  FERRADALKAMKQYKGV---PLDGRPMDIQLVASQIDLEHH 120

>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 = 67.6 bits (165), Expect = 2e-14
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +  G L   VS  ++  +    G +  L +        K  +F +Y T E++  A   +N
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLN 84

Query: 165 GKHKME--GSSVPLVVKWADT 183
           GK  ++  G  + L + + + 
Sbjct: 85  GKEVVDDLGQKITLYLNFVEK 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 = 56.1 bits (135), Expect = 3e-10
 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           +  G +   ++  QLL + ++  LVD + +  +K         F    + +E+ +A    
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83

Query: 77  HNKKTLP--GASSPLQVKYADG 96
           + K+ +   G    L + + + 
Sbjct: 84  NGKEVVDDLGQKITLYLNFVEK 105

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.9 bits (164), Expect = 3e-14
 Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
            +IG +P   +EA++  LF  +G I D +         KGC F+KY+T EQA   + A+ 
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVALA 84

Query: 165 GKHKMEGSSVPLVVKWADTEKER 187
                +G    L   W    KER
Sbjct: 85  NF-PFQGR--NLRTGWG---KER 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 55.4 bits (134), Expect = 4e-10
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 6/63 (9%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           ++G +P   TEA L+ +F+ F  + +     +K      GCCF+   + ++A   + A 
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVAL 83

Query: 77 HNK 79
           N 
Sbjct: 84 ANF 86

>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 = 66.1 bits (162), Expect = 6e-14
 Identities = 19/100 (19%), Positives = 45/100 (45%), Gaps = 9/100 (9%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            +++G +P + +E ++  L S  G + +L+++    QT  SKG AF+++   E + +A+ 
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF-DPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANN 201
            +NG  ++      L   ++                  ++
Sbjct: 63  NLNGY-QLGSR--FLKCGYS---SNSDISGVSLEHHHHHH 96

>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 = 57.2 bits (139), Expect = 6e-11
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           +++G +P   TE Q+L +      V  + ++ D  T  S+G  F+     + +  AV  
Sbjct: 4  VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

>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 = 69.3 bits (169), Expect = 6e-14
 Identities = 35/200 (17%), Positives = 65/200 (32%), Gaps = 46/200 (23%)

Query: 17  LFVGQV-PKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L V  + P+ +T   L  +F  +      ++ + K     +    V      +A  A++ 
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYG-----DVQRVKILFNKKENALVQMADGNQAQLAMSH 91

Query: 76  CHNKKTLPG--------------------ASSPLQVKYADGELERLEHK----------- 104
             N   L G                        L   Y +  L R +             
Sbjct: 92  L-NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 150

Query: 105 ---LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
              L +  +P +VSE ++  LFS  G +          Q  +  A ++  + E+A+ AL 
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---QKDRKMALIQMGSVEEAVQALI 207

Query: 162 AINGKHKMEGSSVPLVVKWA 181
            ++     E     L V ++
Sbjct: 208 DLHNHDLGENH--HLRVSFS 225

>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 = 55.4 bits (133), Expect = 4e-09
 Identities = 28/123 (22%), Positives = 51/123 (41%), Gaps = 9/123 (7%)

Query: 105 LFIGML-PKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           L +  L P+ V+   +  LF +YG ++ ++IL       K  A ++     QA  A+  +
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQLAMSHL 92

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGAL-PMGYAP 222
           NG HK+ G   P+ +  +  +  +  R  Q+ Q    +  N+        G+       P
Sbjct: 93  NG-HKLHGK--PIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 149

Query: 223 PYN 225
           P  
Sbjct: 150 PSA 152

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 66.2 bits (162), Expect = 8e-14
 Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 6/88 (6%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAAL 160
             LF+  + +   E E+   F  YG IK++ +    ++T  SKG A ++YET +QALAA 
Sbjct: 27  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL-DRRTGFSKGYALVEYETHKQALAAK 85

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQ 188
           EA+NG  ++ G    + V W   +  ++
Sbjct: 86  EALNGA-EIMGQ--TIQVDWCFVKGPKR 110

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
           E +   + S E   LFV  + +   E ++   F ++  +  +++  D+ T  S+G   V 
Sbjct: 15  ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 74

Query: 63  CPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
             + ++A  A  A  N   + G    +QV + 
Sbjct: 75  YETHKQALAAKEAL-NGAEIMG--QTIQVDWC 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 65.8 bits (161), Expect = 9e-14
 Identities = 25/85 (29%), Positives = 46/85 (54%), Gaps = 10/85 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +LF+   P +V E+E++ +F  +G +K+++IL        G AF+++E  E A  A+E +
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEV 85

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQ 188
           +GK        PL V ++    +R 
Sbjct: 86  HGK-SFANQ--PLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 51.5 bits (124), Expect = 9e-09
 Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 11/98 (11%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
                ++      +LFV   P  + E++L  +F  F  + EV I+         G  FV 
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVE 71

Query: 63  CPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
               + A KA+   H  K+      PL+V Y+    +R
Sbjct: 72  FEEAESAAKAIEEVHG-KSFAN--QPLEVVYSKLPAKR 106

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 67.6 bits (165), Expect = 1e-13
 Identities = 21/92 (22%), Positives = 43/92 (46%), Gaps = 3/92 (3%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
             KL +  L   VS+A++  LF+ +GT+K   +       S G A + +E +  AL A++
Sbjct: 88  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
              G   ++G   P+ ++   ++ + +     
Sbjct: 148 QYKGV-PLDGR--PMDIQLVASQIDLEHHHHH 176

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 60.6 bits (147), Expect = 3e-11
 Identities = 19/102 (18%), Positives = 39/102 (38%), Gaps = 4/102 (3%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
                  +  E   KL V  +   +++A +  +F EF  + +  +  D++ R S G   V
Sbjct: 76  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADV 134

Query: 62  ICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEH 103
               R +A KA+              P+ ++    +++   H
Sbjct: 135 HFERRADALKAMKQYKGVPL---DGRPMDIQLVASQIDLEHH 173

>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 = 64.9 bits (159), Expect = 1e-13
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 5/86 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
           K+ IG L +NV++  +  +FS YG IK + +   R     SKG A++++E  ++A  AL+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 162 AINGKHKMEGSSVPLVVKWADTEKER 187
            ++G  +++G    +          R
Sbjct: 66  HMDGG-QIDGQ--EITATAVLAPWPR 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 = 56.4 bits (137), Expect = 1e-10
 Identities = 12/70 (17%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDK-TTRASRGCCFVICPSRQEA 69
          S +  K+ +G++ +++T+  ++ +F  +  +  +++  ++     S+G  +V   +  EA
Sbjct: 1  SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 70 DKAVNACHNK 79
          +KA+      
Sbjct: 61 EKALKHMDGG 70

>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 = 65.8 bits (161), Expect = 1e-13
 Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 3/108 (2%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
             KLFIG L +  +E  + A+F  +G I ++ +++     S+G AF+ +E    A  A +
Sbjct: 7   PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK 66

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQH 209
            +NGK  + G    + V+ A     +   R +   S  N  P+   +H
Sbjct: 67  DMNGK-SLHGK--AIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
          M E+    K       LF+G + +   E  L A+F +   + EV +IKD+T++ SRG  F
Sbjct: 1  MVEADHPGK-------LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK-SRGFAF 52

Query: 61 VICPSRQEADKAVNACHNK 79
          +   +  +A  A    + K
Sbjct: 53 ITFENPADAKNAAKDMNGK 71

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L++  L  + SE  +   F+        ++     +  +  AF+ +  +E A+ A++A+
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKAL 71

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRA 192
           NGK  ++GS  P+ V  A    +  +  +
Sbjct: 72  NGK-VLDGS--PIEVTLAKPVDKDSSGPS 97

>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 = 50.0 bits (120), Expect = 3e-08
 Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 10/93 (10%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
            S  E   S  ++ L+V  +    +E  +   F          + K       R   FV
Sbjct: 4  GSSGDEDTMSSVKI-LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFV 56

Query: 62 ICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
             +R++A +A+ A  N K L G  SP++V  A
Sbjct: 57 HFSNREDAVEAMKAL-NGKVLDG--SPIEVTLA 86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 65.5 bits (160), Expect = 1e-13
 Identities = 13/103 (12%), Positives = 39/103 (37%), Gaps = 6/103 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           ++    L  NV E  +  +   YG +++++IL   + +   G A + + +   A   ++ 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 163 INGKHKMEGSSVPLVVKWAD--TEKERQARRAQKAQSQANNLP 203
           ++    + G+   +  +      ++ +              +P
Sbjct: 68  LHLT-SVMGN--IIHAQLDIKGQQRMKYYELIVNGSYTPQTVP 107

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 62.4 bits (152), Expect = 2e-12
 Identities = 15/64 (23%), Positives = 29/64 (45%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++   ++  ++ E  L  M +++  V+EV I+    TR   G   V+  S + A + V  
Sbjct: 8  EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 76 CHNK 79
           H  
Sbjct: 68 LHLT 71

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 22/93 (23%), Positives = 46/93 (49%), Gaps = 9/93 (9%)

Query: 103 HKLFIGMLPKNVSEAE----VSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           H ++I  L + + + E    + A+FS +G I D+ + R  +   +G AF+ ++    A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATN 66

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
           AL ++ G         P+ +++A T+ +  A+ 
Sbjct: 67  ALRSMQGFP-FYDK--PMRIQYAKTDSDIIAKM 96

>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 = 43.0 bits (102), Expect = 9e-06
 Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 10/82 (12%)

Query: 17 LFVGQVPKHMTEAQL----LAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKA 72
          +++  + + + + +L     A+F  F  + ++ + +   +   RG  FVI      A  A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 67

Query: 73 VNACHNKKTLPGASSPLQVKYA 94
          + +       P    P++++YA
Sbjct: 68 LRSMQGF---PFYDKPMRIQYA 86

>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 = 65.5 bits (160), Expect = 2e-13
 Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 5/96 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             L+I  LP  ++  E+  +F  YG I+ +++    +  ++G A++ YE    A  A++ 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDH 66

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQ 198
           ++G + +      LVV + +  +  Q    +K + Q
Sbjct: 67  LSGFN-VSNR--YLVVLYYNANRAFQKMDTKKKEEQ 99

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
          +   E    L++  +P  +T  ++  +F ++  + ++ +     T  +RG  +V+     
Sbjct: 2  RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIF 58

Query: 68 EADKAVNACHNKK 80
          +A  AV+      
Sbjct: 59 DAKNAVDHLSGFN 71

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 21/79 (26%), Positives = 37/79 (46%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
             S      +  +  ++V  +P  +T   L  +F ++  V +V I+KDK TR S+G  F
Sbjct: 3  SGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62

Query: 61 VICPSRQEADKAVNACHNK 79
          ++   +  A     A +NK
Sbjct: 63 ILFLDKDSAQNCTRAINNK 81

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 96  GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETK 153
           G L   +  +++  LP +++  ++  +FS YG +  + I+  + +++ SKG AF+ +  K
Sbjct: 10  GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRK-SKGVAFILFLDK 68

Query: 154 EQALAALEAINGK 166
           + A     AIN K
Sbjct: 69  DSAQNCTRAINNK 81

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 64.7 bits (158), Expect = 2e-13
 Identities = 16/90 (17%), Positives = 33/90 (36%), Gaps = 3/90 (3%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFA--LVDEVNIIKDKTTRASRGCCFVICPS 65
                   + +  +  H     ++     +A   V+ + +IKDK T+ +RG  FV   S
Sbjct: 3  HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS 62

Query: 66 RQEADKAVNACHNKKTLPG-ASSPLQVKYA 94
            +A + +    +           + V +A
Sbjct: 63 AMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 10/68 (14%), Positives = 30/68 (44%), Gaps = 3/68 (4%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGT--IKDLQILRGSQ-QTSKGCAFLKYETKEQALAA 159
             + +  +  +     +    S Y +  + ++++++  Q Q ++G AF++  +   A   
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 160 LEAINGKH 167
           L+ +   H
Sbjct: 70  LQILQSLH 77

>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 = 65.4 bits (160), Expect = 2e-13
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 3/98 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            +F+  L   V   ++  +FS+ G +    IL      S+G   + +E   +A+ A+   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANN 201
           NG+  +     P+ VK  +    +      +   Q+  
Sbjct: 77  NGQ-LLFDR--PMHVKMDERALPKGDFFPPERPQQSGP 111

>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 = 53.9 bits (130), Expect = 2e-09
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 9   KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
           ++      +FV  +   +   +L  +F    +V   +I++DK  + SRG   V      E
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGTVTFEQSIE 68

Query: 69  ADKAVNACHNKKTLPGASSPLQVKYADGELERLEH 103
           A +A++  + +        P+ VK  +  L + + 
Sbjct: 69  AVQAISMFNGQLL---FDRPMHVKMDERALPKGDF 100

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 22/65 (33%), Positives = 40/65 (61%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           +HKLFI  LP + ++ E+  +   +GT+KDL+++       KG A+++YE + QA  A+ 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76

Query: 162 AINGK 166
            ++G 
Sbjct: 77  KMDGM 81

>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 = 3e-12
 Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
           +S E+ KLF+  +P   T+ +L  + K    V ++ ++ ++  +  +G  +V   +  +
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQ 70

Query: 69 ADKAVNACHNK 79
          A +AV      
Sbjct: 71 ASQAVMKMDGM 81

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 67.9 bits (165), Expect = 2e-13
 Identities = 26/168 (15%), Positives = 57/168 (33%), Gaps = 33/168 (19%)

Query: 55  SRGCCFV--ICPSRQE-----ADKAVNACHNKKTLPGASSPLQVK---YADGELERLEHK 104
           ++G C +   C              +          G       +      G   +    
Sbjct: 77  AKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKT 136

Query: 105 LFIGMLPKNVS---------EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQ 155
           L++G +   ++         E+ +  +FS  G I  ++ +       K C F+K++ +  
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQAN 191

Query: 156 ALAALEAINGK---------HKMEGSSVPLVVKWADTEKERQARRAQK 194
           A  A EA++ +                  L+VKWA+ + +  A++  +
Sbjct: 192 AEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDPAAQKRLQ 239

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 43.6 bits (102), Expect = 4e-05
 Identities = 18/90 (20%), Positives = 32/90 (35%), Gaps = 16/90 (17%)

Query: 17  LFVGQVP---------KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
           L+VG +              E+++  +F     +D +  ++ K       C FV    + 
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQA 190

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYADGE 97
            A+ A  A  N +TL   S        +G 
Sbjct: 191 NAEFAKEAMSN-QTLLLPSDKEWDDRREGT 219

>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 = 65.6 bits (160), Expect = 3e-13
 Identities = 18/79 (22%), Positives = 43/79 (54%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
            ++++++K  ++   L+VG +  + TE Q+  +F +   + ++ +  DK  + + G CFV
Sbjct: 27  GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86

Query: 62  ICPSRQEADKAVNACHNKK 80
              SR +A+ A+   +  +
Sbjct: 87  EYYSRADAENAMRYINGTR 105

>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 = 60.2 bits (146), Expect = 3e-11
 Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L++G L    +E ++  LFS  G IK + +      +T+ G  F++Y ++  A  A+  
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 163 INGKHKMEGSSVPLVVKWADTEKE-RQARRAQK 194
           ING  +++     +   W    KE RQ  R + 
Sbjct: 101 INGT-RLDDR--IIRTDWDAGFKEGRQYGRGRS 130

>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 = 63.8 bits (156), Expect = 4e-13
 Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 7/93 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR----GSQQTSKGCAFLKYETKEQALAA 159
            LFI  L  + +E  +  +FS  G IK   I +         S G  F++Y+  EQA  A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
           L+ + G   ++G    L V+ ++   +  +  +
Sbjct: 67  LKQLQGH-TVDGH--KLEVRISERATKPASGPS 96

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 19/93 (20%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 11  SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRA---SRGCCFVICPSRQ 67
           S     LF+  +    TE  L  +F +   +    I K K       S G  FV     +
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           +A KA+               L+V+ ++   + 
Sbjct: 62  QAQKALKQLQGHTV---DGHKLEVRISERATKP 91

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 63.0 bits (154), Expect = 6e-13
 Identities = 18/78 (23%), Positives = 37/78 (47%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          + S   + + +    L V  +  + TE  L  +F ++  + +V+I+ D+ +R SRG  FV
Sbjct: 3  SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

Query: 62 ICPSRQEADKAVNACHNK 79
             +  +A +A    +  
Sbjct: 63 YFENVDDAKEAKERANGM 80

>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 = 55.3 bits (134), Expect = 4e-10
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAA 159
              L +  L    +E ++  +FS YG I D+ I+   QQ+  S+G AF+ +E  + A  A
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY-DQQSRRSRGFAFVYFENVDDAKEA 73

Query: 160 LEAINGK 166
            E  NG 
Sbjct: 74  KERANGM 80

>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 = 63.5 bits (155), Expect = 6e-13
 Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 11/89 (12%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           ++ G +   +++  +   FS +G I ++++        KG +F+++ T E A  A+ ++N
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82

Query: 165 GKHKMEGSSVPLVVKWADTEKERQARRAQ 193
           G   +EG    +   W    KE     + 
Sbjct: 83  GT-TIEGH--VVKCYWG---KESPDMTSG 105

>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 = 48.1 bits (115), Expect = 2e-07
 Identities = 13/71 (18%), Positives = 30/71 (42%), Gaps = 6/71 (8%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
          +SS +   ++ G +   +T+  +   F  F  + E+ +  +K      G  FV   + + 
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHES 73

Query: 69 ADKAVNACHNK 79
          A  A+ + +  
Sbjct: 74 AAHAIVSVNGT 84

>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 = 63.4 bits (155), Expect = 7e-13
 Identities = 16/72 (22%), Positives = 34/72 (47%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
           + +++   + V  + +   E  L  +F+ F  +  + + KDKTT  S+G  F+    R+
Sbjct: 9  NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68

Query: 68 EADKAVNACHNK 79
          +A +A+      
Sbjct: 69 DAARAIAGVSGF 80

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAA 159
              + +  L ++  E ++  LF  +G+I  + + +  + T  SKG AF+ +  +E A  A
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAK-DKTTGQSKGFAFISFHRREDAARA 73

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           +  ++G    +   + L V+WA         
Sbjct: 74  IAGVSG-FGYDH--LILNVEWAKPSTNSGPS 101

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.0 bits (154), Expect = 7e-13
 Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S      + +  KLFVG +     E  L  +F ++  + EV ++KD+ T+ SRG  FV  
Sbjct: 2  SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 64 PSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           +  +A  A+ A  N K++ G    ++V  A
Sbjct: 62 ENIDDAKDAMMAM-NGKSVDG--RQIRVDQA 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 = 58.8 bits (143), Expect = 3e-11
 Identities = 26/91 (28%), Positives = 49/91 (53%), Gaps = 6/91 (6%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAA 159
           E KLF+G L  + +E  +  +FS YG I ++ ++  R +Q+ S+G  F+ +E  + A  A
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR-SRGFGFVTFENIDDAKDA 70

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           + A+NG   ++G    + V  A    + ++ 
Sbjct: 71  MMAMNG-KSVDGR--QIRVDQAGKSSDNRSG 98

>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 = 63.9 bits (156), Expect = 7e-13
 Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 6/90 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            LF+  + +  +E ++   F+ YG IK++ +   R +    KG   ++YET ++A AA+E
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY-LKGYTLVEYETYKEAQAAME 82

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARR 191
            +NG+  + G   P+ V W       + +R
Sbjct: 83  GLNGQ-DLMGQ--PISVDWCFVRGPPKGKR 109

>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 = 58.9 bits (143), Expect = 4e-11
 Identities = 17/70 (24%), Positives = 31/70 (44%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
          S E   LFV  V +  TE  +   F E+  +  +++  D+ T   +G   V   + +EA 
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78

Query: 71 KAVNACHNKK 80
           A+   + + 
Sbjct: 79 AAMEGLNGQD 88

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 63.1 bits (154), Expect = 8e-13
 Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 4/99 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFS-IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAAL 160
           E+ LF+G L  +V +  +   F  +Y + +  +++      SKG  F+K+  + +   AL
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQA 199
               G   +   S P+ +  A   K  + +  +   S  
Sbjct: 69  TECQG--AVGLGSKPVRLSVA-IPKASRVKPVESGPSSG 104

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 17 LFVGQVPKHMTEAQLLAMF-KEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          LFVG +   + +  L   F K +       ++ D+T   S+G  FV      E  +A+  
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGV-SKGYGFVKFTDELEQKRALTE 70

Query: 76 CHNKKTLPGASSPLQVKYA 94
          C     L   S P+++  A
Sbjct: 71 CQGAVGL--GSKPVRLSVA 87

>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 = 63.0 bits (154), Expect = 8e-13
 Identities = 26/101 (25%), Positives = 54/101 (53%), Gaps = 6/101 (5%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYET 152
           D  ++R    +F+G +P   +E ++  +FS  G +   +++   ++T   KG  F +Y+ 
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY-DRETGKPKGYGFCEYQD 59

Query: 153 KEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
           +E AL+A+  +NG+ +  G    L V  A +EK ++  ++ 
Sbjct: 60  QETALSAMRNLNGR-EFSGR--ALRVDNAASEKNKEELKSL 97

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 3/105 (2%)

Query: 7   EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
           +         +FVG +P   TE QL  +F E   V    ++ D+ T   +G  F     +
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 67  QEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLP 111
           + A  A+    N +   G    L+V  A  E  + E K      P
Sbjct: 61  ETALSAMRNL-NGREFSG--RALRVDNAASEKNKEELKSLGTGAP 102

>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 = 62.2 bits (152), Expect = 1e-12
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEF--ALVDEVNIIKDKTTRASRGCCFVICPSRQEADK 71
          R+ L++G +    T+  L           + E+   +++    S+G   V   S   + K
Sbjct: 1  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 72 AVNACHNKKTLPGASSPLQVKYA 94
           ++    K+ L G      V  +
Sbjct: 61 LMDLL-PKRELHG--QNPVVTPS 80

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 15/93 (16%), Positives = 38/93 (40%), Gaps = 11/93 (11%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGT--IKDLQIL--RGSQQTSKGCAFLKYETKEQALA 158
             L+IG L    ++ +++      G   I +++    R + Q SKG A +   ++  +  
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ-SKGFALVGVGSEASSKK 60

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
            ++ +  + ++ G     VV  +    + +   
Sbjct: 61  LMDLLPKR-ELHGQ--NPVVTPS---NKLEHHH 87

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 26/99 (26%), Positives = 48/99 (48%), Gaps = 12/99 (12%)

Query: 85  ASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTS 142
              P   +  +G        LF+  + +  +E ++   F+ YG IK++ +   R +    
Sbjct: 12  GDEPGPQRSVEG------WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY-L 64

Query: 143 KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           KG   ++YET ++A AA+E +NG+  + G   P+ V W 
Sbjct: 65  KGYTLVEYETYKEAQAAMEGLNGQ-DLMGQ--PISVDWC 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 57.7 bits (140), Expect = 7e-11
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 11  SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
           S E   LFV  V +  TE  +   F E+  +  +++  D+ T   +G   V   + +EA 
Sbjct: 20  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79

Query: 71  KAVNACHNKKTLPGASSPLQVKYA 94
            A+    N + L G   P+ V + 
Sbjct: 80  AAMEGL-NGQDLMG--QPISVDWC 100

>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 = 25/84 (29%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEF-ALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
          SS     L++G +  +M E  +   F      V  V II+++ T    G CFV       
Sbjct: 5  SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64

Query: 69 ADKAVNACHNKKTLPGASSPLQVK 92
          A+K ++   N K LPGA+   + K
Sbjct: 65 AEKCLHKI-NGKPLPGATPAKRFK 87

>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 = 49.6 bits (119), Expect = 4e-08
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYG-TIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALE 161
            L++G L   + E  +S  F+  G T+  ++I+R        G  F+++     A   L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 162 AINGKHKMEGS--SVPLVVKWA 181
            INGK  + G+  +    + +A
Sbjct: 71  KINGK-PLPGATPAKRFKLNYA 91

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 20/108 (18%), Positives = 46/108 (42%), Gaps = 5/108 (4%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSK 143
           G+S         G     + ++++G LP ++   ++  +F  YG I+D+ +     +   
Sbjct: 4   GSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGP 61

Query: 144 GCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
             AF+++E    A  A+   +G    +G    L V++  + +   +  
Sbjct: 62  PFAFVEFEDPRDAEDAVYGRDGY-DYDGYR--LRVEFPRSGRGTGSGP 106

>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 = 47.7 bits (114), Expect = 3e-07
 Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 3  ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
                 +     +++VG +P  +    +  +F ++  + ++++   K  R      FV 
Sbjct: 11 GGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVE 67

Query: 63 CPSRQEADKAVNACHNK 79
              ++A+ AV      
Sbjct: 68 FEDPRDAEDAVYGRDGY 84

>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 = 62.5 bits (152), Expect = 3e-12
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 3/100 (3%)

Query: 9   KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
              +    L V  +P  + E QL  +F+ +  ++ V I+ D+ TR SRG  FV   S   
Sbjct: 37  PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96

Query: 69  ADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIG 108
           A +A+    N   +      L+V  A    +R      +G
Sbjct: 97  AQQAIAGL-NGFNILN--KRLKVALAASGHQRPGIAGAVG 133

>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 = 56.7 bits (137), Expect = 3e-10
 Identities = 28/141 (19%), Positives = 52/141 (36%), Gaps = 12/141 (8%)

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALF 123
            S+ +           +       P      + ++ R    L +  +P  V E ++  LF
Sbjct: 7   VSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLR---NLMVNYIPTTVDEVQLRQLF 63

Query: 124 SIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
             YG I+ ++I+  R ++Q S+G  F+K+++   A  A+  +NG   +      L V  A
Sbjct: 64  ERYGPIESVKIVCDRETRQ-SRGYGFVKFQSGSSAQQAIAGLNGF-NILN--KRLKVALA 119

Query: 182 DTEKERQARRAQKAQSQANNL 202
                   R          N 
Sbjct: 120 ---ASGHQRPGIAGAVGDGNG 137

>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 = 61.1 bits (149), Expect = 3e-12
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KL +G +    +  E+ A F  YG + +  I++         AF+  E  E A+ A+  +
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGL 64

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARR 191
           +   + +G    + V+ + T + R A  
Sbjct: 65  DNT-EFQGK--RMHVQLS-TSRLRTASG 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 = 49.5 bits (119), Expect = 4e-08
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 11/93 (11%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
             S +   KL VG +    T  +L A F+E+  V E +I+        +   FV     +
Sbjct: 4   GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAE 55

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           +A +A+    N     G    + V+ +   L  
Sbjct: 56  DAVEAIRGLDN-TEFQG--KRMHVQLSTSRLRT 85

>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 = 61.5 bits (150), Expect = 3e-12
 Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 6/89 (6%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAAL 160
             L++  L   V+E ++ +LF+ +   K   I      T   +G AF+ +  KE A  AL
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQF-RMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQA 189
             +NG  K+ G    LV+++   +K+R +
Sbjct: 85  HLVNGY-KLYGK--ILVIEFGKNKKQRSS 110

>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 = 58.5 bits (142), Expect = 5e-11
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            L++  +   +TE  L+++F  F       I     T   RG  F+  P+++ A +A++ 
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 76  CHNKKTLPGASSPLQVKYA 94
            +           L +++ 
Sbjct: 87  VNGY---KLYGKILVIEFG 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 = 60.7 bits (148), Expect = 5e-12
 Identities = 23/89 (25%), Positives = 46/89 (51%), Gaps = 4/89 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L++  L   + +  +   FS +GTI   +++    + SKG  F+ + + E+A  A+  +
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR-SKGFGFVCFSSPEEATKAVTEM 75

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRA 192
           NG+     ++ PL V  A  ++ERQ+  +
Sbjct: 76  NGR---IVATKPLYVALAQRKEERQSGPS 101

>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 = 57.6 bits (140), Expect = 7e-11
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 5/91 (5%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S  ++ +  + V L+V  +   + + +L   F  F  +    ++ +     S+G  FV  
Sbjct: 5  SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCF 62

Query: 64 PSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           S +EA KAV   + +     A+ PL V  A
Sbjct: 63 SSPEEATKAVTEMNGRIV---ATKPLYVALA 90

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 61.2 bits (149), Expect = 5e-12
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 3/93 (3%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
           A +  ++    E   LF+  +P+  T+  L + F  F  V    +  DK T  S+   FV
Sbjct: 28  AAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFV 87

Query: 62  ICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
              +   A  A+ A +  +     +  L+V+  
Sbjct: 88  SFDNPDSAQVAIKAMNGFQV---GTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 25/106 (23%), Positives = 49/106 (46%), Gaps = 8/106 (7%)

Query: 81  TLPGASSPLQVKYADGELERLEH----KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR 136
           T P AS  L    A    +++E      LFI  LP+  ++ ++++ F  +G +   ++  
Sbjct: 15  TSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI 74

Query: 137 GSQ-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
             Q   SK   F+ ++  + A  A++A+NG  ++      L V+  
Sbjct: 75  DKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF-QVGTK--RLKVQLK 117

>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 = 60.7 bits (148), Expect = 5e-12
 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 11/100 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA- 162
            +F+G +   + E E+ + F+ YG++K+++I+      SKG  F+ +         +E+ 
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70

Query: 163 --INGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN 200
              +GK         L +  A  ++       Q      N
Sbjct: 71  INFHGK--------KLKLGPAIRKQNLSTYHVQPRPLIFN 102

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           +FVG +   M E ++ + F  +  V EV II D+T   S+G  FV   +  +  K V +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV-SKGYGFVSFYNDVDVQKIVES 69

Query: 76 CHN 78
            N
Sbjct: 70 QIN 72

>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 = 60.8 bits (148), Expect = 6e-12
 Identities = 21/64 (32%), Positives = 33/64 (51%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
            KL +  L   VS+A++  LF+ +GT+K   +       S G A + +E K  AL A++ 
Sbjct: 30  GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 89

Query: 163 INGK 166
            NG 
Sbjct: 90  YNGV 93

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
                    E   KL V  +   +++A +  +F EF  + +  +  D++ R S G   V 
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVH 76

Query: 63  CPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
              + +A KA+   +     P    P+ ++  
Sbjct: 77  FERKADALKAMKQYNGV---PLDGRPMNIQLV 105

>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 = 60.3 bits (147), Expect = 6e-12
 Identities = 16/71 (22%), Positives = 28/71 (39%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
            S    +LFV  +    +E  L  +F  +  + E++   D  T+  +G  FV     + 
Sbjct: 3  SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 69 ADKAVNACHNK 79
          A KA      +
Sbjct: 63 AVKAYAEVDGQ 73

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
           +LF+  L    SE ++  LFS YG + +L       +++  KG AF+ +   E A+ A  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKK-PKGFAFVTFMFPEHAVKAYA 68

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQKA 195
            ++G+   +G    L V  + T K+  ++    +
Sbjct: 69  EVDGQV-FQGR--MLHVLPS-TIKKEASQSGPSS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.7 bits (148), Expect = 6e-12
 Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 4/85 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L++G L ++V+E  +  LFS  G  K  +++     ++    F+++     A AAL A+
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAAM 75

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQ 188
           NG+ K+ G    + V WA T   ++
Sbjct: 76  NGR-KILGK--EVKVNWATTPSSQK 97

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L+VG + + +TE  +L +F +        +I + T+      CFV     ++A  A+ A
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74

>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 = 60.4 bits (147), Expect = 8e-12
 Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 2   AESKKEKKSSEER--VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCC 59
                +  S EER    +F  Q+   +    L   F     V +V II D+ +R S+G  
Sbjct: 11  VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70

Query: 60  FVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL 101
           +V     Q    A+      + L G   P+ V+ +  E  RL
Sbjct: 71  YVEFCEIQSVPLAIGL--TGQRLLG--VPIIVQASQAEKNRL 108

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 26/110 (23%), Positives = 52/110 (47%), Gaps = 7/110 (6%)

Query: 83  PGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQ 140
            G S   +        ER    +F   L   +   ++   FS  G ++D++I+  R S++
Sbjct: 6   SGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR 65

Query: 141 TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
            SKG A++++   +    A+  + G  ++ G  VP++V+ +  EK R + 
Sbjct: 66  -SKGIAYVEFCEIQSVPLAI-GLTG-QRLLG--VPIIVQASQAEKNRLSG 110

>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 = 59.9 bits (146), Expect = 8e-12
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 11/88 (12%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KLFIG LP+  +E E+ +LF  YG + +  I+       K   F+  E K  A  A+  +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARR 191
           +   K+ G    + V+ +   K + +  
Sbjct: 63  HHY-KLHGV--NINVEAS-KNKSKASSG 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 = 49.1 bits (118), Expect = 4e-08
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 11/91 (12%)

Query: 10  SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
            S   VKLF+G +P+  TE ++ ++F+++  V E +IIK           FV    +  A
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAA 55

Query: 70  DKAVNACHNKKTLPGASSPLQVKYADGELER 100
           + A+   H+ K L G    + V+ +  + + 
Sbjct: 56  EDAIRNLHHYK-LHG--VNINVEASKNKSKA 83

>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 = 59.5 bits (145), Expect = 9e-12
 Identities = 17/64 (26%), Positives = 27/64 (42%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L++  +    T+  L+ + + +  +     I DKTT   +G  FV   S   A KAV A
Sbjct: 7  GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 76 CHNK 79
              
Sbjct: 67 LKAS 70

>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 = 53.3 bits (129), Expect = 2e-09
 Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            L+I  L    ++ ++  L   YG I   + +  + + +  KG  F+ +++   A  A+ 
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNK-CKGYGFVDFDSPSAAQKAVT 65

Query: 162 AINGK 166
           A+   
Sbjct: 66  ALKAS 70

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 21/100 (21%), Positives = 38/100 (38%), Gaps = 3/100 (3%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
              +   +K   E   LF+  +P+   +  LL MF  F  V    +  DK T  S+   F
Sbjct: 12  SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 71

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           V   +   A  A+ + +  +        L+V+    + + 
Sbjct: 72  VSYDNPVSAQAAIQSMNGFQI---GMKRLKVQLKRSKNDS 108

>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 = 57.7 bits (140), Expect = 7e-11
 Identities = 22/112 (19%), Positives = 49/112 (43%), Gaps = 5/112 (4%)

Query: 83  PGASSPLQVKYADGELERLEH-KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-Q 140
               +   +  A  + E  E   LFI  LP+   + ++  +F  +G +   ++    Q  
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN 64

Query: 141 TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            SK   F+ Y+    A AA++++NG  ++      L V+   ++ + ++  +
Sbjct: 65  LSKCFGFVSYDNPVSAQAAIQSMNGF-QIGMK--RLKVQLKRSKNDSKSGPS 113

>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 = 59.9 bits (146), Expect = 1e-11
 Identities = 23/99 (23%), Positives = 49/99 (49%), Gaps = 6/99 (6%)

Query: 94  ADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYE 151
               +   +  L++G L + V +  + A F  +G I D+QI     +++  +G AF+++E
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK-HRGFAFVEFE 62

Query: 152 TKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
             E A AA++ +N   ++ G    + V  A   + +++ 
Sbjct: 63  LAEDAAAAIDNMNES-ELFGR--TIRVNLAKPMRIKESG 98

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S      +  +  L+VG + + + +  L A F  F  + ++ I  D  T   RG  FV  
Sbjct: 2  SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 64 PSRQEADKAVNACHNKK 80
             ++A  A++  +  +
Sbjct: 62 ELAEDAAAAIDNMNESE 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 = 59.5 bits (145), Expect = 1e-11
 Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 10/89 (11%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
            K+F+G +    +  E+ +LF   G + +  ++       K  AF+  E +  A AA+  
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQ 62

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARR 191
           +NGK +++G    + V+ +   +++    
Sbjct: 63  LNGK-EVKGK--RINVELSTKGQKKSGPS 88

>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 = 51.1 bits (123), Expect = 1e-08
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 11/93 (11%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
             SS    K+FVG V    T  +L ++F+    V E +++K           FV      
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEA 54

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           +A  A+   +  K + G    + V+ +    ++
Sbjct: 55  DAKAAIAQLNG-KEVKG--KRINVELSTKGQKK 84

>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 = 60.0 bits (146), Expect = 1e-11
 Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 4/89 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
             +L +  +P    + ++  +F  +G I D++I+  +++ SKG  F+ +E    A  A E
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFENSADADRARE 73

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQAR 190
            ++G   +EG    + V  A       + 
Sbjct: 74  KLHGT-VVEGR--KIEVNNATARVMTNSG 99

>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 = 58.1 bits (141), Expect = 4e-11
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S    +S     +L V  +P    +  L  MF +F  + +V II ++    S+G  FV  
Sbjct: 5  SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 62

Query: 64 PSRQEADKAVNACHNK 79
           +  +AD+A    H  
Sbjct: 63 ENSADADRAREKLHGT 78

>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 = 59.1 bits (144), Expect = 1e-11
 Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 6/88 (6%)

Query: 96  GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETK 153
           G +   +  L++G L + V +  + A F  +G I D+QI     +++  +G AF+++E  
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK-HRGFAFVEFELA 59

Query: 154 EQALAALEAINGKHKMEGSSVPLVVKWA 181
           E A AA++ +N   ++ G    + V  A
Sbjct: 60  EDAAAAIDNMNES-ELFGR--TIRVNLA 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 = 57.9 bits (141), Expect = 4e-11
 Identities = 16/70 (22%), Positives = 32/70 (45%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
          +  +  L+VG + + + +  L A F  F  + ++ I  D  T   RG  FV     ++A 
Sbjct: 4  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 71 KAVNACHNKK 80
           A++  +  +
Sbjct: 64 AAIDNMNESE 73

>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 = 60.1 bits (146), Expect = 1e-11
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 11/119 (9%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-- 141
           G+S     K            +F+G L   ++  ++ A F+ +G I D ++++    T  
Sbjct: 1   GSSGSSGQKKDTSN----HFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVK-DMATGK 55

Query: 142 SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN 200
           SKG  F+ +  K  A  A++ + G+         +   WA T K    +   ++ ++ +
Sbjct: 56  SKGYGFVSFFNKWDAENAIQQMGGQ---WLGGRQIRTNWA-TRKPPAPKSTYESNTKQS 110

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 19/78 (24%), Positives = 37/78 (47%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          + S  +KK +     +FVG +   +T   + A F  F  + +  ++KD  T  S+G  FV
Sbjct: 3  SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62

Query: 62 ICPSRQEADKAVNACHNK 79
             ++ +A+ A+     +
Sbjct: 63 SFFNKWDAENAIQQMGGQ 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 8/88 (9%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+++G L     + E+   FS YG ++ + I R       G AF+++E    A  A+  +
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR----NPPGFAFVEFEDPRDAEDAVRGL 57

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARR 191
           +GK  + GS   + V+ + T   R++R 
Sbjct: 58  DGK-VICGSR--VRVELS-TGMPRRSRF 81

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 5/66 (7%)

Query: 15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          +K++VG +     + +L   F  +  +  V I ++       G  FV     ++A+ AV 
Sbjct: 1  MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVR 55

Query: 75 ACHNKK 80
              K 
Sbjct: 56 GLDGKV 61

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S    ++  +  +L V  +P    +  L  MF +F  + +V II ++    S+G  FV  
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 76

Query: 64 PSRQEADKAVNACHNK 79
           +  +AD+A    H  
Sbjct: 77 ENSADADRAREKLHGT 92

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 57.7 bits (140), Expect = 8e-11
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +L +  +P    + ++  +F  +G I D++I+  +++ SKG  F+ +E    A  A E +
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFENSADADRAREKL 89

Query: 164 NGK 166
           +G 
Sbjct: 90  HGT 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 59.1 bits (144), Expect = 1e-11
 Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 12/94 (12%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++F+  LP + +   +   F+  G +    I   + + SKGC  +K+E+ E A  A   +
Sbjct: 10  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-SKGCGVVKFESPEVAERACRMM 68

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQS 197
           NG  K+ G    + V        R  R A    S
Sbjct: 69  NGM-KLSGR--EIDV--------RIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 48.3 bits (116), Expect = 8e-08
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++FV  +P   T   L   F E   V   +I  +     S+GC  V   S + A++A   
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67

Query: 76 CHNK 79
           +  
Sbjct: 68 MNGM 71

>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 = 60.1 bits (146), Expect = 2e-11
 Identities = 17/78 (21%), Positives = 36/78 (46%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
           +     + + +    L V  +  + TE  L  +F ++  + +V+I+ D+ +R SRG  FV
Sbjct: 34  SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 62  ICPSRQEADKAVNACHNK 79
              +  +A +A    +  
Sbjct: 94  YFENVDDAKEAKERANGM 111

>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 = 53.6 bits (129), Expect = 3e-09
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 3/65 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            L +  L    +E ++  +FS YG I D+ I+   QQ+  S+G AF+ +E  + A  A E
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVY-DQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 162 AINGK 166
             NG 
Sbjct: 107 RANGM 111

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
              LFIG L  N S AE+    S      DL ++     T++   ++ +E+ E    ALE
Sbjct: 17  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE 76

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            + G  K+ G+   + ++     K R   R 
Sbjct: 77  -LTGL-KVFGN--EIKLEKP---KGRDGTRG 100

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 17/94 (18%), Positives = 40/94 (42%), Gaps = 5/94 (5%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
          M E   E   S     LF+G +  + + A+L     E    +++ ++  +T   +R   +
Sbjct: 4  MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGT-NRKFGY 62

Query: 61 VICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
          V   S ++ +KA+        + G  + ++++  
Sbjct: 63 VDFESAEDLEKALEL--TGLKVFG--NEIKLEKP 92

>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 = 59.1 bits (144), Expect = 2e-11
 Identities = 18/69 (26%), Positives = 34/69 (49%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
          S     L+VG +  ++TE  L  +F+ F  +D + ++KD  T  S+G  F+     + A 
Sbjct: 2  SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 71 KAVNACHNK 79
          +A+   +  
Sbjct: 62 RALEQLNGF 70

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 9/91 (9%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            L++G L  N++E  +  +F  +G I ++ ++    + + SKG  F+ +   E A  ALE
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGR-SKGYGFITFSDSECARRALE 65

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +NG  ++ G   P+ V       ER    +
Sbjct: 66  QLNGF-ELAGR--PMRVGHV---TERLDGGS 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 59.9 bits (145), Expect = 2e-11
 Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 9/94 (9%)

Query: 103 HKLFIGMLPKNVSEAE----VSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
             + I  +   V + +    + AL S  G I D+ +       + G A++ + T+E A A
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDD--NSGKAYIVFATQESAQA 87

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            +EA  G    +G+  PLV+ +++T + + A   
Sbjct: 88  FVEAFQGYP-FQGN--PLVITFSETPQSQVAEDG 118

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 47.2 bits (112), Expect = 6e-07
 Identities = 16/113 (14%), Positives = 40/113 (35%), Gaps = 13/113 (11%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCF 60
            +       +E    + +  +   + + +L A+     +   ++  I    +  + G  +
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAY 76

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYA---------DGELERLEHK 104
           ++  +++ A   V A       P   +PL + ++         DG LE   H 
Sbjct: 77  IVFATQESAQAFVEAFQGY---PFQGNPLVITFSETPQSQVAEDGSLEHHHHH 126

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 22/108 (20%), Positives = 48/108 (44%), Gaps = 11/108 (10%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTS 142
           G+S P+  +  D         +++G L + VSE  +  LF   G + +  + +       
Sbjct: 4   GSSGPISERNQDA-------TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQH 56

Query: 143 KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           +G  F+++ ++E A  A++ ++   K+ G   P+ V  A    +  + 
Sbjct: 57  QGYGFVEFLSEEDADYAIKIMDMI-KLYGK--PIRVNKASAHNKNLSG 101

>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 = 57.3 bits (139), Expect = 8e-11
 Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 3/87 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            ++VG + + ++E  L  +F +   V   ++ KD+ T   +G  FV   S ++AD A+  
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76

Query: 76  CHNKKTLPGASSPLQVKYADGELERLE 102
               K L G   P++V  A    + L 
Sbjct: 77  MDMIK-LYG--KPIRVNKASAHNKNLS 100

>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 = 59.8 bits (145), Expect = 3e-11
 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 9/98 (9%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKD------LQILRGSQQTSKGCAFLKYETKEQA 156
            ++++  L K+V E ++  +F  Y             I    +   KG AF+    ++ A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 157 LAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
             AL+  NG   + G   P+VV++A + + +Q  +  K
Sbjct: 106 AKALKEANGY-VLFGK--PMVVQFARSARPKQDPKEGK 140

>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 = 48.7 bits (116), Expect = 2e-07
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 8/98 (8%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNI-----IKDKTTRASR 56
               +  +  E   +++V  + KH+ E  L  +F  +             I+       +
Sbjct: 33  LSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMK 92

Query: 57  GCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           G  F+  P+ + A KA+   +          P+ V++A
Sbjct: 93  GQAFIGLPNEKAAAKALKEANGY---VLFGKPMVVQFA 127

>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 = 58.5 bits (142), Expect = 3e-11
 Identities = 19/74 (25%), Positives = 38/74 (51%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          A +   +K S   ++L+VG +  ++TE  L  +F+ F  ++ + ++ D  T  S+G  F+
Sbjct: 14 AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73

Query: 62 ICPSRQEADKAVNA 75
               + A KA+  
Sbjct: 74 TFSDSECAKKALEQ 87

>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 = 55.4 bits (134), Expect = 4e-10
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 7/86 (8%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAAL 160
            +L++G L  N++E  +  +F  +G I+ +Q++    + + SKG  F+ +   E A  AL
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR-SKGYGFITFSDSECAKKAL 85

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKE 186
           E +NG  ++ G   P+ V    TE+ 
Sbjct: 86  EQLNGF-ELAGR--PMKVGHV-TERT 107

>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 = 58.5 bits (142), Expect = 3e-11
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 11/89 (12%)

Query: 104 KLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           ++FIG L    V +++V  +FS YG +    +        KG AF++Y  +  A AA+  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLG 81

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARR 191
            NG+  + G    L +  A   K  ++  
Sbjct: 82  ENGR-VLAGQ--TLDINMAGEPKPDRSGP 107

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 10/65 (15%), Positives = 28/65 (43%), Gaps = 9/65 (13%)

Query: 16 KLFVGQVPKH-MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
          ++F+G +    + ++ +  +F ++  V   ++         +G  FV   + + A  AV 
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 75 ACHNK 79
            + +
Sbjct: 81 GENGR 85

>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 = 59.9 bits (145), Expect = 4e-11
 Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            L +  L    S   +  +F  YG + D+ I R  + T  S+G AF+++  K  A  A++
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR-DRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRA 192
           A++G   ++G    L V+ A   +   +  +
Sbjct: 131 AMDGA-VLDGR--ELRVQMARYGRPPDSHHS 158

>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 = 59.5 bits (144), Expect = 6e-11
 Identities = 18/78 (23%), Positives = 35/78 (44%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
           +         E    L V  +    +   L  +F+++  V +V I +D+ T+ SRG  FV
Sbjct: 58  SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117

Query: 62  ICPSRQEADKAVNACHNK 79
               +++A+ A++A    
Sbjct: 118 RFHDKRDAEDAMDAMDGA 135

>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 = 57.8 bits (140), Expect = 4e-11
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            + +  LP++ +  EV  L   Y  +K   + R     +K  AF+     EQA  A++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-----NKRTAFVTLLNGEQAQNAIQMF 60

Query: 164 NGKHKMEGSSVPLVVKWADTEK 185
           +  +   G    L+V+   T+ 
Sbjct: 61  HQ-YSFRG--KDLIVQLQPTDA 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 = 46.2 bits (110), Expect = 5e-07
 Identities = 13/87 (14%), Positives = 30/87 (34%), Gaps = 10/87 (11%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
          S     + V  +P+     ++  + K++        +K      ++   FV   + ++A 
Sbjct: 2  SSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQ 54

Query: 71 KAVNACHNKKTLPGASSPLQVKYADGE 97
           A+   H      G    L V+    +
Sbjct: 55 NAIQMFHQYS-FRG--KDLIVQLQPTD 78

>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 = 58.0 bits (141), Expect = 5e-11
 Identities = 17/70 (24%), Positives = 31/70 (44%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
            +  + L V  +    +   L  +F+++  V +V I ++  T+A RG  FV    R++A
Sbjct: 9  DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 70 DKAVNACHNK 79
            A  A    
Sbjct: 69 QDAEAAMDGA 78

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 9/90 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            L +  L    S   +  +F  YG + D+ I R    T   +G AF+++  +  A  A  
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR-EPHTKAPRGFAFVRFHDRRDAQDAEA 73

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARR 191
           A++G  +++G    L V+ A   +  +   
Sbjct: 74  AMDGA-ELDGR--ELRVQVA---RYGRRDL 97

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 59.0 bits (143), Expect = 5e-11
 Identities = 18/77 (23%), Positives = 35/77 (45%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
              +     E    L V  +    +   L  +F+++  V +V I +D+ T+ SRG  FV 
Sbjct: 36  SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95

Query: 63  CPSRQEADKAVNACHNK 79
              +++A+ A++A    
Sbjct: 96  FHDKRDAEDAMDAMDGA 112

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 55.5 bits (134), Expect = 7e-10
 Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            L +  L    S   +  +F  YG + D+ I R  + T  S+G AF+++  K  A  A++
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR-DRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRA 192
           A++G   ++G    L V+ A   +   +  +
Sbjct: 108 AMDGA-VLDGR--ELRVQMARYGRPPDSHHS 135

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 59.0 bits (143), Expect = 5e-11
 Identities = 18/79 (22%), Positives = 34/79 (43%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
             S     S+  +  L+VG + + + +  L A F  F  + ++ I  D  T   RG  FV
Sbjct: 51  GGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 110

Query: 62  ICPSRQEADKAVNACHNKK 80
                ++A  A++  +  +
Sbjct: 111 EFELAEDAAAAIDNMNESE 129

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 57.5 bits (139), Expect = 2e-10
 Identities = 25/105 (23%), Positives = 48/105 (45%), Gaps = 7/105 (6%)

Query: 78  NKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG 137
            ++ + G S               +  L++G L + V +  + A F  +G I D+QI   
Sbjct: 42  TERHVDGGSGGSGGSGGS---ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 98

Query: 138 SQ-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
            + +  +G AF+++E  E A AA++ +N   ++ G    + V  A
Sbjct: 99  YETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGR--TIRVNLA 140

>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 = 57.7 bits (140), Expect = 5e-11
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 10/85 (11%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L++     +++   +   FS +G I DL +        + CAF+ YE  E A  A+  +N
Sbjct: 18  LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESADQAVAELN 70

Query: 165 GKHKMEGSSVPLVVKWADTEKERQA 189
           G  ++E     L V  A  +    +
Sbjct: 71  GT-QVESV--QLKVNIARKQPMLDS 92

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          + S  E+++  +   L+V      MT   L   F  F  + ++++   +       C FV
Sbjct: 3  SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFV 54

Query: 62 ICPSRQEADKAVNACHNK 79
               + AD+AV   +  
Sbjct: 55 TYEKMESADQAVAELNGT 72

>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 = 57.7 bits (140), Expect = 6e-11
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          + S      S+    LFV  + +  TE  L   F          I+ D+ T +S+G  FV
Sbjct: 3  SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFV 59

Query: 62 ICPSRQEADKAVNACHNKK 80
             S ++A  A  A  + +
Sbjct: 60 DFNSEEDAKAAKEAMEDGE 78

>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 = 45.7 bits (109), Expect = 1e-06
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 12/91 (13%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGT---IKDLQILRGSQQTSKGCAFLKYETKEQALAAL 160
            LF+  L ++ +E  +   F        + D    R +   SKG  F+ + ++E A AA 
Sbjct: 17  TLFVKGLSEDTTEETLKESFDGSVRARIVTD----RETGS-SKGFGFVDFNSEEDAKAAK 71

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQARR 191
           EA+    +++G+   + + WA   K      
Sbjct: 72  EAMEDG-EIDGN--KVTLDWA-KPKGEGGSG 98

>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 = 57.1 bits (139), Expect = 6e-11
 Identities = 18/64 (28%), Positives = 33/64 (51%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           LFVG +  ++ +  L   FK+F      +++ D  T +SRG  FV   S+ +A  A+++
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 76 CHNK 79
             +
Sbjct: 63 MQGQ 66

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 20/85 (23%), Positives = 42/85 (49%), Gaps = 7/85 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
            LF+G L  NV +  +   F  + +     ++    QT  S+G  F+ + +++ A  A++
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW-DMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 162 AINGKHKMEGSSVPLVVKWADTEKE 186
           ++ G+   + +  PL + WA  + E
Sbjct: 62  SMQGQ---DLNGRPLRINWA-AKLE 82

>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 = 58.1 bits (141), Expect = 7e-11
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 2  AESKKEKKSSEERV-KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
              + KK  +E+  KLF+G +    TE  L   ++++  + +  +++D  ++ SRG  F
Sbjct: 14 TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73

Query: 61 VICPSRQEADKAVNA 75
          V   S  E D A+ A
Sbjct: 74 VTFSSMAEVDAAMAA 88

>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 = 45.3 bits (108), Expect = 2e-06
 Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           KLFIG L    +E  +   +  +G + D  ++R    + S+G  F+ + +  +  AA+ A
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 163 ----INGK 166
               I+G+
Sbjct: 89  RPHSIDGR 96

>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 = 59.5 bits (143), Expect = 1e-10
 Identities = 20/161 (12%), Positives = 52/161 (32%), Gaps = 18/161 (11%)

Query: 30  QLLAMFKEF-ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP 88
           +++  F     L  + N+I +  +++      +     +                     
Sbjct: 49  EIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVK 108

Query: 89  LQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFL 148
            +  Y  G              P + +  ++       G + ++Q+ R   +  KG  F+
Sbjct: 109 NRSVYIKG-------------FPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFV 155

Query: 149 KYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQA 189
            +++ E A   +E    K+K       L++ + D    ++ 
Sbjct: 156 VFDSIESAKKFVETPGQKYK----ETDLLILFKDDYFAKKN 192

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 55.9 bits (136), Expect = 1e-10
 Identities = 19/60 (31%), Positives = 29/60 (48%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+FVG +  + T   +   F++F  VD+  ++ DKTT   RG  FV   S    +K    
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 46.7 bits (112), Expect = 2e-07
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
           K+F+G L  N +  +V   F  +G + D  ++  + + +  +G  F+ +E+++      E
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNR-HRGFGFVTFESEDIVEKVCE 59

Query: 162 A----INGK 166
                IN K
Sbjct: 60  IHFHEINNK 68

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 11/93 (11%)

Query: 100 RLEHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
             + +LFIG LP KNVS+ ++  +FS YG I  + I            F++++  +    
Sbjct: 8   PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRD 60

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
           A+E  + +    G    L+++ + +    Q   
Sbjct: 61  AIECESQE-MNFGK--KLILEVSSSNARPQFDH 90

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 16/97 (16%)

Query: 1  MAESKKEKKSSEERVKLFVGQVP-KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCC 59
          M E       S    +LF+G +P K++++  L  +F  +  + ++NI             
Sbjct: 1  MTEMHNIPPKS----RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFG 48

Query: 60 FVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADG 96
          F+   + Q    A+     +    G    L ++ +  
Sbjct: 49 FIQFDNPQSVRDAIECESQEM-NFG--KKLILEVSSS 82

>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 = 59.7 bits (144), Expect = 1e-10
 Identities = 24/151 (15%), Positives = 54/151 (35%), Gaps = 9/151 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGT--IKDLQIL--RGSQQTSKGCAFLKYETKEQALA 158
             L+IG L    ++ +++      G   I +++    R + Q SKG A +   ++  +  
Sbjct: 69  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ-SKGFALVGVGSEASSKK 127

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQHPSLFGALPM 218
            ++ +  + ++ G     VV   + +   Q     +  +Q+  +       P   G+   
Sbjct: 128 LMDLLPKR-ELHGQ--NPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPG-GSSRA 183

Query: 219 GYAPPYNGYGYQASGSYGLMQYRLPPMQNQP 249
            +     G G       G  ++  P     P
Sbjct: 184 AFPQGGRGRGRFPGAVPGGDRFPGPAGPGGP 214

>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 = 53.6 bits (128), Expect = 1e-08
 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD--EVNIIKDKTTRASRGCC 59
           A        + +R+ L++G +    T+  L        + D  E+   +++    S+G  
Sbjct: 56  AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115

Query: 60  FVICPSRQEADKAVNACHNK 79
            V   S   + K ++    +
Sbjct: 116 LVGVGSEASSKKLMDLLPKR 135

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 55.6 bits (135), Expect = 2e-10
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+F+G +    T+  L   F +F  V E  +++D  T+ SRG  FV    +   DK +  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+FIG L    ++  +   F  +G +K+  ++R    + S+G  F+ +  +      L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 163 INGKHKMEGSSV 174
              +H+++  ++
Sbjct: 62  --SRHELDSKTI 71

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 1/79 (1%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
            S       E    +FVG +   + E  L  +F +   + +V I KD+  +  +   FV
Sbjct: 4  GSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFV 62

Query: 62 ICPSRQEADKAVNACHNKK 80
               +    A+   +  +
Sbjct: 63 CFKHPESVSYAIALLNGIR 81

>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 = 54.6 bits (132), Expect = 6e-10
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           E  +  +F+G L   V E  +  LF   G +  + I +  +   K   F+ ++  E    
Sbjct: 13  EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSY 72

Query: 159 ALEAINGKHKMEGSSVPLVVKWA 181
           A+  +NG  ++ G   P+ V   
Sbjct: 73  AIALLNGI-RLYGR--PINVSGP 92

>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 = 56.2 bits (136), Expect = 2e-10
 Identities = 19/102 (18%), Positives = 40/102 (39%), Gaps = 12/102 (11%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE--------VNIIKDKTT 52
          M         S+    +FV  + +++T   +   FK+  ++          +N+  D+ T
Sbjct: 1  MGHHHHHHSHSDNN-TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59

Query: 53 RASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
             +G   V       A  A++    K+   G  +P++V +A
Sbjct: 60 GKLKGEATVSFDDPPSAKAAIDWFDGKE-FSG--NPIKVSFA 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 = 53.5 bits (129), Expect = 2e-09
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 12/96 (12%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-------QT--SKGC 145
                   + +F+  L +NV+   V+  F   G IK  +             +T   KG 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 146 AFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           A + ++    A AA++  +GK +  G+  P+ V +A
Sbjct: 66  ATVSFDDPPSAKAAIDWFDGK-EFSGN--PIKVSFA 98

>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 = 57.0 bits (138), Expect = 2e-10
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
             S +EKK  ++R  ++VG V    T   L A F     ++ + I+ DK +   +G  +
Sbjct: 24 QPLSAEEKKEIDKR-SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAY 82

Query: 61 VICPSRQEADKAVN 74
          +    R   D AV 
Sbjct: 83 IEFAERNSVDAAVA 96

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 22/130 (16%), Positives = 47/130 (36%), Gaps = 15/130 (11%)

Query: 69  ADKAVNACHNKKTLPGASSPLQVKYADGELERLEH--KLFIGMLPKNVSEAEVSALFSIY 126
           A        + K   GA +    +    E ++      +++G +    +  ++ A FS  
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 127 GTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV---PLVVKWA 181
           G+I  + IL  + S    KG A++++  +    AA+        M+ +      + V   
Sbjct: 61  GSINRITILCDKFSGH-PKGYAYIEFAERNSVDAAVA-------MDETVFRGRTIKVLPK 112

Query: 182 DTEKERQARR 191
            T     +  
Sbjct: 113 RTNMPGISST 122

>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 = 56.0 bits (136), Expect = 2e-10
 Identities = 24/67 (35%), Positives = 35/67 (52%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
           S  +  K+FVG +P +  E +L   FK+F +V EV +I D   +  RG  F+     Q 
Sbjct: 5  SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS 64

Query: 69 ADKAVNA 75
           D+AVN 
Sbjct: 65 VDQAVNM 71

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 46.0 bits (110), Expect = 7e-07
 Identities = 19/92 (20%), Positives = 41/92 (44%), Gaps = 7/92 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
           K+F+G +P N  E E+   F  +G + ++ ++    +    +G  F+ +E ++    A+ 
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIY-DAEKQRPRGFGFITFEDEQSVDQAVN 70

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
                H + G  V   VK A+    + +  + 
Sbjct: 71  --MHFHDIMGKKVE--VKRAEPRDSKSSGPSS 98

>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 = 57.6 bits (139), Expect = 2e-10
 Identities = 20/92 (21%), Positives = 43/92 (46%), Gaps = 12/92 (13%)

Query: 100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 159
            L+ K+++G L  N ++ E+   F  YG ++ + + R       G AF+++E    A  A
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADA 126

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
           +  ++G+  + G    + V+ +        +R
Sbjct: 127 VRELDGR-TLCGC--RVRVELS-----NGEKR 150

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           K++VG +  +  + +L   F  +  +  V + ++       G  FV     ++A  AV  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 76  CHNKKTLPGASSPLQVKYADG 96
             + +TL G    ++V+ ++G
Sbjct: 130 L-DGRTLCG--CRVRVELSNG 147

>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 = 55.7 bits (135), Expect = 2e-10
 Identities = 18/70 (25%), Positives = 31/70 (44%)

Query: 6  KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS 65
             K+ E+  K+FVG +    ++  L   F +F  V +  I  D  T  SRG  F++   
Sbjct: 3  NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 66 RQEADKAVNA 75
              +K ++ 
Sbjct: 63 AASVEKVLDQ 72

>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 = 46.8 bits (112), Expect = 3e-07
 Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G L  + S+ ++   F+ +G + D  I        S+G  F+ ++        L+ 
Sbjct: 13  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72

Query: 163 ----INGK 166
               ++G+
Sbjct: 73  KEHRLDGR 80

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 57.2 bits (138), Expect = 3e-10
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD--EVNIIKDKTTRASRGCC 59
           A           R  ++VG      T+ QL+ + +   + D  E+   +++    S+G  
Sbjct: 43  AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA 102

Query: 60  FVICPSRQEADKAVNACHNK 79
            V+  S     K +     K
Sbjct: 103 EVVVASENSVHKLLELLPGK 122

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.1 bits (122), Expect = 4e-08
 Identities = 21/120 (17%), Positives = 45/120 (37%), Gaps = 9/120 (7%)

Query: 83  PGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGT--IKDLQIL--RGS 138
           P   +P  + Y    L      +++G      ++ ++  +    G   + +L+    R +
Sbjct: 37  PNNKTP-AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRAN 95

Query: 139 QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQ 198
            Q SKG A +   ++      LE + GK  + G    + V+ A  +   Q     + +  
Sbjct: 96  GQ-SKGYAEVVVASENSVHKLLELLPGKV-LNGE--KVDVRPATRQNLSQFEAQARKREC 151

>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 = 55.7 bits (135), Expect = 3e-10
 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 5/90 (5%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAA 159
              +FIG L   + E  +   FS +G I     +     T  SKG AF+ + + + + AA
Sbjct: 5   SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQA 189
           +EA+NG       + P+ V +A  +  + +
Sbjct: 65  IEAMNG---QYLCNRPITVSYAFKKDSKGS 91

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEF-ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
           +F+G +   + E  L   F  F  ++    I++D  T  S+G  F+   S   +D A+ 
Sbjct: 7  GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 75 ACHNK 79
          A + +
Sbjct: 67 AMNGQ 71

>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 = 54.8 bits (133), Expect = 4e-10
 Identities = 15/58 (25%), Positives = 25/58 (43%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          K+FVG +     E ++   F  F  V+ + +  D  T   RG CF+     +   K +
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

>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 = 11/69 (15%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G L  +  E ++   F  +G ++ +++   ++    +G  F+ ++ +E     +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 163 ----INGKH 167
               +    
Sbjct: 61  KYHNVGLSK 69

>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 = 55.3 bits (134), Expect = 4e-10
 Identities = 21/74 (28%), Positives = 31/74 (41%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S   K++ ++   L V  +P   TE  L   F  F  V  V + KD  T  S+G  FV  
Sbjct: 5  SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 64 PSRQEADKAVNACH 77
             +   K ++  H
Sbjct: 65 TEYETQVKVMSQRH 78

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 16/91 (17%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L +  LP   +E ++   FS +G +  +Q+ +  +   SKG  F+++   E     ++ 
Sbjct: 17  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE---TQVKV 73

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
           ++ +H ++G       K  ++++ + +  + 
Sbjct: 74  MSQRHMIDGRWC--DCKLPNSKQSQDSGPSS 102

>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 = 55.3 bits (134), Expect = 4e-10
 Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 10/94 (10%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
            R    L    L  N++E E+  +F     I+   ++    + SKG A+++++++  A  
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIR---LVSQDGK-SKGIAYIEFKSEADAEK 68

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            LE   G  +++G    + + +     E+   R 
Sbjct: 69  NLEEKQGA-EIDGR--SVSLYYT---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 = 51.9 bits (125), Expect = 6e-09
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 5/80 (6%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
          M E     K       L    +  ++TE +L  +F++      + I        S+G  +
Sbjct: 3  MLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAY 57

Query: 61 VICPSRQEADKAVNACHNKK 80
          +   S  +A+K +      +
Sbjct: 58 IEFKSEADAEKNLEEKQGAE 77

>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 = 55.4 bits (134), Expect = 4e-10
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
              L +  L  + +E  +  +F     IK   + +     SKG AF+++ + E A  AL 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARR 191
           + N + ++EG    + ++     +      
Sbjct: 72  SCNKR-EIEGR--AIRLELQ-GPRGSPNSG 97

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 3  ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
           S      S E   L +  +    TE  L  +F++      + + +++  + S+G  F+ 
Sbjct: 4  GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGK-SKGYAFIE 59

Query: 63 CPSRQEADKAVNACHNKK 80
            S ++A +A+N+C+ ++
Sbjct: 60 FASFEDAKEALNSCNKRE 77

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 10/101 (9%)

Query: 92  KYADGELERLEHKLFIGMLPKNVSEAEVSAL-------FSIYGTIKDLQILRGSQQTSKG 144
           K    E + ++  + +  +P+ V    +  L       FS +G I +        + +KG
Sbjct: 5   KDRPQEADGIDSVIVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGK-TKG 62

Query: 145 CAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEK 185
             FL+Y +   A+ A++  +G +K++      V  + D +K
Sbjct: 63  YIFLEYASPAHAVDAVKNADG-YKLDKQHTFRVNLFTDFDK 102

>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 = 13/82 (15%), Positives = 28/82 (34%), Gaps = 8/82 (9%)

Query: 5  KKEKKSSEERVKLFVGQVPK------HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGC 58
           + +++      + V  VP+         +  +  +F +F  +   N    +    ++G 
Sbjct: 6  DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI--TNDFYPEEDGKTKGY 63

Query: 59 CFVICPSRQEADKAVNACHNKK 80
           F+   S   A  AV      K
Sbjct: 64 IFLEYASPAHAVDAVKNADGYK 85

>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 = 55.3 bits (134), Expect = 5e-10
 Identities = 18/70 (25%), Positives = 30/70 (42%)

Query: 6  KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS 65
          +         K+F+G +    T+  L   F +F  V E  +++D  T+ SRG  FV    
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 76

Query: 66 RQEADKAVNA 75
          +   DK +  
Sbjct: 77 QAGVDKVLAQ 86

>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 = 44.6 bits (106), Expect = 3e-06
 Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 6/88 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+FIG L    ++  +   F  +G +K+  ++R    + S+G  F+ +  +      L  
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQAR 190
              +H+++  ++    K A   +  Q +
Sbjct: 87  --SRHELDSKTI--DPKVA-FPRRAQPK 109

>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 = 55.2 bits (133), Expect = 5e-10
 Identities = 20/110 (18%), Positives = 40/110 (36%), Gaps = 17/110 (15%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
            R +  +    LP     AE+   FS +G++  + +           A +++    +A  
Sbjct: 7   GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARK 61

Query: 159 ALEAINGKHKMEGSSVPLVVKWA---------DTEKERQARRAQKAQSQA 199
           A   +    K      PL ++WA           +  +  + A+KA+S  
Sbjct: 62  AFRHLAYS-KFHHV--PLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGP 108

>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 = 46.7 bits (111), Expect = 6e-07
 Identities = 13/79 (16%), Positives = 22/79 (27%), Gaps = 9/79 (11%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
            S    +S   +  +    +P     A++   F  F  +  V + +            V
Sbjct: 1  GSSGSSGRS---KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIV 51

Query: 62 ICPSRQEADKAVNACHNKK 80
                EA KA       K
Sbjct: 52 EFLEPLEARKAFRHLAYSK 70

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 54.8 bits (132), Expect = 5e-10
 Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 7/104 (6%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSK 143
           G+S         GE   L   +++G LP++   +++       G++     LR + Q  +
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQGPR 56

Query: 144 GCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKER 187
             AFL Y     A  A+  + G  ++      L V  A  ++++
Sbjct: 57  RRAFLHYPDSAAAQQAVSCLQGL-RLGTD--TLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 43.7 bits (103), Expect = 5e-06
 Identities = 17/96 (17%), Positives = 31/96 (32%), Gaps = 8/96 (8%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
                 + +     ++VG +P+    + L    +E   V         T +  R   F+
Sbjct: 7  GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRL-----TWQGPRRRAFL 61

Query: 62 ICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGE 97
            P    A +AV+       L      L+V  A  +
Sbjct: 62 HYPDSAAAQQAVSCL-QGLRLGT--DTLRVALARQQ 94

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 54.7 bits (132), Expect = 6e-10
 Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 106 FIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAIN 164
            I      V +  +++LFS  G + +++         +KG  F++  +   A   +++ +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 165 GKHKMEGSSVPLVVKWADTEK 185
           GK +++      +    D E+
Sbjct: 76  GK-RLDLKHRLFLYTMKDVER 95

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 14/63 (22%), Positives = 28/63 (44%)

Query: 18 FVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH 77
           +      + +  L ++F +   V  +    D+ T  ++G  FV C S  +A K + + H
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 78 NKK 80
           K+
Sbjct: 76 GKR 78

>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 = 54.5 bits (132), Expect = 6e-10
 Identities = 17/64 (26%), Positives = 32/64 (50%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           +FVG +   +T A + A F  F  + +  ++KD  T  S+G  FV   ++ +A+ A+  
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 76 CHNK 79
             +
Sbjct: 68 MGGQ 71

>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 = 54.1 bits (131), Expect = 9e-10
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAA 159
              +F+G L   ++ A ++A F+ +G I D ++++    T  SKG  F+ +  K  A  A
Sbjct: 6   HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVK-DMATGKSKGYGFVSFFNKWDAENA 64

Query: 160 LEAINGKHKMEGSSVPLVVKWA 181
           ++ + G+         +   WA
Sbjct: 65  IQQMGGQ---WLGGRQIRTNWA 83

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 22/73 (30%), Positives = 33/73 (45%)

Query: 3  ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
           S      ++E  KLFVG +    T+  L + F ++  V +  I+KDKTT  SRG  FV 
Sbjct: 5  SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVK 64

Query: 63 CPSRQEADKAVNA 75
                    + +
Sbjct: 65 FKDPNCVGTVLAS 77

>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 = 44.9 bits (107), Expect = 2e-06
 Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 8/88 (9%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTS 142
           G+S    +  +  +      KLF+G L  + ++  + + FS YG + D  I++      S
Sbjct: 1   GSSGSSGMNNSGADEIG---KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQS 57

Query: 143 KGCAFLKYETKEQALAALEA----INGK 166
           +G  F+K++        L +    ++G+
Sbjct: 58  RGFGFVKFKDPNCVGTVLASRPHTLDGR 85

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           ++VG V    T  +L A F     V+ V I+ DK +   +G  ++    ++    ++
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

>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 = 51.7 bits (125), Expect = 6e-09
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 13/93 (13%)

Query: 98  LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQ 155
           +E     +++G +    +  E+ A F   G++  + IL  + S    KG A++++  KE 
Sbjct: 2   MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGH-PKGFAYIEFSDKES 60

Query: 156 ALAALEAINGKHKMEGSSV---PLVVKWADTEK 185
              +L        ++ S      + V    T +
Sbjct: 61  VRTSLA-------LDESLFRGRQIKVIPKRTNR 86

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + I  L   V EA++      +G I  + ++       K  A +++E    A  A+    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78

Query: 165 GK 166
             
Sbjct: 79  DN 80

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 18/94 (19%), Positives = 33/94 (35%), Gaps = 9/94 (9%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
           E+  +   +     + +  +   + EA L+   +EF  +  V ++  K          V
Sbjct: 9  MENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALV 62

Query: 62 ICPSRQEADKAVNACH-NKKTLPGASSPLQVKYA 94
                 A  AVN    N+  + G   P  V Y+
Sbjct: 63 EFEDVLGACNAVNYAADNQIYIAG--HPAFVNYS 94

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 20/93 (21%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + I  LP +V+E EV +L   +G + +L +L+G     K  AF++  T+E A   +    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 165 GKHKMEGSSVPLVVKWADTEKERQARRAQKAQS 197
               +     P+ +++++ ++ +      +A++
Sbjct: 74  SVTPVLRGQ-PIYIQFSNHKELKTDSSPNQARA 105

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 12/78 (15%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          + + ++P  +TE +++++   F  V  + ++K K         F+   + + A+  VN  
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNYY 72

Query: 77 HNKKTLPGASSPLQVKYA 94
           +   +     P+ ++++
Sbjct: 73 TSVTPVL-RGQPIYIQFS 89

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 53.6 bits (129), Expect = 3e-09
 Identities = 26/115 (22%), Positives = 47/115 (40%), Gaps = 16/115 (13%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-------QQT--SKGCAFLKYETKE 154
            +F+  L +NV+   V+  F   G IK  +            ++T   KG A + ++   
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 155 QALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPNADSQH 209
            A AA++  +GK    G+  P+ V +A     R+A   +   +    L +    H
Sbjct: 69  SAKAAIDWFDGKE-FSGN--PIKVSFA----TRRADFNRGGGNGRGGLEHHHHHH 116

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 19/96 (19%), Positives = 42/96 (43%), Gaps = 12/96 (12%)

Query: 7  EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE--------VNIIKDKTTRASRGC 58
          E+ +S+    +FV  + +++T   +   FK+  ++          +N+  D+ T   +G 
Sbjct: 1  EQDNSDNN-TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 59

Query: 59 CFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
            V       A  A++    K+   G  +P++V +A
Sbjct: 60 ATVSFDDPPSAKAAIDWFDGKE-FSG--NPIKVSFA 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 = 52.7 bits (127), Expect = 3e-09
 Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAAL 160
              + +  +P  VS  E+   F  Y  I   + +    +    G A + +E++++A AA+
Sbjct: 15  PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74

Query: 161 EAINGKH 167
             +N + 
Sbjct: 75  IDLNDRP 81

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALV-DEVNIIKDKTTRASRGCCFVICPSRQE 68
                 + V  +P  ++  ++L  F  + ++   V +  ++      G   V   SR E
Sbjct: 11 GKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM-PTGEAMVAFESRDE 69

Query: 69 ADKAVNACHNKK 80
          A  AV   +++ 
Sbjct: 70 ATAAVIDLNDRP 81

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAAL 160
              + +  +P  VS  E+   F  Y  I   + +    +    G A + +E++++A AA+
Sbjct: 15  PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74

Query: 161 EAINGKH 167
             +N + 
Sbjct: 75  IDLNDRP 81

>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 = 51.1 bits (123), Expect = 1e-08
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALV-DEVNIIKDKTTRASRGCCFVICPSRQE 68
                 + V  +P  ++  ++L  F  + ++   V +  ++      G   V   SR E
Sbjct: 11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM-PTGEAMVAFESRDE 69

Query: 69 ADKAVNACHNKK 80
          A  AV   +++ 
Sbjct: 70 ATAAVIDLNDRP 81

>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 = 52.6 bits (127), Expect = 3e-09
 Identities = 17/92 (18%), Positives = 43/92 (46%), Gaps = 7/92 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQIL--RGSQQTSKGCAFLKYETKEQALAALE 161
            +++G L  + +  +V  LFS +G + +++++  R +++  KG  F++ +  E    A+ 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKK-PKGFGFVEMQE-ESVSEAIA 60

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
            ++      G    + V  A+ +K  +     
Sbjct: 61  KLDNT-DFMGR--TIRVTEANPKKSLEHHHHH 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 = 52.2 bits (126), Expect = 4e-09
 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           ++VG +    T  Q+  +F +F  V  V +I D+ T+  +G  FV     +   +A+  
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 76 CHNK 79
            N 
Sbjct: 62 LDNT 65

>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 = 52.8 bits (127), Expect = 4e-09
 Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 12/107 (11%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT---------SKGC 145
           D + +     +++  L  +V+  +++  F   G +K  +                  KG 
Sbjct: 8   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67

Query: 146 AFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
           A + YE    A AA+E  +GK   +GS   L V  A  +    +  +
Sbjct: 68  ATVSYEDPPTAKAAVEWFDGKD-FQGS--KLKVSLARKKPPMNSGPS 111

>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 = 46.6 bits (111), Expect = 7e-07
 Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 8/86 (9%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE--------VNIIKDKTTR 53
          + S  +     +   ++V  +   +T   L   FK+  +V          ++I  DK T 
Sbjct: 3  SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 54 ASRGCCFVICPSRQEADKAVNACHNK 79
            +G   V       A  AV     K
Sbjct: 63 KPKGDATVSYEDPPTAKAAVEWFDGK 88

>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 = 52.3 bits (126), Expect = 4e-09
 Identities = 27/107 (25%), Positives = 49/107 (45%), Gaps = 15/107 (14%)

Query: 85  ASSPLQVKYADGELERLEH---KLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQ 140
            SS     ++ G + R  H   +LFIG LP KNVS+ ++  +FS YG I  + I      
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------ 55

Query: 141 TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKER 187
                 F++++  +    A+E  + +    G    L+++ + +   R
Sbjct: 56  -KNAFGFIQFDNPQSVRDAIEXESQE-MNFGK--KLILEVS-SSNAR 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 = 52.7 bits (127), Expect = 5e-09
 Identities = 23/67 (34%), Positives = 34/67 (50%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
          +      K+FVG +P H T+A L   F+ F  ++E  +I D+ T  SRG  FV    R  
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71

Query: 69 ADKAVNA 75
          A++A   
Sbjct: 72 AERACKD 78

>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 = 46.9 bits (112), Expect = 5e-07
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 5/93 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G LP + ++A +   F  +G I++  ++   Q   S+G  F+    +  A  A + 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQKA 195
            N    ++G      V  A    + ++ +   A
Sbjct: 79  PN--PIIDGRKA--NVNLAYLGAKPRSLQTGFA 107

>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 = 51.8 bits (125), Expect = 6e-09
 Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 5/73 (6%)

Query: 5  KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICP 64
          +          K+FVG+  + MT  +L   F ++  V +V I K       R   FV   
Sbjct: 2  RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFA 56

Query: 65 SRQEADKAVNACH 77
            + A        
Sbjct: 57 DDKVAQSLCGEDL 69

>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 = 49.5 bits (119), Expect = 3e-08
 Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 9/85 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           K+F+G   ++++  E+   F  YG + D+ I +      +  AF+ +   +    A    
Sbjct: 13  KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDK---VAQSLC 65

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQ 188
                ++G SV   +  A+ +  + 
Sbjct: 66  GEDLIIKGISV--HISNAEPKHNKL 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 = 51.7 bits (124), Expect = 8e-09
 Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 5/62 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + +  L ++V EA++      +GTI  + ++       K  A +++E  + A   +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAA 72

Query: 165 GK 166
             
Sbjct: 73  DV 74

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 11/78 (14%), Positives = 25/78 (32%), Gaps = 7/78 (8%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          + V  + + + EA L+   ++F  +  V ++  K          V   +   A + V   
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECVTFA 71

Query: 77 HNKKTLPGASSPLQVKYA 94
           +              Y+
Sbjct: 72 ADVPVYIA-GQQAFFNYS 88

>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 = 15/71 (21%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT--TRASRGCCFVICPSR 66
            S    K+FVG +P  + E ++ A F+ F  +      K ++      +G  F++    
Sbjct: 3  SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62

Query: 67 QEADKAVNACH 77
                ++AC 
Sbjct: 63 SSVQALIDACL 73

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 6/89 (6%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR---GSQQTSKGCAFLKYETKEQ 155
                K+F+G LP ++ E E++A F  +G +      +    S    KG AFL ++ +  
Sbjct: 5   SSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESS 64

Query: 156 ALAALEA---INGKHKMEGSSVPLVVKWA 181
             A ++A    +GK  +  SS  +  K  
Sbjct: 65  VQALIDACLEEDGKLYLCVSSPTIKDKPV 93

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 5/62 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           L I  LP  V+E EV AL   +G + ++ +L+G     K  AFL+  T+E A+  +   +
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 165 GK 166
             
Sbjct: 73  AV 74

>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 = 46.0 bits (109), Expect = 8e-07
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L + ++P  +TE +++A+   F  V  + ++K K         F+   + + A   VN  
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNYY 71

Query: 77 HNKKTLPGASSPLQVKYA 94
                   + P+ ++Y+
Sbjct: 72 SAVTPH-LRNQPIYIQYS 88

>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 = 50.3 bits (121), Expect = 2e-08
 Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           +FVG+    MTE +L   F ++  V +V I K       R   FV     Q A      
Sbjct: 7  GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE 61

Query: 76 CH 77
            
Sbjct: 62 DL 63

>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 = 46.8 bits (112), Expect = 3e-07
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            +F+G    +++E E+   FS YG + D+ I +      +  AF+ +   +    A    
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQ---IAQSLC 59

Query: 164 NGKHKMEGSSV 174
                ++G SV
Sbjct: 60  GEDLIIKGISV 70

>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 = 14/109 (12%), Positives = 43/109 (39%), Gaps = 5/109 (4%)

Query: 92  KYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKY 150
              +G++   +    I  +P ++++ +V          ++ + +L  +     G A +++
Sbjct: 5   SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF 64

Query: 151 ETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQA 199
           + ++ A  +       H+ + +     V     E  R+  +   AQ ++
Sbjct: 65  KNEDDARKSER----LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKS 109

>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 = 48.6 bits (116), Expect = 1e-07
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE-VNIIKDKTTRASRGCCFVI 62
          S  E   +  +V   +  +P  +T+  +L   +   + +  V+++ D   +   G   V 
Sbjct: 5  SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ-GLGQALVQ 63

Query: 63 CPSRQEADKAVNACHNKKTLPG 84
            +  +A K+     ++K L G
Sbjct: 64 FKNEDDARKSERL--HRKKLNG 83

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 11/94 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC-AFLKYETKEQALAALEA 162
            +F+   P+ V  A++S  F  +G +  + + +      KG  A ++        A L  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK-----DKGVFAIVEMGDVGAREAVLS- 63

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQKAQ 196
              +H + G  +   V+    +KE Q+  ++  +
Sbjct: 64  -QSQHSLGGHRLR--VRPR-EQKEFQSPASKSPK 93

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 5/60 (8%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           +FV   P+ +  AQL   F  F  V  V + KDK   A      V        +  ++ 
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFA-----IVEMGDVGAREAVLSQ 64

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 49.5 bits (118), Expect = 7e-08
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + I  LP +V+E EV +L   +G + +L +L+G     K  AF++  T+E A   +    
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88

Query: 165 GK 166
             
Sbjct: 89  SV 90

>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 = 46.4 bits (110), Expect = 8e-07
 Identities = 12/78 (15%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           + + ++P  +TE +++++   F  V  + ++K K         F+   + + A+  VN  
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNYY 87

Query: 77  HNKKTLPGASSPLQVKYA 94
            +   +     P+ ++++
Sbjct: 88  TSVTPVLR-GQPIYIQFS 104

>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 = 48.8 bits (117), Expect = 9e-08
 Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 13/95 (13%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
             F+G LP +V+E  +   F     I  +++ R        KG  + ++E  +  L+AL 
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 74

Query: 162 AINGKHKMEGSSV---PLVVKWADTEKERQARRAQ 193
                  +   S+    + V  AD  +++ +  + 
Sbjct: 75  ------SLNEESLGNKRIRVDVADQAQDKDSGPSS 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 = 48.8 bits (117), Expect = 1e-07
 Identities = 15/100 (15%), Positives = 37/100 (37%), Gaps = 6/100 (6%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDK-TTRASRGCCF 60
           + S   +         F+G +P  +TE  +   F+    +  V + ++       +G  +
Sbjct: 3   SGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGY 61

Query: 61  VICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
                      A++   N+++L      ++V  AD   ++
Sbjct: 62  AEFEDLDSLLSALSL--NEESLGNK--RIRVDVADQAQDK 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          + S  ++  +E     +VG +P +  +  + A+FK+ + +  V +++DK T   +G C+V
Sbjct: 3  SGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61

Query: 62 ICPSRQEADKAVN 74
                   +A+ 
Sbjct: 62 EFDEVDSLKEALT 74

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 12/93 (12%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEA 162
             ++G LP N  + ++ A+F     I+ ++++R       KG  +++++  +    AL  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74

Query: 163 INGKHKMEGSSV---PLVVKWADTEKERQARRA 192
                  +G+ +    L V  A+  K+ ++  +
Sbjct: 75  ------YDGALLGDRSLRVDIAEGRKQDKSGPS 101

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 6/67 (8%)

Query: 100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 159
           R E+++ +  LP + S  ++       G +    + R       G   +++  KE    A
Sbjct: 13  RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYA 66

Query: 160 LEAINGK 166
           +  ++  
Sbjct: 67  VRKLDNT 73

>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 = 38.6 bits (90), Expect = 4e-04
 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 7/65 (10%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++ V  +P   +   L    +E   V   ++ +D       G   V    +++   AV  
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69

Query: 76 CHNKK 80
            N K
Sbjct: 70 LDNTK 74

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 9/69 (13%)

Query: 105 LFIGMLPKNVSEAEVSAL-------FSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQAL 157
           + +  +P+ V    +  L       FS +G I +        + +KG  FL+Y +   A+
Sbjct: 4   IVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGK-TKGYIFLEYASPAHAV 61

Query: 158 AALEAINGK 166
            A++  +G 
Sbjct: 62  DAVKNADGY 70

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 8/70 (11%)

Query: 17 LFVGQVPKH------MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
          + V  VP+         +  +  +F +F  +      ++     ++G  F+   S   A 
Sbjct: 4  IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61

Query: 71 KAVNACHNKK 80
           AV      K
Sbjct: 62 DAVKNADGYK 71

>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 = 52.2 bits (124), Expect = 1e-07
 Identities = 21/82 (25%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAI 163
           LF+  +  + +E+++   F +YG IK + ++   +    +G AF++YE +    +A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 164 NGKHKMEGSSVPLVVKWADTEK 185
           +G  K++G  V + V+   T K
Sbjct: 165 DG-KKIDGRRVLVDVERGRTVK 185

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 44.8 bits (105), Expect = 2e-05
 Identities = 15/64 (23%), Positives = 29/64 (45%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
           LFV +V    TE++L   F+ +  +  ++++  K +   RG  F+     ++   A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 77  HNKK 80
             KK
Sbjct: 165 DGKK 168

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 20/116 (17%), Positives = 41/116 (35%), Gaps = 9/116 (7%)

Query: 77  HNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR 136
           H+         P        +L    +++ +  LP+  S  ++  L              
Sbjct: 5   HHHHHHSSGLVPRGSHM--SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETT--FSS 60

Query: 137 GSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            + +   G   L++ ++E  + ALE +N   +  GS   + V+  D       RR+
Sbjct: 61  VNTRDFDGTGALEFPSEEILVEALERLNN-IEFRGS--VITVE-RDDNPPP-IRRS 111

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 7  EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
            K   +R ++ +  +P+  +   L  + +E +L           TR   G   +  PS 
Sbjct: 21 MSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDGTGALEFPSE 77

Query: 67 QEADKAVNACHNKK 80
          +   +A+   +N +
Sbjct: 78 EILVEALERLNNIE 91

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           H + +   P NV+E  V    +       ++I+R +     G  F+ +  +E+   AL+ 
Sbjct: 11  HTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK- 68

Query: 163 INGKHK 168
               ++
Sbjct: 69  ---CNR 71

>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 = 43.8 bits (104), Expect = 4e-06
 Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 3/71 (4%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
          S      + +   P ++TE  ++        V  + I+++       G  FV   + +E 
Sbjct: 6  SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNAHGN-KTGYIFVDFSNEEEV 63

Query: 70 DKAVNACHNKK 80
           +A+  C+ + 
Sbjct: 64 KQAL-KCNREY 73

>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 = 47.5 bits (113), Expect = 4e-07
 Identities = 19/117 (16%), Positives = 39/117 (33%), Gaps = 5/117 (4%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTS 142
           G S   Q +            +++  LP       V   F     ++D + I  G    +
Sbjct: 7   GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA 66

Query: 143 KGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQA 199
            G  F+++  +    AAL     +HK    +  + V     +   +     + + Q+
Sbjct: 67  TGEGFVEFRNEADYKAALC----RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 119

>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 = 45.6 bits (108), Expect = 2e-06
 Identities = 10/72 (13%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 3  ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE-VNIIKDKTTRASRGCCFV 61
          +  + +   E    +++  +P       ++  FK+  +V++ + I      + + G  FV
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGFV 72

Query: 62 ICPSRQEADKAV 73
             +  +   A+
Sbjct: 73 EFRNEADYKAAL 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 = 46.7 bits (111), Expect = 4e-07
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 5/64 (7%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFAL-----VDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
          +L+VG +P  +TE  ++  F              N +        +   F+   S  E  
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 71 KAVN 74
          +A+ 
Sbjct: 68 QAMA 71

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 7/69 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQ------ILRGSQQTSKGCAFLKYETKEQAL 157
           +L++G +P  ++E  +   F+    +  L       +L       K  AFL++ + ++  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 158 AALEAINGK 166
            A+ A +G 
Sbjct: 68  QAM-AFDGI 75

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 46.8 bits (111), Expect = 5e-07
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 105 LFIGMLPKNVSEAEV---SALFSIYGTIKDLQILR----GSQQTSKGCAFLKYETKEQAL 157
           +F+  L + +++ EV      F  +G I  + I         Q     A++ Y   E AL
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 158 AALEAINGK 166
            A++ +N  
Sbjct: 78  RAIQCVNNV 86

>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 = 46.5 bits (111), Expect = 5e-07
 Identities = 14/94 (14%), Positives = 34/94 (36%), Gaps = 6/94 (6%)

Query: 3  ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDK-TTRASRGCCFV 61
             + +         F+G +P  +TE  +   F+    +  V + ++       +G  + 
Sbjct: 8  HHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 66

Query: 62 ICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD 95
                    A++   N+++L      ++V  AD
Sbjct: 67 EFEDLDSLLSALSL--NEESLGNR--RIRVDVAD 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 = 45.3 bits (108), Expect = 2e-06
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
             F+G LP +V+E  +   F     I  +++ R        KG  + ++E  +  L+AL 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 162 AINGKHKMEGSSVPLVVKWADTEKE 186
            +N +  +      + V  AD  ++
Sbjct: 80  -LNEE-SLGNR--RIRVDVADQAQD 100

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 13/92 (14%), Positives = 29/92 (31%), Gaps = 7/92 (7%)

Query: 100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 159
           R E+++ +  LP + S  ++       G +    + R       G   +++  KE    A
Sbjct: 14  RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYA 67

Query: 160 LEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
           +  ++   K               +  R    
Sbjct: 68  VRKLDNT-KFRSHEGETAYIRVKVDGPRSPSY 98

>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 = 44.3 bits (105), Expect = 3e-06
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 5/68 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           H + +  LP   +E ++   FS       + I  G      G A +++ T E A+AA+  
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA- 73

Query: 163 INGKHKME 170
              K K  
Sbjct: 74  ---KDKAN 78

>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 = 43.2 bits (102), Expect = 9e-06
 Identities = 14/79 (17%), Positives = 25/79 (31%), Gaps = 3/79 (3%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
          + S      S     + +  +P   TE  +   F     +  V+I      R   G   V
Sbjct: 3  SGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGR-VTGEADV 60

Query: 62 ICPSRQEADKAVNACHNKK 80
             + ++A  A+ A     
Sbjct: 61 EFATHEDAVAAM-AKDKAN 78

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 44.5 bits (105), Expect = 4e-06
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE-VNIIKDKTTRASRGCCFV 61
                   S     + +  +P   T+ +++  F    +V   + +  D   +   G  FV
Sbjct: 31  GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAFV 89

Query: 62  ICPSRQEADKAVNACHNKK 80
              S++ A+KA+   H ++
Sbjct: 90  QFASQELAEKAL-GKHKER 107

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 44.1 bits (104), Expect = 7e-06
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 5/70 (7%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTI-KDLQILRGSQQTSKGCAFLKYETKEQALAAL 160
           +  + +  LP   ++ E+   FS    +   + +    +    G AF+++ ++E A  AL
Sbjct: 42  DGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101

Query: 161 EAINGKHKME 170
                KHK  
Sbjct: 102 G----KHKER 107

>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 = 43.6 bits (103), Expect = 7e-06
 Identities = 10/69 (14%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           +  + +  +P +  E +V   F     +  + +L+     + G   +K+ + +    AL+
Sbjct: 16  DLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK 74

Query: 162 AINGKHKME 170
               +++M 
Sbjct: 75  ----RNRML 79

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 3  ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
           S K    + + + + V  +P    E  +   F     VD V+++KD   R + G   V 
Sbjct: 5  SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR-NNGNGLVK 62

Query: 63 CPSRQEADKAV 73
            S Q+  +A+
Sbjct: 63 FLSPQDTFEAL 73

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 15/127 (11%), Positives = 27/127 (21%), Gaps = 4/127 (3%)

Query: 217 PMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGFHGIIPPVNQGNAMRGASPDLSSNMG 276
              Y      YG  A+      Q+  P      G          G   +GA P +     
Sbjct: 6   KRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGM----SYGQMGMPPQGAVPSMGQQQF 61

Query: 277 PRNYAMPPSGFVGSGYPAVPGLQYPMPYPGGMLGHRPLNNSPGSVSPAVANSNPSTSSSG 336
                      +     ++  +            +          +P      P  + + 
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 337 GTGSGGQ 343
           G  S   
Sbjct: 122 GQPSAAM 128

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 42.5 bits (99), Expect = 2e-04
 Identities = 24/166 (14%), Positives = 39/166 (23%), Gaps = 4/166 (2%)

Query: 192 AQKAQSQANNLPNADSQHPSLFGALPMGYAPPYNGYGYQASGSYGLMQYRLPPMQNQPGF 251
            Q AQ      P A        G  P G  P      +       L Q       +    
Sbjct: 24  QQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDM 83

Query: 252 HGIIPPVNQGNAMRGASPDLSSNMGPRNYAMPPSGFVGSGYPAVPG---LQYPMPYPGGM 308
           H    P+   NA       +      +    P +        A  G         YP  +
Sbjct: 84  HLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDL 143

Query: 309 LGHRPLNNSPGSV-SPAVANSNPSTSSSGGTGSGGQIEGFLSIYSV 353
           L   P   +  ++  P +              +        ++ +V
Sbjct: 144 LTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAV 189

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           H + +  LP   +E ++   FS       + I  G      G A +++ T E+A+AA+  
Sbjct: 47  HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS- 104

Query: 163 INGKHKME 170
              K +  
Sbjct: 105 ---KDRAN 109

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 14/80 (17%), Positives = 25/80 (31%), Gaps = 3/80 (3%)

Query: 1   MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
            +   +    S     + +  +P   TE  +   F     V  V+I      R   G   
Sbjct: 33  GSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGPDGR-VTGEAD 90

Query: 61  VICPSRQEADKAVNACHNKK 80
           V   + +EA  A+ +     
Sbjct: 91  VEFATHEEAVAAM-SKDRAN 109

>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 = 42.3 bits (99), Expect = 3e-05
 Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 77  HNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFS---IYGTIKDLQ 133
            +  ++ G     +     G        + +  LP + S  +V    S   I+     + 
Sbjct: 19  SHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVH 78

Query: 134 ILRGSQQTSKGCAFLKYETKEQALAALE 161
            +   +    G AF++  +++    AL+
Sbjct: 79  FIYTREGRQSGEAFVELGSEDDVKMALK 106

>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 = 9e-05
 Identities = 12/84 (14%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE---VNIIKDKTTRASRGC 58
             S        E   + +  +P   +   +     +  + D    V+ I  +  R   G 
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-QSGE 90

Query: 59  CFVICPSRQEADKAVNACHNKKTL 82
            FV   S  +   A+    +++++
Sbjct: 91  AFVELGSEDDVKMAL--KKDRESM 112

>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 = 41.4 bits (97), Expect = 3e-05
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 7/99 (7%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFS---IYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
              +    LP + +  +V   FS   I      +  L       +G A ++ E+++    
Sbjct: 11  VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQK 70

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQS 197
           ALE    KH+M      + V   + E      ++ + +S
Sbjct: 71  ALE----KHRMYMGQRYVEVYEINNEDVDALMKSLQVKS 105

>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 = 38.3 bits (89), Expect = 4e-04
 Identities = 13/79 (16%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 5  KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVN---IIKDKTTRASRGCCFV 61
           K ++  ++   +    +P   T   +L  F +  + +  N    + ++  +  RG   +
Sbjct: 2  SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK-RRGDALI 60

Query: 62 ICPSRQEADKAVNACHNKK 80
             S Q+  KA+   H   
Sbjct: 61 EMESEQDVQKAL-EKHRMY 78

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 20/117 (17%), Positives = 44/117 (37%), Gaps = 8/117 (6%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFS---IYGTIKDLQILRGSQQ 140
           G+S    +       E   + + +  LP + S  +V    S   I+  +  +  +   + 
Sbjct: 1   GSSGSSGMMLGPEGGE--GYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREG 58

Query: 141 TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQS 197
              G AF++ E+++    AL+    +  M    +  V K   TE +   + +    +
Sbjct: 59  RQSGEAFVELESEDDVKLALKK--DRESMGHRYIE-VFKSHRTEMDWVLKHSGPNSA 112

>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 = 38.4 bits (89), Expect = 5e-04
 Identities = 11/75 (14%), Positives = 23/75 (30%), Gaps = 5/75 (6%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE---VNIIKDKTTRASRGCCFVICPS 65
              E   + +  +P   +   +     +  + D    V+ I  +  R   G  FV   S
Sbjct: 12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QSGEAFVELES 70

Query: 66 RQEADKAVNACHNKK 80
            +   A+     + 
Sbjct: 71 EDDVKLAL-KKDRES 84

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 2  AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALV----DEVNIIKDKTTRASRG 57
          +    +  S E +V + +  +P   T  +++A F +   +    + +  +     R   G
Sbjct: 11 SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTG 69

Query: 58 CCFVICPSRQEADKAVNACHNKK 80
            FV+    + A  A+   H   
Sbjct: 70 DAFVLFACEEYAQNAL-RKHKDL 91

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 8/83 (9%)

Query: 83  PGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFS----IYGTIKDLQILRGS 138
            G S+ +    +       +  + +  LP   +  EV A F     I G  + +  +   
Sbjct: 8   GGTSNEVAQFLSKEN----QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63

Query: 139 QQTSKGCAFLKYETKEQALAALE 161
                G AF+ +  +E A  AL 
Sbjct: 64  DGRPTGDAFVLFACEEYAQNALR 86

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 9/88 (10%)

Query: 84  GASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTS 142
           G+S        +      +  + +  LP   S+ E+   FS    + + + +    Q  S
Sbjct: 1   GSSGS----SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRS 56

Query: 143 KGCAFLKYETKEQALAALEAINGKHKME 170
            G AF+++ ++E A  AL+    KHK  
Sbjct: 57  TGEAFVQFASQEIAEKALK----KHKER 80

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALV-DEVNIIKDKTTRASRGCCFVI 62
          S      +     + +  +P   ++ +++  F    +V + + +  D   R S G  FV 
Sbjct: 5  SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR-STGEAFVQ 63

Query: 63 CPSRQEADKAVNACHNKK 80
            S++ A+KA+   H ++
Sbjct: 64 FASQEIAEKAL-KKHKER 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 = 40.6 bits (95), Expect = 6e-05
 Identities = 14/89 (15%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 77  HNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR 136
            N +    ++  L+   +D E++    + F         E   + +   YG ++++ +  
Sbjct: 11  RNPQNSSQSADGLRSAVSDVEMQEHYDEFF---------EEVFTEMEEKYGEVEEMNVCD 61

Query: 137 GSQQTSKGCAFLKYETKEQALAALEAING 165
                  G  ++K+  +E A  A+  +N 
Sbjct: 62  NLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

>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 = 41.2 bits (96), Expect = 1e-04
 Identities = 30/161 (18%), Positives = 63/161 (39%), Gaps = 8/161 (4%)

Query: 65  SRQEADKAVNACH-NKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALF 123
           S Q A +AVN+       L  +++ +    A      +   + +  L   V+   +  +F
Sbjct: 9   SAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLR-IIVENLFYPVTLDVLHQIF 67

Query: 124 SIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT 183
           S +GT+  +       + ++  A L+Y     A  A  +++G++        L + ++  
Sbjct: 68  SKFGTVLKI---ITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC-TLRIDFSKL 123

Query: 184 EKERQARRAQKAQSQAN-NLPNADSQHPSLFGALPMGYAPP 223
                     K++     +LP+ DSQ PSL   +   +   
Sbjct: 124 TSLNVKYNNDKSRDYTRPDLPSGDSQ-PSLDQTMAAAFGLS 163

>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 = 39.5 bits (92), Expect = 2e-04
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 105 LFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           + +  LP    S++ V  L   YG IK+  ++R   Q     AF++ ET+E A+A ++
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ-----AFIEMETREDAMAMVD 80

>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 = 37.9 bits (88), Expect = 6e-04
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 6/61 (9%)

Query: 105 LFIGMLPKNVS-EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           + I    +  +   ++  L   +G I +  IL          AF++  T E A AA++  
Sbjct: 18  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYY 72

Query: 164 N 164
            
Sbjct: 73  T 73

>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 = 37.3 bits (86), Expect = 8e-04
 Identities = 19/91 (20%), Positives = 30/91 (32%), Gaps = 10/91 (10%)

Query: 10 SSEERVKLFVGQVPKHMTEAQ----LLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS 65
          SS     + V  +   ++  +    L   F     V  V +         +    V   +
Sbjct: 5  SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMEN 61

Query: 66 RQEADKAVNACHNKKTLPGASSPLQVKYADG 96
           Q+A  AVN+ H  K     S  + V  A G
Sbjct: 62 LQDAIGAVNSLHRYKI---GSKKILVSLATG 89

>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 = 40.6 bits (94), Expect = 8e-04
 Identities = 32/247 (12%), Positives = 66/247 (26%), Gaps = 62/247 (25%)

Query: 10  SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC------ 63
           S+     + +      +T  ++ ++  ++         +D            +       
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR----PQDLPREVLTTNPRRLSIIAESI 337

Query: 64  ---PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVS 120
               +  +  K VN C    T+  +S  L V     E  ++  +L +   P +       
Sbjct: 338 RDGLATWDNWKHVN-CDKLTTIIESS--LNVLEPA-EYRKMFDRLSV--FPPSA------ 385

Query: 121 ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW 180
               I      L ++            +        +         +K+   S  LV K 
Sbjct: 386 ---HI--PTILLSLIWFD---------VIKSDVMVVV---------NKLHKYS--LVEKQ 420

Query: 181 ADTEKERQARRAQKAQSQANNLPNADSQHPSLFGA--LPMGY-----APPYN-GYGYQAS 232
                        + + +  N       H S+     +P  +      PPY   Y Y   
Sbjct: 421 PKESTISIPSIYLELKVKLENEYAL---HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477

Query: 233 GSYGLMQ 239
           G + L  
Sbjct: 478 G-HHLKN 483

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 18/104 (17%), Positives = 42/104 (40%), Gaps = 5/104 (4%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + +  L   V+   +  +FS +GT+  +       + ++  A L+Y     A  A  +++
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITF---TKNNQFQALLQYADPVSAQHAKLSLD 87

Query: 165 GKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN-NLPNADS 207
           G++        L + ++            K++     +LP+ DS
Sbjct: 88  GQNIYNACC-TLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 130

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	354
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
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	99.98
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.98
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.98
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	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
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.9
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.82
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.82
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.8
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.8
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.8
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.8
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.8
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.78
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.78
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.78
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.78
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.78
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.77
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.77
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.77
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.77
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.76
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.76
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.76
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.75
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.74
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.74
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.74
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.74
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.74
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.74
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.74
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.73
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.73
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.73
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.73
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.73
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.73
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.73
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.73
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.73
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.73
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.72
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.72
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.72
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.72
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.72
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.72
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.72
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.72
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.72
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.71
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2div_A	99	TRNA selenocysteine associated protein; structural	99.71
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.71
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.71
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.71
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.71
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.71
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.71
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.71
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.7
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.7
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.7
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.7
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.54
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.7
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.7
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.7
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.7
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.7
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.69
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.69
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.69
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.69
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.69
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.69
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.69
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.69
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.69
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.69
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.69
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.68
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.68
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.68
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.68
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.68
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.68
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.68
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.68
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.68
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.68
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.67
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.67
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.67
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.67
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.67
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.67
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.67
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.67
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.67
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.67
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.67
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.67
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.67
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.67
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.66
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.66
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.66
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.66
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.66
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.66
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.65
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.65
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.65
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.65
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.65
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.65
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.63
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.63
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.63
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.63
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.63
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.63
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.63
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.62
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.62
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.62
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.62
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.61
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.61
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.4
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.6
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.6
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.6
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.6
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.59
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.59
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.58
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.57
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.56
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.55
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.55
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.54
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.54
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.54
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.53
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.53
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.53
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.52
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.52
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.51
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.47
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.46
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.44
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.44
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.44
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.43
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.43
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.42
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.41
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.41
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.36
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.33
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.2
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.15
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.15
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.14
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.97
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.87
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.85
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.8
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.7
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.64
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.22
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.14
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.09
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.79
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.71
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.55
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.36
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.3
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.25
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.15
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.01
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.93
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.78
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.74
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.68
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.63
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.69
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.38
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.1
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.13
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	83.8

>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=9e-38  Score=273.03  Aligned_cols=175  Identities=25%  Similarity=0.404  Sum_probs=152.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||+++||++|+++|++||+|++|+|++|+.|++++|||||+|.+.++|++||+.+++.. +.+  +.+
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~-~~g--~~i   87 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDV-IKG--KPV   87 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhh-cCC--ccc
Confidence            45577899999999999999999999999999999999999999999999999999999999999998766 444  777


Q ss_pred             eeeccccccc---cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC
Q 018554           90 QVKYADGELE---RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK  166 (354)
Q Consensus        90 ~v~~~~~~~~---~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  166 (354)
                      ++.++.....   ...++|||+||++++|+++|+++|+.||.|++++|++|.. .++|||||+|.+.++|.+|++.|||.
T Consensus        88 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a~~Ai~~lng~  166 (213)
T 4f02_A           88 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGM  166 (213)
T ss_dssp             EEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHHHHHHHHhCCC
Confidence            7777654332   2367899999999999999999999999999999999854 36999999999999999999999998


Q ss_pred             cccCCCceeEEEEecCChHHHHHHH
Q 018554          167 HKMEGSSVPLVVKWADTEKERQARR  191 (354)
Q Consensus       167 ~~~~g~~~~l~v~~a~~~~~~~~~~  191 (354)
                      . ++|  +.|+|+||++++++..+.
T Consensus       167 ~-~~g--~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          167 L-LND--RKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             E-ETT--EECEEEECCCHHHHHHHH
T ss_pred             E-ECC--EEEEEEEcCCCcccchhh
Confidence            7 666  799999999887665443

>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=2e-37  Score=261.68  Aligned_cols=170  Identities=42%  Similarity=0.790  Sum_probs=157.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCC--CcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR--ASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg--~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      +.++|||+|||+++|+++|+++|++||+|.+|++++++.++  +++|||||+|.+.++|++|++.+++..++.+..+.+.
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            67899999999999999999999999999999999999887  8999999999999999999999999887777788888


Q ss_pred             eecccccccc--ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554           91 VKYADGELER--LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus        91 v~~~~~~~~~--~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      +.+++.+...  ..++|||+||+.++|+++|+++|+.||.|+++.++++.++.++|||||+|.+.++|.+|++.|||..+
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT  161 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCC
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcc
Confidence            8887655433  47899999999999999999999999999999999998899999999999999999999999999987


Q ss_pred             cCCCceeEEEEecC
Q 018554          169 MEGSSVPLVVKWAD  182 (354)
Q Consensus       169 ~~g~~~~l~v~~a~  182 (354)
                      .+|..++|.|+||+
T Consensus       162 ~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          162 MEGCSSPMVVKFAD  175 (175)
T ss_dssp             CTTCSSCCEEEECC
T ss_pred             cCCCCCCeEEEecC
Confidence            87767899999986

>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=1.9e-35  Score=247.44  Aligned_cols=165  Identities=28%  Similarity=0.531  Sum_probs=151.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      .+++|||+|||.++++++|+++|++||.|.+|++++++.+|+++|||||+|.+.++|++|++.+++.. +.+  +.++|.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~-~~g--~~l~v~   77 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLR-LQT--KTIKVS   77 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCc-cCC--ceEEEE
Confidence            36899999999999999999999999999999999999999999999999999999999999998866 444  788898


Q ss_pred             ccccccc-cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554           93 YADGELE-RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus        93 ~~~~~~~-~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ++..... ...++|||+||+.++++++|+++|++||.|++++++++. ++.++|||||+|.+.++|.+|++.|||.. ++
T Consensus        78 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~  156 (167)
T 1fxl_A           78 YARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK-PS  156 (167)
T ss_dssp             ECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CT
T ss_pred             ecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCc-cC
Confidence            8875543 346889999999999999999999999999999999985 88899999999999999999999999986 78


Q ss_pred             CCceeEEEEec
Q 018554          171 GSSVPLVVKWA  181 (354)
Q Consensus       171 g~~~~l~v~~a  181 (354)
                      |+.++|.|+||
T Consensus       157 g~~~~i~v~~A  167 (167)
T 1fxl_A          157 GATEPITVKFA  167 (167)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCccceEEEeC
Confidence            87788999986

>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=1.6e-35  Score=248.45  Aligned_cols=165  Identities=29%  Similarity=0.523  Sum_probs=151.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ..++|||+|||+++++++|+++|++||.|.+|++++++.+++++|||||+|.+.++|++|++.+++.. +.+  +.++|.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~-~~g--~~l~v~   78 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGIT-VRN--KRLKVS   78 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCE-eCC--cEEEEE
Confidence            57899999999999999999999999999999999999999999999999999999999999998866 444  788999


Q ss_pred             ccccccc-cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554           93 YADGELE-RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus        93 ~~~~~~~-~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ++..+.. ...++|||+||+.++++++|+++|+.||.|+++.++++. ++.++|+|||+|.+.++|.+|++.|||.. ++
T Consensus        79 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~  157 (168)
T 1b7f_A           79 YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI-PE  157 (168)
T ss_dssp             ECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CT
T ss_pred             ecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCE-ec
Confidence            8876543 346899999999999999999999999999999999996 88999999999999999999999999986 77


Q ss_pred             CCceeEEEEec
Q 018554          171 GSSVPLVVKWA  181 (354)
Q Consensus       171 g~~~~l~v~~a  181 (354)
                      |..++|+|+||
T Consensus       158 g~~~~l~V~~A  168 (168)
T 1b7f_A          158 GGSQPLSVRLA  168 (168)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCCeEEEEEeC
Confidence            77789999986

>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=8.2e-35  Score=250.37  Aligned_cols=174  Identities=24%  Similarity=0.401  Sum_probs=146.3

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      +..+..+.++|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|++. ++.. +.+  
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~-~~g--   81 (196)
T 1l3k_A            6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHK-VDG--   81 (196)
T ss_dssp             --CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCE-ETT--
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCE-ECC--
Confidence            344567889999999999999999999999999999999999999999999999999999999999977 4544 555  


Q ss_pred             ccceeecccccccc-------ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHH
Q 018554           87 SPLQVKYADGELER-------LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALA  158 (354)
Q Consensus        87 ~~l~v~~~~~~~~~-------~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~  158 (354)
                      +.|.|.++......       ..++|||+||+.++|+++|+++|+.||.|++|.|+++. ++.++|||||+|++.++|.+
T Consensus        82 ~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~  161 (196)
T 1l3k_A           82 RVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK  161 (196)
T ss_dssp             EECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             EEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHH
Confidence            77888877544322       24799999999999999999999999999999999995 88999999999999999999


Q ss_pred             HHHHhCCCcccCCCceeEEEEecCChHHHH
Q 018554          159 ALEAINGKHKMEGSSVPLVVKWADTEKERQ  188 (354)
Q Consensus       159 Ai~~l~g~~~~~g~~~~l~v~~a~~~~~~~  188 (354)
                      |++. ++.. ++|  +.|.|+||.++.+..
T Consensus       162 A~~~-~~~~-~~G--~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          162 IVIQ-KYHT-VNG--HNCEVRKALSKQEMA  187 (196)
T ss_dssp             HHHC-SCCE-ETT--EECEEEECC------
T ss_pred             HHHh-CCcE-ECC--EEEEEEecCChhHhc
Confidence            9986 6765 676  689999998876554

>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=2.7e-34  Score=250.89  Aligned_cols=169  Identities=20%  Similarity=0.348  Sum_probs=148.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||.++|+++|+++|++||+|.+|++++|+.+++++|||||+|.+.++|++|++.|++.. +.+  +.|
T Consensus        24 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g--~~l  100 (216)
T 2qfj_A           24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVM-LGG--RNI  100 (216)
T ss_dssp             HHHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCC-CC---CCC
T ss_pred             ccCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCe-eCC--eeE
Confidence            34567899999999999999999999999999999999999999999999999999999999999998866 555  778


Q ss_pred             eeeccccccc------------cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHH
Q 018554           90 QVKYADGELE------------RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQA  156 (354)
Q Consensus        90 ~v~~~~~~~~------------~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A  156 (354)
                      +|.++.....            ...++|||+||+.++|+++|+++|+.||.|++|+|+++ .++.++|||||+|++.++|
T Consensus       101 ~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A  180 (216)
T 2qfj_A          101 KVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS  180 (216)
T ss_dssp             EEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             EEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHH
Confidence            8887654432            23579999999999999999999999999999999999 5889999999999999999


Q ss_pred             HHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          157 LAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       157 ~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      .+|++.|||.. ++|  +.|+|.|+...
T Consensus       181 ~~A~~~l~g~~-~~g--~~i~V~~a~~~  205 (216)
T 2qfj_A          181 QDAVSSMNLFD-LGG--QYLRVGKAVTP  205 (216)
T ss_dssp             HHHHHHHTTCB-CSS--SBCEEEECSSC
T ss_pred             HHHHHHccCCE-eCC--cEEEEEEecCC
Confidence            99999999987 666  67999998754

>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=2.8e-34  Score=240.04  Aligned_cols=162  Identities=22%  Similarity=0.418  Sum_probs=146.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      ++|||+|||.++|+++|+++|++||.|.+|++++|+. ++++|||||+|.+.++|++|++.+++.. +.+  +.+.+.++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~-~~g--~~i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQ-IEN--NIVKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCc-cCC--CeeEEEEc
Confidence            6899999999999999999999999999999999985 7799999999999999999999998876 444  78888887


Q ss_pred             cccc---ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554           95 DGEL---ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus        95 ~~~~---~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ....   ....++|||+||+.++|+++|+++|+.||.|.++.++++ .++.++|+|||+|.+.++|.+|++.|||.. ++
T Consensus        77 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~  155 (166)
T 3md3_A           77 FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD-LN  155 (166)
T ss_dssp             CCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE-ET
T ss_pred             CCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-cC
Confidence            5543   334679999999999999999999999999999999998 688999999999999999999999999987 56


Q ss_pred             CCceeEEEEecCC
Q 018554          171 GSSVPLVVKWADT  183 (354)
Q Consensus       171 g~~~~l~v~~a~~  183 (354)
                      |  +.|+|+||+.
T Consensus       156 g--~~i~v~~a~~  166 (166)
T 3md3_A          156 G--RPLRINWAAK  166 (166)
T ss_dssp             T--EECEEEESCC
T ss_pred             C--cEEEEEecCC
Confidence            5  7899999863

>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=1.1e-34  Score=243.11  Aligned_cols=163  Identities=26%  Similarity=0.395  Sum_probs=144.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ++++|||+|||.++|+++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|++|++.  . ..+.|  +.+.+.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~-~~~~g--~~i~v~   76 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--Q-HILDG--KVIDPK   76 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--C-CEETT--EECCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--c-cccCC--eEcccc
Confidence            578999999999999999999999999999999999999999999999999999999999985  2 34555  677777


Q ss_pred             ccccccc-cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554           93 YADGELE-RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus        93 ~~~~~~~-~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ++..+.. ...++|||+||+.++|+++|+++|+.||.|+++.++++ .++.++|||||+|.+.++|.+|++ +++.. ++
T Consensus        77 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~-~~  154 (167)
T 2cjk_A           77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFID-FK  154 (167)
T ss_dssp             ECCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEEC-SS
T ss_pred             cccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEE-eC
Confidence            7665433 33679999999999999999999999999999999998 479999999999999999999998 78765 66


Q ss_pred             CCceeEEEEecCCh
Q 018554          171 GSSVPLVVKWADTE  184 (354)
Q Consensus       171 g~~~~l~v~~a~~~  184 (354)
                      |  +.|.|+||+++
T Consensus       155 g--~~i~V~~a~pk  166 (167)
T 2cjk_A          155 D--RKIEIKRAEPR  166 (167)
T ss_dssp             S--SCEEEEECCCC
T ss_pred             C--eEEEEeecCCC
Confidence            6  68999999764

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=1.4e-32  Score=250.49  Aligned_cols=177  Identities=21%  Similarity=0.258  Sum_probs=159.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||+++|+++|+++|+.||.|.+|.+++|+.+|+++|||||+|.+.++|.+|++.+++.. +.+  +.|.|
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~-~~g--~~i~v  169 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP-LGP--RTLYV  169 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCE-eCC--cEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999999998866 555  88999


Q ss_pred             ecccccccc----ccceEEEecCCCCC-CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC
Q 018554           92 KYADGELER----LEHKLFIGMLPKNV-SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK  166 (354)
Q Consensus        92 ~~~~~~~~~----~~~~l~V~~l~~~~-t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  166 (354)
                      .++..+...    ..++|||+||+.++ |+++|+++|+.||.|++++|+++.++.++|+|||+|.+.++|.+|++.|||.
T Consensus       170 ~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  249 (284)
T 3smz_A          170 HWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGL  249 (284)
T ss_dssp             EECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCC
Confidence            998765432    36799999999995 9999999999999999999999999999999999999999999999999998


Q ss_pred             cccCCCceeEEEEecCChHHHHHHHHHH
Q 018554          167 HKMEGSSVPLVVKWADTEKERQARRAQK  194 (354)
Q Consensus       167 ~~~~g~~~~l~v~~a~~~~~~~~~~~~~  194 (354)
                      . ++|  +.|.|+|++++..++....++
T Consensus       250 ~-~~g--~~l~v~~a~~~~~~~~~~~~~  274 (284)
T 3smz_A          250 S-LGG--SHLRVSFCAPGPPGRSMLAAL  274 (284)
T ss_dssp             E-ETT--EECEEEECCSSSCHHHHHHHH
T ss_pred             c-cCC--eEEEEEEecCCCcccchhhhh
Confidence            7 565  799999999887766555444

>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=1.5e-32  Score=238.01  Aligned_cols=160  Identities=18%  Similarity=0.289  Sum_probs=136.9

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVP-KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp-~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .+.++|||+||+ +++++++|+++|++||.|.+|+|+++     .+|||||+|.+.++|++||+.||+.. +.+  +.|+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~-~~g--~~l~   73 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNF-MFG--QKMN   73 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCE-ETT--EECE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCE-ECC--ceEE
Confidence            357899999999 89999999999999999999999876     36899999999999999999999877 555  7788


Q ss_pred             eeccccccc--------------------------------------cccceEEEecCCCCCCHHHHHHhhccCCCe--e
Q 018554           91 VKYADGELE--------------------------------------RLEHKLFIGMLPKNVSEAEVSALFSIYGTI--K  130 (354)
Q Consensus        91 v~~~~~~~~--------------------------------------~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v--~  130 (354)
                      |.+++.+..                                      ...++|||+||++++|+++|+++|++||.|  .
T Consensus        74 v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~  153 (205)
T 3tyt_A           74 VCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPT  153 (205)
T ss_dssp             EEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCS
T ss_pred             EEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceE
Confidence            887642110                                      113579999999999999999999999998  8


Q ss_pred             EEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC--ceeEEEEec
Q 018554          131 DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS--SVPLVVKWA  181 (354)
Q Consensus       131 ~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~--~~~l~v~~a  181 (354)
                      +++++.+. +.++|+|||+|++.++|.+||+.|||.. ++|.  ..++.|+||
T Consensus       154 ~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~-~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          154 SVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQ-MKNPNGPYPYTLKLC  204 (205)
T ss_dssp             EEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCE-ECCSSSSSCEECEEE
T ss_pred             EEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCC-ccCCCCCcceEEEec
Confidence            99999876 4457999999999999999999999987 5543  457888875

>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=7.1e-33  Score=234.10  Aligned_cols=164  Identities=21%  Similarity=0.327  Sum_probs=142.5

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .+..+.++|||+|||.++++++|+++|++||.|.. .++++..+++++|||||+|.+.++|++|+ .+++.. +.+  +.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g--~~   82 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLK-VFG--NE   82 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEE-ETT--EE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCE-eCC--eE
Confidence            46678999999999999999999999999998776 45566667899999999999999999999 588866 444  88


Q ss_pred             ceeeccccccc---cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554           89 LQVKYADGELE---RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus        89 l~v~~~~~~~~---~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      |+|.++..+..   ...++|||+||+.++|+++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|++.|||
T Consensus        83 l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 1fje_B           83 IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQG  158 (175)
T ss_dssp             EEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTE
T ss_pred             EEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCC
Confidence            99988875433   347899999999999999999999999988766    56788899999999999999999999999


Q ss_pred             CcccCCCceeEEEEecCCh
Q 018554          166 KHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       166 ~~~~~g~~~~l~v~~a~~~  184 (354)
                      .. ++|  +.|.|+||+++
T Consensus       159 ~~-~~g--~~i~v~~a~~k  174 (175)
T 1fje_B          159 AE-IDG--RSVSLYYTGEK  174 (175)
T ss_dssp             EE-ETT--EEEEEEECSSC
T ss_pred             CE-ECC--eEEEEEecCCC
Confidence            76 666  78999999764

>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=99.98  E-value=1.7e-31  Score=242.98  Aligned_cols=162  Identities=21%  Similarity=0.425  Sum_probs=141.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLL----AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~----~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .+....++|||+|||+++++++|+    ++|++||.|.+|++++   +++++|||||+|.+.++|++|++.||+.. +.+
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g   79 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFP-FYD   79 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCe-eCC
Confidence            456789999999999999999977    8999999999999886   57899999999999999999999998866 555


Q ss_pred             CCccceeeccccccc-----------------------------------------------------------------
Q 018554           85 ASSPLQVKYADGELE-----------------------------------------------------------------   99 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~-----------------------------------------------------------------   99 (354)
                        +.|+|.|++.+..                                                                 
T Consensus        80 --~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (282)
T 3pgw_A           80 --KPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHM  157 (282)
T ss_pred             --cEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccC
Confidence              7888887754331                                                                 


Q ss_pred             -----------------------------------------------cccceEEEecCCCCCCHHHHHHhhccCCCeeEE
Q 018554          100 -----------------------------------------------RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL  132 (354)
Q Consensus       100 -----------------------------------------------~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i  132 (354)
                                                                     ...++|||+||+.++|+++|+++|++||.|++|
T Consensus       158 ~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v  237 (282)
T 3pgw_A          158 PGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEV  237 (282)
T ss_pred             CCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEE
Confidence                                                           124679999999999999999999999999999


Q ss_pred             EEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          133 QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       133 ~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      +|+.++    +|||||+|.+.++|.+|++.|||..+..|  +.|+|+||+
T Consensus       238 ~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~~l~v~~ak  281 (282)
T 3pgw_A          238 RLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQN--NAMKISFAK  281 (282)
T ss_pred             EEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCC--CEEEEEEec
Confidence            999764    58999999999999999999999874325  689999986

>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=99.98  E-value=1.6e-31  Score=225.02  Aligned_cols=157  Identities=27%  Similarity=0.443  Sum_probs=138.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEF----A-------LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~----G-------~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      ++.++|||+|||.++|+++|+++|++|    |       .|.++.+.+      ++|||||+|.+.++|++|+ .+++..
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~   74 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGII   74 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcE
Confidence            367899999999999999999999999    6       677776644      5789999999999999999 888766


Q ss_pred             cCCCCCccceeeccccccc-cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHH
Q 018554           81 TLPGASSPLQVKYADGELE-RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALA  158 (354)
Q Consensus        81 ~~~g~~~~l~v~~~~~~~~-~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~  158 (354)
                       +.+  +.++|.++..... ...++|||+||+.++|+++|+++|++||.|+++.+.++. ++.++|||||+|.+.++|.+
T Consensus        75 -~~g--~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~  151 (172)
T 2g4b_A           75 -FQG--QSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ  151 (172)
T ss_dssp             -ETT--EECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHH
T ss_pred             -ecC--ceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHH
Confidence             555  7888888765432 336899999999999999999999999999999999994 89999999999999999999


Q ss_pred             HHHHhCCCcccCCCceeEEEEec
Q 018554          159 ALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       159 Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      |++.|||.. ++|  +.|.|+||
T Consensus       152 A~~~l~g~~-~~g--~~l~V~~A  171 (172)
T 2g4b_A          152 AIAGLNGMQ-LGD--KKLLVQRA  171 (172)
T ss_dssp             HHHHHTTCE-ETT--EECEEEEC
T ss_pred             HHHHcCCCE-ECC--eEEEEEeC
Confidence            999999987 565  78999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.98  E-value=1e-32  Score=237.61  Aligned_cols=160  Identities=26%  Similarity=0.440  Sum_probs=137.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEF----A-------LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~----G-------~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      ...++|||+|||+++|+++|+++|++|    |       .|.++.+      ++++|||||+|.+.++|++|+ .|++..
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~   74 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGII   74 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCE
Confidence            357999999999999999999999999    4       5555554      456899999999999999999 887765


Q ss_pred             cCCCCCccceeeccccccc---------------------cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-
Q 018554           81 TLPGASSPLQVKYADGELE---------------------RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-  138 (354)
Q Consensus        81 ~~~g~~~~l~v~~~~~~~~---------------------~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-  138 (354)
                       +.+  +.|+|.++.....                     ...++|||+||+.++++++|+++|++||.|.++.+.++. 
T Consensus        75 -~~g--~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~  151 (198)
T 2yh0_A           75 -FQG--QSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA  151 (198)
T ss_dssp             -ETT--EEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTT
T ss_pred             -EcC--ceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCC
Confidence             555  7888888754311                     235899999999999999999999999999999999995 


Q ss_pred             CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          139 QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       139 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      ++.++|||||+|.+.++|.+|++.|||.. ++|  +.|.|+|++++
T Consensus       152 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~~a~~~  194 (198)
T 2yh0_A          152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQ-LGD--KKLLVQRASVG  194 (198)
T ss_dssp             TCSEEEEEEEEESSSSHHHHHHHHHTTCE-ETT--EECEEEESCCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEECCCC
Confidence            89999999999999999999999999987 565  78999999765

>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=4.7e-31  Score=232.90  Aligned_cols=165  Identities=20%  Similarity=0.338  Sum_probs=142.1

Q ss_pred             cccccCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554            5 KKEKKSSEERVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ........+.++|||+|||. ++++++|+++|++||.|.+|+|++|+     +|||||+|.+.++|++|++.|++.. +.
T Consensus        25 ~~p~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~-~~   98 (229)
T 2adc_A           25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHK-LH   98 (229)
T ss_dssp             CCGGGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCB-CS
T ss_pred             CCCCCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCe-EC
Confidence            34445567889999999999 99999999999999999999999985     6899999999999999999998866 45


Q ss_pred             CCCccceeecccccc------------------------------------ccccceEEEecCCCCCCHHHHHHhhccCC
Q 018554           84 GASSPLQVKYADGEL------------------------------------ERLEHKLFIGMLPKNVSEAEVSALFSIYG  127 (354)
Q Consensus        84 g~~~~l~v~~~~~~~------------------------------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G  127 (354)
                      +  +.|+|.+++.+.                                    ....++|||+||+.++++++|+++|+.||
T Consensus        99 g--~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G  176 (229)
T 2adc_A           99 G--KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG  176 (229)
T ss_dssp             S--SBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTS
T ss_pred             C--eEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcC
Confidence            5  788888775331                                    01157899999999999999999999999


Q ss_pred             -CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC-CCceeEEEEecCCh
Q 018554          128 -TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME-GSSVPLVVKWADTE  184 (354)
Q Consensus       128 -~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~-g~~~~l~v~~a~~~  184 (354)
                       .|.+|+++.+    ++|+|||+|++.++|.+|++.|||.. ++ |  +.|+|+|+++.
T Consensus       177 ~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~-~~~g--~~l~v~~a~~~  228 (229)
T 2adc_A          177 GVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHD-LGEN--HHLRVSFSKST  228 (229)
T ss_dssp             CCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCB-SSSS--CBCEEEECSSC
T ss_pred             CCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCc-cCCC--CeEEEEEecCC
Confidence             9999999763    27899999999999999999999987 45 5  68999998753

>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=3.5e-31  Score=238.30  Aligned_cols=163  Identities=26%  Similarity=0.424  Sum_probs=145.2

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||+|||.++|+++|+++|+.||.|.+|.+.++      +|||||+|.+.++|.+|++.+++.. +.+  +
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~-i~g--~   86 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTI-LKS--R   86 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCE-ETT--E
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcE-ECC--c
Confidence            344567789999999999999999999999999999999654      6899999999999999999998876 544  8


Q ss_pred             cceeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHh-CCC
Q 018554           88 PLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI-NGK  166 (354)
Q Consensus        88 ~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~  166 (354)
                      .|+|.++..     .++|||+||+..+|+++|+++|+.||.|++|.|+.+.++.++|||||+|.+.++|.+|++.| ++.
T Consensus        87 ~l~v~~a~~-----~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~  161 (261)
T 3sde_A           87 PLRIRFATH-----GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGA  161 (261)
T ss_dssp             ECEEEECCC-----SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSC
T ss_pred             eeEeeeccc-----CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCe
Confidence            889988864     46899999999999999999999999999999999999999999999999999999999999 555


Q ss_pred             cccCCCceeEEEEecCCh
Q 018554          167 HKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       167 ~~~~g~~~~l~v~~a~~~  184 (354)
                      .++.+..++|.|++++..
T Consensus       162 ~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          162 FLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             EESSSSCCBCEEEECCCE
T ss_pred             EEecCCCceEEEeecccc
Confidence            555556689999998755

>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=1.2e-30  Score=238.57  Aligned_cols=165  Identities=19%  Similarity=0.330  Sum_probs=141.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ...++|||+|||.++++++|+++|+.|| .|.+|.+++++. ++++|||||+|.+.++|.+|++.|++.. +.+  +.|.
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~  190 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLK-IEG--YTLV  190 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCE-ETT--EECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCE-eCC--cEEE
Confidence            4689999999999999999999999999 999999999986 8899999999999999999999998876 555  8888


Q ss_pred             eecccccccc--------ccceEEEecCCCC-CCHHHHHHhhccCCCeeEEEEeeCCC--CCcceEEEEEeCCHHHHHHH
Q 018554           91 VKYADGELER--------LEHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQ--QTSKGCAFLKYETKEQALAA  159 (354)
Q Consensus        91 v~~~~~~~~~--------~~~~l~V~~l~~~-~t~~~l~~~F~~~G~v~~i~i~~~~~--~~~~g~afV~f~~~~~A~~A  159 (354)
                      |.++.+....        ..++|||+||+.+ +|+++|+++|+.||.|++|+|+++..  +.++|||||+|.+.++|.+|
T Consensus       191 v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A  270 (292)
T 2ghp_A          191 TKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA  270 (292)
T ss_dssp             EEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHH
T ss_pred             EEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHH
Confidence            8887654322        2579999999999 99999999999999999999999876  99999999999999999999


Q ss_pred             HHHhCCCcccCCCceeEEEEecCCh
Q 018554          160 LEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       160 i~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      + .|||.. ++|  +.|.|.||+++
T Consensus       271 ~-~l~g~~-~~g--~~i~V~~a~~k  291 (292)
T 2ghp_A          271 L-QMNRSL-LGN--REISVSLADKK  291 (292)
T ss_dssp             G-GGTTEE-ETT--EEEEEEECCCC
T ss_pred             H-HhcCCE-ECC--cEEEEEEecCC
Confidence            9 999987 665  78999999864

>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=1.2e-30  Score=225.01  Aligned_cols=156  Identities=21%  Similarity=0.368  Sum_probs=136.6

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           13 ERVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        13 ~~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      +.++|||+|||. ++++++|+++|++||.|.+|++++|+     +|||||+|.+.++|++|++.|++.. +.+  +.|+|
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~-~~g--~~l~v   73 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHK-LHG--KPIRI   73 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCC-CSS--CCCEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCe-ecC--eEEEE
Confidence            468999999999 99999999999999999999999875     6899999999999999999998866 455  77888


Q ss_pred             ecccccc------------------------------------ccccceEEEecCCCCCCHHHHHHhhccCC-CeeEEEE
Q 018554           92 KYADGEL------------------------------------ERLEHKLFIGMLPKNVSEAEVSALFSIYG-TIKDLQI  134 (354)
Q Consensus        92 ~~~~~~~------------------------------------~~~~~~l~V~~l~~~~t~~~l~~~F~~~G-~v~~i~i  134 (354)
                      .+++.+.                                    ....++|||+||+.++++++|+++|+.|| .|.++++
T Consensus        74 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i  153 (198)
T 1qm9_A           74 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF  153 (198)
T ss_dssp             EECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEE
T ss_pred             EEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEE
Confidence            7765331                                    01267899999999999999999999999 9999999


Q ss_pred             eeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC-CCceeEEEEecCC
Q 018554          135 LRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME-GSSVPLVVKWADT  183 (354)
Q Consensus       135 ~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~-g~~~~l~v~~a~~  183 (354)
                      +.+.    +|+|||+|.+.++|.+|++.|||.. ++ |  +.|+|+|+++
T Consensus       154 ~~~~----~g~afV~f~~~~~A~~A~~~l~g~~-~~~g--~~l~v~~a~~  196 (198)
T 1qm9_A          154 FQKD----RKMALIQMGSVEEAVQALIDLHNHD-LGEN--HHLRVSFSKS  196 (198)
T ss_dssp             SSTT----SSCEEEECSSHHHHHHHHHHHTSSC-CSSC--CSCCEEEECC
T ss_pred             EeCC----CcEEEEEeCCHHHHHHHHHHhcCCc-cCCC--CeEEEEeecc
Confidence            7643    7899999999999999999999987 45 5  6889999875

>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=1.8e-30  Score=237.45  Aligned_cols=164  Identities=18%  Similarity=0.243  Sum_probs=135.4

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||+++|+++|+++|+.||+|.+|+|++|+.+  ++|||||+|.+.++|.+|++ +++.. +.+  +
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~-~~g--~  108 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKV-VGQ--N  108 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCE-ETT--E
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcE-eCC--c
Confidence            345677899999999999999999999999999999999999853  58999999999999999995 77655 555  7


Q ss_pred             cceeeccccccccccceEEEecCCCCCCHHHHHHhhccCC-CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC
Q 018554           88 PLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYG-TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK  166 (354)
Q Consensus        88 ~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G-~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~  166 (354)
                      .+.+.++.      .++|||+||+.++++++|+++|+.|| .|.+|.++++..+.++|||||+|.+.++|.+|++.|||.
T Consensus       109 ~i~v~~~~------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  182 (292)
T 2ghp_A          109 EIIVSHLT------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL  182 (292)
T ss_dssp             ECEEEECC------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EEEEEECC------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            78888763      57899999999999999999999999 999999999987889999999999999999999999998


Q ss_pred             cccCCCceeEEEEecCChHH
Q 018554          167 HKMEGSSVPLVVKWADTEKE  186 (354)
Q Consensus       167 ~~~~g~~~~l~v~~a~~~~~  186 (354)
                      . ++|  +.|.|.|+++...
T Consensus       183 ~-~~g--~~l~v~~a~~~~~  199 (292)
T 2ghp_A          183 K-IEG--YTLVTKVSNPLEK  199 (292)
T ss_dssp             E-ETT--EECEEEECCCC--
T ss_pred             E-eCC--cEEEEEECCCCcc
Confidence            7 565  7899999987644

>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=99.97  E-value=3e-29  Score=228.36  Aligned_cols=158  Identities=22%  Similarity=0.411  Sum_probs=141.6

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      +...++++|||+|||.++|+++|+++|+.|| |.+|.+      ++++|||||+|.+.++|.+|++.+++.. +.+  +.
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g--~~   86 (284)
T 3smz_A           17 RQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSR-LRE--RE   86 (284)
T ss_dssp             HHHHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCE-ETT--EE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCe-eCC--eE
Confidence            3455789999999999999999999999999 999888      4578999999999999999999998877 555  78


Q ss_pred             ceeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 018554           89 LQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus        89 l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                      +.|.++..     .++|||+||+.++|+++|+++|+.||.|.++.++++ .++.++|||||+|.+.++|.+|++.|+|..
T Consensus        87 i~v~~~~~-----~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~  161 (284)
T 3smz_A           87 LSVQLQPT-----DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP  161 (284)
T ss_dssp             CEEEECCC-----SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             EEEEecCC-----CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCE
Confidence            88887543     478999999999999999999999999999999998 489999999999999999999999999976


Q ss_pred             ccCCCceeEEEEecCCh
Q 018554          168 KMEGSSVPLVVKWADTE  184 (354)
Q Consensus       168 ~~~g~~~~l~v~~a~~~  184 (354)
                       ++|  +.|.|.|++..
T Consensus       162 -~~g--~~i~v~~a~~~  175 (284)
T 3smz_A          162 -LGP--RTLYVHWTDAG  175 (284)
T ss_dssp             -ETT--EECEEEECCGG
T ss_pred             -eCC--cEEEEEECCCC
Confidence             555  78999999764

>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=99.90  E-value=1.2e-23  Score=174.69  Aligned_cols=137  Identities=20%  Similarity=0.286  Sum_probs=108.4

Q ss_pred             EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC----Cccceeecc-------ccccccccceEEEecCC
Q 018554           43 EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA----SSPLQVKYA-------DGELERLEHKLFIGMLP  111 (354)
Q Consensus        43 ~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~----~~~l~v~~~-------~~~~~~~~~~l~V~~l~  111 (354)
                      +++|+++..  +++|||||+|.+.++|++|++.+++...+.+.    .........       ........++|||+||+
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            567788764  69999999999999999999988654322221    011111110       11122336899999999


Q ss_pred             CCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          112 KNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       112 ~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      +++|+++|+++|+.||.|++|+|++| .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+|++..
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~~a~~~  150 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV-LDG--RELRVQMARYG  150 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEE-SSS--SEEEEEEECCS
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEEEEECCCC
Confidence            99999999999999999999999999 489999999999999999999999999976 666  68999999765

>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=99.88  E-value=6e-23  Score=161.13  Aligned_cols=101  Identities=18%  Similarity=0.281  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ..++|||+|||+++||++|+++|++||.|.+|+|++|+  +++||||||+|.+.++|++||+.|++.. +.+  +.|+|.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~-~~g--~~i~V~   78 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGML-LND--RKVFVG   78 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEE
Confidence            46789999999999999999999999999999999996  4589999999999999999999998876 555  788898


Q ss_pred             ccccccccc---------cceEEEecCCCCCCHHH
Q 018554           93 YADGELERL---------EHKLFIGMLPKNVSEAE  118 (354)
Q Consensus        93 ~~~~~~~~~---------~~~l~V~~l~~~~t~~~  118 (354)
                      +++.+..+.         ..+|||+||+.++|++-
T Consensus        79 ~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           79 RFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             ESSCCCC----------------------------
T ss_pred             ECCCccccccccccccCCCCceEeCCCCCCccccc
Confidence            876544322         45799999999999874

>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=99.86  E-value=2e-21  Score=148.02  Aligned_cols=83  Identities=27%  Similarity=0.456  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||.++|+++|+++|++||+|.+|+|++|+.||+++|||||+|.+.++|++|++.||+.. +.|  +.|+
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~-~~g--r~l~   92 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR-LQS--KTIK   92 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCE-ECC--EEEE
Confidence            4456899999999999999999999999999999999999999999999999999999999999999876 555  8899


Q ss_pred             eecccc
Q 018554           91 VKYADG   96 (354)
Q Consensus        91 v~~~~~   96 (354)
                      |+|+++
T Consensus        93 V~~AkP   98 (99)
T 4fxv_A           93 VSYARP   98 (99)
T ss_dssp             EEECCB
T ss_pred             EEEeeC
Confidence            999865

>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=99.85  E-value=3.3e-21  Score=158.43  Aligned_cols=121  Identities=21%  Similarity=0.395  Sum_probs=103.6

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHh-cCCccCCCCCccceeecccccc-----------------ccccceEEEecCCCCC
Q 018554           53 RASRGCCFVICPSRQEADKAVNAC-HNKKTLPGASSPLQVKYADGEL-----------------ERLEHKLFIGMLPKNV  114 (354)
Q Consensus        53 g~~~G~aFV~f~~~~~A~~Ai~~l-~~~~~~~g~~~~l~v~~~~~~~-----------------~~~~~~l~V~~l~~~~  114 (354)
                      .+-+|+++|+|.+.++|++|++.+ |+.. +.|   .+.+.++..+.                 ....++|||+||++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~-~~G---~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~   85 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNG-VDG---EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNG   85 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHT-CCC---EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCC
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCC-CCC---ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCC
Confidence            467899999999999999999999 7755 544   67777665421                 1236899999999999


Q ss_pred             CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          115 SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       115 t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      |+++|+++|++||.|++|+|+++    ++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+|++++
T Consensus        86 t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~~a~~~  148 (150)
T 2i2y_A           86 NKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRT-LCG--CRVRVELSNGE  148 (150)
T ss_dssp             SCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSC-SSS--SCCEEEECCCC
T ss_pred             CHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEEEcCCC
Confidence            99999999999999999999987    58999999999999999999999977 666  68999998765

>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=99.83  E-value=2.1e-20  Score=144.24  Aligned_cols=96  Identities=38%  Similarity=0.655  Sum_probs=86.8

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ........+.++|||+|||.++++++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++|++.||+..++.+
T Consensus         4 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   83 (106)
T 2dgp_A            4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPG   83 (106)
T ss_dssp             CCCSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTT
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCC
Confidence            34456677889999999999999999999999999999999999999999999999999999999999999999887766


Q ss_pred             CCccceeecccccccc
Q 018554           85 ASSPLQVKYADGELER  100 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~~  100 (354)
                      ..+.|+|.+++.+..+
T Consensus        84 ~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           84 MNRPIQVKPADSESRG   99 (106)
T ss_dssp             CSSCCEEEECCCCSCC
T ss_pred             CCceEEEEECCccccc
Confidence            6799999999876543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.83  E-value=1.9e-20  Score=145.36  Aligned_cols=85  Identities=19%  Similarity=0.234  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+||+++++|++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++||+.||+.. +.+  +.|+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~-~~g--r~i~   79 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTS-VMG--NIIH   79 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEE
Confidence            3567899999999999999999999999999999999999999999999999999999999999999877 555  7888


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |.++....
T Consensus        80 V~~a~~~~   87 (110)
T 3s8s_A           80 AQLDIKGQ   87 (110)
T ss_dssp             EEECSTTH
T ss_pred             EEECCCCc
Confidence            88876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.83  E-value=2.9e-21  Score=144.87  Aligned_cols=84  Identities=20%  Similarity=0.365  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +++|||+|||.++||++|+++|++|| +|.+|+|++|+.|+++||||||+|.+.++|++|++.+++...+.|  +.|+|.
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g--r~i~V~   78 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILG--QKVSMH   78 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETT--EEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECC--EEEEEE
Confidence            47899999999999999999999999 899999999999999999999999999999999998766555666  889999


Q ss_pred             ccccccc
Q 018554           93 YADGELE   99 (354)
Q Consensus        93 ~~~~~~~   99 (354)
                      +++++..
T Consensus        79 ~a~~~~~   85 (91)
T 2lxi_A           79 YSDPKPK   85 (91)
T ss_dssp             CCCSCCC
T ss_pred             EcCCCCC
Confidence            9887654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.82  E-value=8.1e-21  Score=143.26  Aligned_cols=86  Identities=20%  Similarity=0.396  Sum_probs=76.9

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc---cCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFAL--VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK---TLP   83 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~--v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~---~~~   83 (354)
                      .....-.+|||+|||+++|+++|+++|++||.  |.+|++++|+.||++||||||+|.+.++|++|++.||+..   .+.
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~   83 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            34567889999999999999999999999995  6799999999999999999999999999999999999864   355


Q ss_pred             CCCccceeecccc
Q 018554           84 GASSPLQVKYADG   96 (354)
Q Consensus        84 g~~~~l~v~~~~~   96 (354)
                      |  +.|.|+|++.
T Consensus        84 G--r~i~V~~Aks   94 (95)
T 2lkz_A           84 G--KTIGVDFAKS   94 (95)
T ss_dssp             T--EEEEEEECCC
T ss_pred             C--EEEEEEEccC
Confidence            5  8899998864

>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=99.82  E-value=9.5e-20  Score=140.32  Aligned_cols=94  Identities=37%  Similarity=0.653  Sum_probs=83.1

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .........++|||+|||.++++++|+++|++||.|.+|.|++|+ +++++|||||+|.+.++|++||+.||+..+..+.
T Consensus         7 ~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~   85 (105)
T 2dnh_A            7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGA   85 (105)
T ss_dssp             CCCCSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTC
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCC
Confidence            334455678999999999999999999999999999999999998 6999999999999999999999999998865555


Q ss_pred             Cccceeecccccccc
Q 018554           86 SSPLQVKYADGELER  100 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~  100 (354)
                      .+.|+|.+++.+.++
T Consensus        86 ~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           86 SSSLVVKFADTDKES  100 (105)
T ss_dssp             SSCCEEEESCSSCCC
T ss_pred             CccEEEEECccCccc
Confidence            588999999876654

>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=1.1e-19  Score=138.29  Aligned_cols=79  Identities=27%  Similarity=0.528  Sum_probs=73.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||.++|+++|+++|++||.|++|+|++|+ ++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|+|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~-~~g--r~l~V~~   95 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR-LQS--KTIKVSY   95 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            5789999999999999999999999999999999984 79999999999999999999999999987 666  7899999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>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=99.81  E-value=1.4e-19  Score=141.86  Aligned_cols=92  Identities=23%  Similarity=0.334  Sum_probs=81.9

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ....+..+.++|||+|||+++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+.||+.. +.+ 
T Consensus        17 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g-   94 (115)
T 2cpz_A           17 GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ-IGM-   94 (115)
T ss_dssp             SCCCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE-ETT-
T ss_pred             ccCcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCE-ECC-
Confidence            334556678999999999999999999999999999999999999999999999999999999999999998866 555 


Q ss_pred             Cccceeecccccccc
Q 018554           86 SSPLQVKYADGELER  100 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~  100 (354)
                       +.|+|.+++.+...
T Consensus        95 -~~l~V~~a~~~~~~  108 (115)
T 2cpz_A           95 -KRLKVQLKRSKNDS  108 (115)
T ss_dssp             -EECEEECCCCSCCC
T ss_pred             -EEEEEEEcCCCCcC
Confidence             88999998766543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.4e-19  Score=136.57  Aligned_cols=88  Identities=33%  Similarity=0.508  Sum_probs=79.3

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+....++|||+|||.++++++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|++|++ +++.. +.+  +
T Consensus         4 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~-~~g--~   79 (99)
T 2dgs_A            4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHD-IMG--K   79 (99)
T ss_dssp             CCCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCB-SSS--C
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCE-ECC--e
Confidence            4566788999999999999999999999999999999999999999999999999999999999998 87765 555  7


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        80 ~l~V~~a~~~~~   91 (99)
T 2dgs_A           80 KVEVKRAEPRDS   91 (99)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEECCCCcc
Confidence            899998876654

>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=99.81  E-value=8.6e-20  Score=142.98  Aligned_cols=106  Identities=17%  Similarity=0.317  Sum_probs=93.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||.++++++|+++|+.||.|.+|.+++|.   +++|||||+|.+.++|.+|++.||+.. +.+  +.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l   77 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFN-VSN--RYL   77 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCB-SSS--CBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCE-ECC--eEE
Confidence            45678999999999999999999999999999999999864   569999999999999999999998876 444  889


Q ss_pred             eeeccccccccccceEEEecCCCCCCHHHHHHhhccCCC
Q 018554           90 QVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGT  128 (354)
Q Consensus        90 ~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~  128 (354)
                      .|.++..+...       .+++...++++|+++|++||.
T Consensus        78 ~v~~a~~~~~~-------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           78 VVLYYNANRAF-------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             EEEECCHHHHT-------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             EEEEecCChhh-------hhhhHhHhHHHHHHHHHHhCC
Confidence            99999876554       467788899999999999984

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.1e-19  Score=139.40  Aligned_cols=91  Identities=21%  Similarity=0.376  Sum_probs=82.4

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ..+.+..+.++|||+|||.++++++|+++|++||+|.+|.|++|+.+++++|||||+|.+.++|++|++.||+.. +.+ 
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g-   84 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG-YDH-   84 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCE-ETT-
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCe-eCC-
Confidence            445667789999999999999999999999999999999999999999999999999999999999999998876 555 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.+++.+..
T Consensus        85 -~~l~v~~a~~~~~   97 (103)
T 2cq0_A           85 -LILNVEWAKPSTN   97 (103)
T ss_dssp             -EECEEEESSCCCC
T ss_pred             -cEEEEEECCCCCC
Confidence             8899999876654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.80  E-value=7.4e-19  Score=136.37  Aligned_cols=85  Identities=15%  Similarity=0.227  Sum_probs=77.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++++|+++|+++|++||.|++|+|++|. ++.++|||||+|++.++|++|++.|||.. ++|  +.|+|.+
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~-~~g--r~i~V~~   82 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTS-VMG--NIIHAQL   82 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEEEEE
Confidence            5789999999999999999999999999999999995 69999999999999999999999999987 566  7899999


Q ss_pred             cCChHHHHH
Q 018554          181 ADTEKERQA  189 (354)
Q Consensus       181 a~~~~~~~~  189 (354)
                      +.....+..
T Consensus        83 a~~~~~~~~   91 (110)
T 3s8s_A           83 DIKGQQRMK   91 (110)
T ss_dssp             CSTTHHHHH
T ss_pred             CCCCcHHHH
Confidence            987765543

>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=99.80  E-value=2.2e-19  Score=138.25  Aligned_cols=92  Identities=24%  Similarity=0.348  Sum_probs=82.7

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .....+....++|||+|||+++++++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|++|++.||+.. +.+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g   84 (105)
T 1x5u_A            6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK-LYG   84 (105)
T ss_dssp             SCCCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB-CSS
T ss_pred             CCCcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCe-ECC
Confidence            3445667788999999999999999999999999999999999999999999999999999999999999998866 555


Q ss_pred             CCccceeeccccccc
Q 018554           85 ASSPLQVKYADGELE   99 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~   99 (354)
                        +.|+|.+++.+..
T Consensus        85 --~~l~v~~a~~~~~   97 (105)
T 1x5u_A           85 --KPIRVNKASAHNK   97 (105)
T ss_dssp             --CBCEEEETTTTSC
T ss_pred             --eEEEEEECCCCCc
Confidence              8899999876654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3e-19  Score=134.84  Aligned_cols=86  Identities=27%  Similarity=0.466  Sum_probs=78.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||.++++++|+++|++||.|.+|++++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~   78 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFE-LAG--RPMR   78 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCC-SSS--SCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCe-eCC--cEEE
Confidence            3578999999999999999999999999999999999999999999999999999999999999998866 555  8899


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.+++.+..
T Consensus        79 V~~a~~~~~   87 (95)
T 2dnz_A           79 VGHVTERLD   87 (95)
T ss_dssp             EEESSCCCC
T ss_pred             EEEcccccC
Confidence            999876654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=2.4e-19  Score=140.47  Aligned_cols=93  Identities=23%  Similarity=0.415  Sum_probs=83.4

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .....+..+.++|||+|||+++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+.|++.. +.+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g   84 (115)
T 2dgo_A            6 SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW-LGG   84 (115)
T ss_dssp             CSSCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCE-ETT
T ss_pred             CcCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            3455677889999999999999999999999999999999999999999999999999999999999999998866 555


Q ss_pred             CCccceeecccccccc
Q 018554           85 ASSPLQVKYADGELER  100 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~~  100 (354)
                        +.|+|.+++.+...
T Consensus        85 --~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           85 --RQIRTNWATRKPPA   98 (115)
T ss_dssp             --EECEEEESSCCCCC
T ss_pred             --EEEEEEEccCCCCC
Confidence              88999998766543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.4e-19  Score=138.88  Aligned_cols=92  Identities=24%  Similarity=0.332  Sum_probs=82.8

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .+...+..+.++|||+|||+++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++|++.||+.. +.+
T Consensus         4 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g   82 (103)
T 2dnm_A            4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAE-LDG   82 (103)
T ss_dssp             CCCSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCC-BTT
T ss_pred             CCCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCE-ECC
Confidence            3455677789999999999999999999999999999999999999999999999999999999999999998876 555


Q ss_pred             CCccceeeccccccc
Q 018554           85 ASSPLQVKYADGELE   99 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~   99 (354)
                        +.|+|.+++....
T Consensus        83 --~~l~V~~a~~~~~   95 (103)
T 2dnm_A           83 --RELRVQVARYGRR   95 (103)
T ss_dssp             --BCCEEEECSSCCS
T ss_pred             --cEEEEEECCcCCC
Confidence              8899999876543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3e-19  Score=137.77  Aligned_cols=88  Identities=24%  Similarity=0.326  Sum_probs=79.1

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        17 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~   93 (106)
T 1p27_B           17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD-LMG--Q   93 (106)
T ss_dssp             BCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCB-SSS--S
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCE-ECC--c
Confidence            3345677899999999999999999999999999999999999999999999999999999999999998876 555  8


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|+|.+++.+.
T Consensus        94 ~l~V~~a~~~~  104 (106)
T 1p27_B           94 PISVDWCFVRG  104 (106)
T ss_dssp             BCEEEESEESS
T ss_pred             EEEEEeecCCC
Confidence            89999887653

>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=99.80  E-value=2.2e-19  Score=133.27  Aligned_cols=83  Identities=24%  Similarity=0.444  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .+.++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|+|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v   80 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW-LGG--RQIRT   80 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEE
Confidence            467899999999999999999999999999999999999999999999999999999999999998866 555  88899


Q ss_pred             eccccc
Q 018554           92 KYADGE   97 (354)
Q Consensus        92 ~~~~~~   97 (354)
                      .+++.+
T Consensus        81 ~~a~~k   86 (87)
T 3bs9_A           81 NWATRK   86 (87)
T ss_dssp             EEEC--
T ss_pred             EecCCC
Confidence            888653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=4.2e-19  Score=136.43  Aligned_cols=89  Identities=22%  Similarity=0.381  Sum_probs=79.2

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~-~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      +.+....++|||+|||+++|+++|+++|++ ||.|.+|.|++|+ +++++|||||+|.+.++|++|++.|++...+.+  
T Consensus         3 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g--   79 (104)
T 2dhg_A            3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGS--   79 (104)
T ss_dssp             CCCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS--
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCC--
Confidence            345678899999999999999999999999 9999999999999 899999999999999999999999988663555  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|+|.++..+..
T Consensus        80 ~~l~v~~a~~~~~   92 (104)
T 2dhg_A           80 KPVRLSVAIPKAS   92 (104)
T ss_dssp             SCCCCCBCCCCCS
T ss_pred             EeEEEEEccCCCc
Confidence            7888888865543

>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=99.80  E-value=2.8e-19  Score=142.94  Aligned_cols=89  Identities=22%  Similarity=0.353  Sum_probs=80.9

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ...+..+.++|||+|||+++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++||+.|++.. +.+  
T Consensus        39 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~-i~g--  115 (129)
T 2kxn_B           39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME-LDG--  115 (129)
T ss_dssp             CSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCC-SSS--
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCE-ECC--
Confidence            44567788999999999999999999999999999999999999999999999999999999999999998866 555  


Q ss_pred             ccceeecccccc
Q 018554           87 SPLQVKYADGEL   98 (354)
Q Consensus        87 ~~l~v~~~~~~~   98 (354)
                      +.|+|.+++.+.
T Consensus       116 ~~l~V~~a~~~~  127 (129)
T 2kxn_B          116 RRIRVDFSITKR  127 (129)
T ss_dssp             SCCEESCCSSSS
T ss_pred             EEEEEEEecCCC
Confidence            889999987654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.1e-19  Score=136.64  Aligned_cols=89  Identities=28%  Similarity=0.439  Sum_probs=80.2

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus         6 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~   82 (102)
T 1x5s_A            6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS-VDG--R   82 (102)
T ss_dssp             CCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCC-TTS--C
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCE-ECC--e
Confidence            3456788999999999999999999999999999999999999999999999999999999999999998876 555  7


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        83 ~l~v~~a~~~~~   94 (102)
T 1x5s_A           83 QIRVDQAGKSSD   94 (102)
T ss_dssp             CCEEEEEECCCC
T ss_pred             EEEEEECCCCCC
Confidence            889988876543

>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=99.80  E-value=1.1e-19  Score=135.94  Aligned_cols=82  Identities=16%  Similarity=0.266  Sum_probs=70.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFA--LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G--~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      .+|||+|||+++|+++|+++|++||  .|.+|++++|+.||+++|||||+|.+.++|++|++.||+.. +.|  +.|+|.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~-~~g--r~i~V~   78 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE-LHG--QNPVVT   78 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSC-SSS--CCCEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCe-eCC--EEEEEE
Confidence            5899999999999999999999999  99999999999999999999999999999999999999876 555  888998


Q ss_pred             ccccccc
Q 018554           93 YADGELE   99 (354)
Q Consensus        93 ~~~~~~~   99 (354)
                      ++.+...
T Consensus        79 ~~~~~~~   85 (90)
T 3p5t_L           79 PSNKLEH   85 (90)
T ss_dssp             CC-----
T ss_pred             ECCCCcc
Confidence            8876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.3e-19  Score=135.44  Aligned_cols=89  Identities=22%  Similarity=0.336  Sum_probs=80.3

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ...+.+..+.++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+
T Consensus         6 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g   84 (95)
T 2cqc_A            6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME-LDG   84 (95)
T ss_dssp             CCCCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEE-ETT
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            4455677788999999999999999999999999999999999999999999999999999999999999998866 555


Q ss_pred             CCccceeecccc
Q 018554           85 ASSPLQVKYADG   96 (354)
Q Consensus        85 ~~~~l~v~~~~~   96 (354)
                        +.|+|.+++.
T Consensus        85 --~~l~v~~a~~   94 (95)
T 2cqc_A           85 --RRIRVSGPSS   94 (95)
T ss_dssp             --EEEEEECCSC
T ss_pred             --EEEEEEecCC
Confidence              8888888753

>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=99.80  E-value=4.4e-19  Score=137.32  Aligned_cols=90  Identities=24%  Similarity=0.436  Sum_probs=80.9

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ...+...+.++|||+|||.++++++|+++|++||.|.+|.+++++.+++++|||||+|.+.++|++|++.|++.. +.| 
T Consensus        18 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~-i~g-   95 (108)
T 2jrs_A           18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFE-LAG-   95 (108)
T ss_dssp             SSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCC-SSS-
T ss_pred             ccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC-
Confidence            334567788999999999999999999999999999999999999999999999999999999999999998866 555 


Q ss_pred             Cccceeecccccc
Q 018554           86 SSPLQVKYADGEL   98 (354)
Q Consensus        86 ~~~l~v~~~~~~~   98 (354)
                       +.|+|.+++.+.
T Consensus        96 -~~l~V~~a~~k~  107 (108)
T 2jrs_A           96 -RPMKVGHVTERT  107 (108)
T ss_dssp             -SCCEEECSCSSC
T ss_pred             -EEEEEEEcccCC
Confidence             889999887653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=4.9e-19  Score=136.77  Aligned_cols=91  Identities=29%  Similarity=0.440  Sum_probs=81.4

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeC-CCCCCcccEEEEEeCCHHHHHHHHHHh-cCCccCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKD-KTTRASRGCCFVICPSRQEADKAVNAC-HNKKTLP   83 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d-~~tg~~~G~aFV~f~~~~~A~~Ai~~l-~~~~~~~   83 (354)
                      ....+....++|||+|||+++++++|+++|++||.|.+|+|++| +.+++++|||||+|.+.++|++||+.| |+.. +.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~-~~   85 (107)
T 2cph_A            7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH-LY   85 (107)
T ss_dssp             CSSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCB-SS
T ss_pred             cccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCe-EC
Confidence            44556778999999999999999999999999999999999999 788999999999999999999999999 7766 55


Q ss_pred             CCCccceeeccccccc
Q 018554           84 GASSPLQVKYADGELE   99 (354)
Q Consensus        84 g~~~~l~v~~~~~~~~   99 (354)
                      +  +.|+|.+++.+..
T Consensus        86 g--~~l~v~~a~~~~~   99 (107)
T 2cph_A           86 G--RRLVLEWADSEVT   99 (107)
T ss_dssp             S--CBCEEEECCCCCC
T ss_pred             C--CEEEEEeCCCCCC
Confidence            5  7899999877654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.1e-19  Score=136.24  Aligned_cols=91  Identities=24%  Similarity=0.390  Sum_probs=81.1

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ..++....+.++|||+|||+++++++|+++|++||.|.+|.|++|  +++++|||||+|.+.++|++|++.||+.. +.+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g   82 (103)
T 2d9p_A            6 SGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRI-VAT   82 (103)
T ss_dssp             CCCCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCB-SSS
T ss_pred             CCCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCE-eCC
Confidence            345566778999999999999999999999999999999999998  79999999999999999999999998877 444


Q ss_pred             CCccceeecccccccc
Q 018554           85 ASSPLQVKYADGELER  100 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~~  100 (354)
                        +.|+|.+++.+..+
T Consensus        83 --~~l~V~~a~~~~~~   96 (103)
T 2d9p_A           83 --KPLYVALAQRKEER   96 (103)
T ss_dssp             --SBCEEEECSSCCCC
T ss_pred             --cEEEEEEecccccC
Confidence              88999998776543

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=2.3e-19  Score=136.59  Aligned_cols=88  Identities=23%  Similarity=0.277  Sum_probs=79.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ....+.++|||+|||+++++++|+++|++||+|.+|.|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~   79 (99)
T 1whw_A            3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV-FQG--RM   79 (99)
T ss_dssp             CCCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEE-SSS--CE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCE-ECC--cE
Confidence            345688999999999999999999999999999999999999899999999999999999999999998866 555  88


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|.+++.+..
T Consensus        80 l~V~~a~~~~~   90 (99)
T 1whw_A           80 LHVLPSTIKKE   90 (99)
T ss_dssp             EEEEECCCCST
T ss_pred             EEEEEcCCCcc
Confidence            99999877654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3.1e-19  Score=135.89  Aligned_cols=89  Identities=27%  Similarity=0.408  Sum_probs=78.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee-EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC-
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD-EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS-   86 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~-~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~-   86 (354)
                      ......++|||+|||.++++++|+++|++||.|. +|+|++|+.+++++|||||+|.+.++|++|++.||+.. +.+.. 
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g~~~   82 (99)
T 2div_A            4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKP-LPGATP   82 (99)
T ss_dssp             CCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSE-ESSCSS
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCc-cCCCCc
Confidence            4456789999999999999999999999999999 99999999999999999999999999999999998866 55522 


Q ss_pred             -ccceeecccccc
Q 018554           87 -SPLQVKYADGEL   98 (354)
Q Consensus        87 -~~l~v~~~~~~~   98 (354)
                       +.|+|.|++...
T Consensus        83 ~~~l~v~~a~~~~   95 (99)
T 2div_A           83 AKRFKLNYATYSG   95 (99)
T ss_dssp             CEECCEEETTCCS
T ss_pred             ceeEEEeecCCCC
Confidence             128888887643

>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=99.79  E-value=3.7e-19  Score=130.83  Aligned_cols=81  Identities=28%  Similarity=0.480  Sum_probs=75.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      +++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|+|.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~-~~g--~~l~v~~   77 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD-LNG--RPLRINW   77 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCe-eCC--cEEEEEe
Confidence            3689999999999999999999999999999999999999999999999999999999999998877 555  8899998


Q ss_pred             cccc
Q 018554           94 ADGE   97 (354)
Q Consensus        94 ~~~~   97 (354)
                      ++.+
T Consensus        78 a~~~   81 (83)
T 3md1_A           78 AAKL   81 (83)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            8764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=5.2e-19  Score=134.94  Aligned_cols=88  Identities=18%  Similarity=0.321  Sum_probs=79.1

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||.|.+|+|++|+ +++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        11 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~   86 (100)
T 2do4_A           11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMT-IKE--N   86 (100)
T ss_dssp             CSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEE-SSS--C
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCE-ECC--E
Confidence            3456678999999999999999999999999999999999999 89999999999999999999999998865 555  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        87 ~l~v~~a~~~~~   98 (100)
T 2do4_A           87 IIKVAISNSGPS   98 (100)
T ss_dssp             EEEEEECCCCSC
T ss_pred             EEEEEECCCCCC
Confidence            899999876643

>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=99.79  E-value=4.4e-19  Score=137.98  Aligned_cols=90  Identities=23%  Similarity=0.332  Sum_probs=80.5

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc------CCc
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH------NKK   80 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~------~~~   80 (354)
                      ...+..+.++|||+|||+++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|++.+|      +..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A            8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            34566788999999999999999999999999999999999999999999999999999999999999998      544


Q ss_pred             cCCCCCccceeeccccccc
Q 018554           81 TLPGASSPLQVKYADGELE   99 (354)
Q Consensus        81 ~~~g~~~~l~v~~~~~~~~   99 (354)
                       +.+  +.|+|.++..+..
T Consensus        88 -~~g--~~l~v~~a~~~~~  103 (111)
T 1x4h_A           88 -LDG--RQLKVDLAVTRDE  103 (111)
T ss_dssp             -SSS--CEEEEECCCCCCC
T ss_pred             -EcC--EEEEEEECCCCcc
Confidence             555  8899999876544

>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=99.79  E-value=3.4e-19  Score=131.68  Aligned_cols=83  Identities=24%  Similarity=0.390  Sum_probs=76.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l   79 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--RTI   79 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCE-ECC--cEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999998876 555  788


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      +|.+++
T Consensus        80 ~v~~ak   85 (85)
T 3mdf_A           80 RVNLAK   85 (85)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            888764

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.8e-19  Score=138.07  Aligned_cols=90  Identities=22%  Similarity=0.326  Sum_probs=81.1

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ......+.++|||+|||+++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  
T Consensus         5 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--   81 (102)
T 2cqb_A            5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--   81 (102)
T ss_dssp             SSCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE-ETT--
T ss_pred             cCCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--
Confidence            44556788999999999999999999999999999999999999999999999999999999999999998866 555  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|+|.+++.+..
T Consensus        82 ~~l~V~~a~~~~~   94 (102)
T 2cqb_A           82 RTIRVNLAKPMRI   94 (102)
T ss_dssp             EEEEEEECCCCCC
T ss_pred             cEEEEEeCCCCCC
Confidence            8899999876654

>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=99.79  E-value=4.8e-19  Score=134.10  Aligned_cols=84  Identities=20%  Similarity=0.301  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ++++|||+|||.++++++|+++|++||.|.+|++++|+.+++++|||||+|.+.++|++|++.|++.. +.+  +.|+|.
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~   77 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ-LGS--RFLKCG   77 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEE
Confidence            46899999999999999999999999999999999999999999999999999999999999998866 555  889999


Q ss_pred             ccccccc
Q 018554           93 YADGELE   99 (354)
Q Consensus        93 ~~~~~~~   99 (354)
                      +++.+..
T Consensus        78 ~a~~~~~   84 (96)
T 2x1f_A           78 YSSNSDI   84 (96)
T ss_dssp             ECSCSSG
T ss_pred             EcCCCCC
Confidence            9876543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.79  E-value=1.1e-19  Score=146.54  Aligned_cols=120  Identities=19%  Similarity=0.271  Sum_probs=77.1

Q ss_pred             EEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccc-cccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEee
Q 018554           58 CCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD-GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR  136 (354)
Q Consensus        58 ~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~-~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~  136 (354)
                      +.|++|+|...+.+|++.+++......  .  ...+.. .......++|||+||++++|+++|+++|+.||.|++|+|++
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~--~--~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   81 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGR--G--SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR   81 (135)
T ss_dssp             ---------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCC
T ss_pred             cccccccCCCchhhhhhhccCCCCCCC--C--CCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            678899999999999999877653222  1  112222 22233468999999999999999999999999999999999


Q ss_pred             CC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          137 GS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       137 ~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      +. ++.++|||||+|++.++|++|++.||+.. ++|  +.|+|+|++..
T Consensus        82 ~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~-i~g--~~l~V~~a~~~  127 (135)
T 2lea_A           82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV-LDG--RELRVQMARYG  127 (135)
T ss_dssp             CSSSSSCCSCCEEECSCHHHHHHHHTTTTTCC-SSS--SCCEEEECCCC
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEECCCC
Confidence            84 78999999999999999999999999987 666  68999999764

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.78  E-value=1.4e-19  Score=138.08  Aligned_cols=85  Identities=20%  Similarity=0.258  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCC------CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           11 SEERVKLFVGQVPK------HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~------~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ....++|||+|||.      ++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++||+.||+..+ .+
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~-~g   81 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL-DL   81 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBS-SS
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCccc-CC
Confidence            34578999999999      999999999999999999999999999999999999999999999999999998775 32


Q ss_pred             CCccceeeccccc
Q 018554           85 ASSPLQVKYADGE   97 (354)
Q Consensus        85 ~~~~l~v~~~~~~   97 (354)
                       .+.|+|.++.++
T Consensus        82 -~r~l~V~~a~~~   93 (100)
T 3ns6_A           82 -KHRLFLYTMKDV   93 (100)
T ss_dssp             -SCBCEEEESHHH
T ss_pred             -CeEEEEEECchh
Confidence             278888888654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.78  E-value=9.3e-19  Score=133.28  Aligned_cols=85  Identities=21%  Similarity=0.405  Sum_probs=77.3

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE--------VNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~--------i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      .......++|||+|||.++++++|+++|++||.|.+        |++++|+.|++++|||||+|.+.++|++|++.||+.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            445678899999999999999999999999999999        999999999999999999999999999999999987


Q ss_pred             ccCCCCCccceeeccc
Q 018554           80 KTLPGASSPLQVKYAD   95 (354)
Q Consensus        80 ~~~~g~~~~l~v~~~~   95 (354)
                      . +.+  +.|+|.+++
T Consensus        87 ~-~~g--~~l~V~~A~   99 (99)
T 2la6_A           87 E-FSG--NPIKVSFAT   99 (99)
T ss_dssp             B-SSS--SBCEEEECC
T ss_pred             E-eCC--cEEEEEecC
Confidence            6 555  788888763

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=4.5e-19  Score=133.64  Aligned_cols=86  Identities=27%  Similarity=0.464  Sum_probs=77.6

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ......+.++|||+|||.++++++|+++|++||+|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--   85 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQ-LFG--   85 (94)
T ss_dssp             CCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEE-ETT--
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCe-eCC--
Confidence            34456788999999999999999999999999999999999999999999999999999999999999998866 555  


Q ss_pred             ccceeeccc
Q 018554           87 SPLQVKYAD   95 (354)
Q Consensus        87 ~~l~v~~~~   95 (354)
                      +.|+|.+++
T Consensus        86 ~~l~v~~ak   94 (94)
T 2e5h_A           86 RVIKASIAI   94 (94)
T ss_dssp             EEEEEEECC
T ss_pred             cEEEEEecC
Confidence            788888764

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=2.5e-19  Score=136.95  Aligned_cols=89  Identities=26%  Similarity=0.385  Sum_probs=77.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      ++|||+|||.++|+++|+++|++||+|.+|.+++|     ++|||||+|.+.++|++|++.|++.. +.+  +.|+|.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V~~a   72 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKV-ICG--SRVRVELS   72 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSC-SSS--CCCEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCe-ECC--cEEEEEEc
Confidence            58999999999999999999999999999999987     67899999999999999999998876 555  77889888


Q ss_pred             ccccccc-----------cceEEEecCC
Q 018554           95 DGELERL-----------EHKLFIGMLP  111 (354)
Q Consensus        95 ~~~~~~~-----------~~~l~V~~l~  111 (354)
                      +.+....           ..+||||+|+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           73 TGMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SSCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             cCCCCcccCCCCCccccCCCceecCCCC
Confidence            6543221           5689999986

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=5.7e-19  Score=134.67  Aligned_cols=83  Identities=17%  Similarity=0.337  Sum_probs=72.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-ccCCCCCcc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK-KTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~-~~~~g~~~~   88 (354)
                      ...+.++|||+|||+++||++|+++|++||+|.+|+|++|      ||||||+|++.++|++|++.+++. ..+.|  +.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G--r~   83 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRG--QP   83 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETT--EE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECC--EE
Confidence            4668899999999999999999999999999999999986      589999999999999999988653 44655  89


Q ss_pred             ceeecccccccc
Q 018554           89 LQVKYADGELER  100 (354)
Q Consensus        89 l~v~~~~~~~~~  100 (354)
                      |+|.|++.+..+
T Consensus        84 l~V~~A~~~~~~   95 (105)
T 1sjq_A           84 IYIQFSNHKELK   95 (105)
T ss_dssp             CCBCCCSSSSCC
T ss_pred             EEEEEcCCCCCC
Confidence            999998765443

>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=99.78  E-value=5.6e-19  Score=137.17  Aligned_cols=89  Identities=20%  Similarity=0.279  Sum_probs=80.0

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~   96 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE-IMG--Q   96 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCE-ETT--E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE-ECC--c
Confidence            3455677899999999999999999999999999999999999999999999999999999999999998876 555  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        97 ~l~V~~a~~~~~  108 (110)
T 1oo0_B           97 TIQVDWCFVKGP  108 (110)
T ss_dssp             ECEEEESEESSC
T ss_pred             EEEEEEcccCCC
Confidence            899999876543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=5.9e-19  Score=142.99  Aligned_cols=90  Identities=27%  Similarity=0.417  Sum_probs=80.9

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+....++|||+|||.++++++|+++|++||+|++|+|++|+.|++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~  112 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN-ILN--K  112 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEE-CSS--C
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--e
Confidence            3456678999999999999999999999999999999999999999999999999999999999999998866 555  7


Q ss_pred             cceeecccccccc
Q 018554           88 PLQVKYADGELER  100 (354)
Q Consensus        88 ~l~v~~~~~~~~~  100 (354)
                      .|+|.+++.+..+
T Consensus       113 ~l~v~~a~~~~~~  125 (139)
T 1u6f_A          113 RLKVALAASGHQR  125 (139)
T ss_dssp             EEEEEESSCCCCC
T ss_pred             EEEEEECCCCCCC
Confidence            8999998876554

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.78  E-value=3.3e-19  Score=140.31  Aligned_cols=86  Identities=23%  Similarity=0.332  Sum_probs=77.0

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ...+..+.++|||+|||+++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  
T Consensus        33 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--  109 (118)
T 2khc_A           33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQ-VGT--  109 (118)
T ss_dssp             SSCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCE-ETT--
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCE-ECC--
Confidence            34456678999999999999999999999999999999999999999999999999999999999999998866 555  


Q ss_pred             ccceeeccc
Q 018554           87 SPLQVKYAD   95 (354)
Q Consensus        87 ~~l~v~~~~   95 (354)
                      +.|+|.+++
T Consensus       110 ~~l~V~~ak  118 (118)
T 2khc_A          110 KRLKVQLKK  118 (118)
T ss_dssp             EECCEEEC-
T ss_pred             EEEEEEecC
Confidence            778887763

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=5.1e-19  Score=134.44  Aligned_cols=86  Identities=23%  Similarity=0.329  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC---CCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT---TRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~---tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++|+.   |++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~   78 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT-VDG--H   78 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE-ETT--E
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCe-eCC--e
Confidence            35789999999999999999999999999999999999887   77999999999999999999999998876 555  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        79 ~l~V~~a~~~~~   90 (98)
T 2cpf_A           79 KLEVRISERATK   90 (98)
T ss_dssp             ECEEECSSCSSC
T ss_pred             EEEEEEccCCCC
Confidence            899999876554

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=3.6e-19  Score=134.69  Aligned_cols=87  Identities=25%  Similarity=0.431  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEV-NIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i-~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ..+.++|||+|||.++++++|+++|++||.|.+| +|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l   78 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY-LCN--RPI   78 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCE-ETT--EEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE-ECC--EEE
Confidence            3568999999999999999999999999999999 999999999999999999999999999999998877 544  889


Q ss_pred             eeecccccccc
Q 018554           90 QVKYADGELER  100 (354)
Q Consensus        90 ~v~~~~~~~~~  100 (354)
                      +|.+++.+..+
T Consensus        79 ~v~~a~~~~~~   89 (96)
T 1x5t_A           79 TVSYAFKKDSK   89 (96)
T ss_dssp             EEEESCCCCCC
T ss_pred             EEEEecccCCC
Confidence            99998766543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.78  E-value=2.3e-19  Score=143.96  Aligned_cols=88  Identities=23%  Similarity=0.412  Sum_probs=78.1

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--EEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC----cc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE--VNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK----KT   81 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~--i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~----~~   81 (354)
                      .......++|||+|||+++||++|+++|++||.|..  |+|++|+.||++||||||+|.+. +|.+|++.||+.    . 
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~-   94 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT-   94 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC-
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc-
Confidence            345577899999999999999999999999999976  99999999999999999999999 999999999987    4 


Q ss_pred             CCCCCccceeeccccccc
Q 018554           82 LPGASSPLQVKYADGELE   99 (354)
Q Consensus        82 ~~g~~~~l~v~~~~~~~~   99 (354)
                      +.+  +.|+|++++.+..
T Consensus        95 ~~g--r~l~V~~a~~~~~  110 (131)
T 2m2b_A           95 IDG--KTINVEFAKGSKR  110 (131)
T ss_dssp             GGG--CCCCCEECCCSCC
T ss_pred             CCC--EEEEEEECCCCCC
Confidence            444  7888888876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.78  E-value=3e-19  Score=134.61  Aligned_cols=80  Identities=16%  Similarity=0.399  Sum_probs=72.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCC--eeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCc---ccCCCcee
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGT--IKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKH---KMEGSSVP  175 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~--v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~---~~~g~~~~  175 (354)
                      -++|||+||++++|+++|+++|++||.  |.+|++++|+ ++.+||||||+|.+.++|++|++.|||..   .++|  ++
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G--r~   86 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG--KT   86 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT--EE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC--EE
Confidence            468999999999999999999999995  6799999994 79999999999999999999999999974   4677  78


Q ss_pred             EEEEecCC
Q 018554          176 LVVKWADT  183 (354)
Q Consensus       176 l~v~~a~~  183 (354)
                      |.|+||+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999975

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.78  E-value=9.7e-19  Score=137.17  Aligned_cols=85  Identities=29%  Similarity=0.464  Sum_probs=77.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +..+.++|||+|||.++++++|+++|++||.|.+|.|++|+ +++++|||||+|.+.++|++|++.|++.. +.+  +.|
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~-~~g--~~l   78 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKS-LHG--KAI   78 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCB-CSS--SBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            35678999999999999999999999999999999999998 89999999999999999999999998877 555  789


Q ss_pred             eeecccccc
Q 018554           90 QVKYADGEL   98 (354)
Q Consensus        90 ~v~~~~~~~   98 (354)
                      +|.+++...
T Consensus        79 ~V~~a~~~~   87 (116)
T 2fy1_A           79 KVEQAKKPS   87 (116)
T ss_dssp             EEEECCCSS
T ss_pred             EEEECCCCC
Confidence            999887544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.8e-19  Score=138.09  Aligned_cols=88  Identities=30%  Similarity=0.436  Sum_probs=79.4

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ....++...++|||+|||+++++++|+++|++||+|.+|+|++|+.|++++|||||+|.+.++|++||+.+++  .+.+ 
T Consensus         9 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~--~~~g-   85 (116)
T 2cqd_A            9 HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP--IIDG-   85 (116)
T ss_dssp             CCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC--EETT-
T ss_pred             CCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC--cCCC-
Confidence            3455677889999999999999999999999999999999999999999999999999999999999999976  4655 


Q ss_pred             Cccceeeccccc
Q 018554           86 SSPLQVKYADGE   97 (354)
Q Consensus        86 ~~~l~v~~~~~~   97 (354)
                       +.|+|.++..+
T Consensus        86 -~~l~V~~a~~~   96 (116)
T 2cqd_A           86 -RKANVNLAYLG   96 (116)
T ss_dssp             -EECEEEESTTT
T ss_pred             -EEEEEEEcccC
Confidence             88899988654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=5.8e-19  Score=135.90  Aligned_cols=90  Identities=27%  Similarity=0.323  Sum_probs=80.3

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ....+..+.++|||+|||+++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++||+. ++.. +.+ 
T Consensus         8 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~-~~g-   84 (105)
T 2dh8_A            8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHT-LDG-   84 (105)
T ss_dssp             CCCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEE-ETT-
T ss_pred             CCcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCe-ECC-
Confidence            3455678899999999999999999999999999999999999999999999999999999999999998 6644 655 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.++..+..
T Consensus        85 -~~l~V~~a~~~~~   97 (105)
T 2dh8_A           85 -RNIDPKPCTPRGM   97 (105)
T ss_dssp             -EEEBCCCSCCSSC
T ss_pred             -EEEEEEEccCCCC
Confidence             7889988876554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.77  E-value=1e-18  Score=134.07  Aligned_cols=89  Identities=22%  Similarity=0.444  Sum_probs=79.1

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .........++|||+|||+++++++|+++|++|| |.+|+|++|+.|++++|||||+|.+.++|++|+ .||+.. +.+ 
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g-   82 (103)
T 2dng_A            7 GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGAL-LGD-   82 (103)
T ss_dssp             CCCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCE-ETT-
T ss_pred             CCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCe-ECC-
Confidence            3445567889999999999999999999999997 999999999999999999999999999999999 898866 555 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.+++.+..
T Consensus        83 -~~l~V~~a~~~~~   95 (103)
T 2dng_A           83 -RSLRVDIAEGRKQ   95 (103)
T ss_dssp             -EECEEEECCCCCC
T ss_pred             -eEEEEEEecCCCC
Confidence             8899999876544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.77  E-value=7.2e-19  Score=145.07  Aligned_cols=83  Identities=22%  Similarity=0.354  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFA--LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G--~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .+.++|||+|||+++|+++|+++|++||  .|.+|+|++|+.||+++|||||+|.+.++|++||+.|++.. +.|  +.|
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~-~~G--r~l  129 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKV-LNG--EKV  129 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCE-ETT--EEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC--eEe
Confidence            3568999999999999999999999999  99999999999999999999999999999999999998876 555  889


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      +|.++..+
T Consensus       130 ~V~~a~~~  137 (156)
T 3n9u_C          130 DVRPATRQ  137 (156)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCCC
Confidence            99988654

>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=99.77  E-value=8e-19  Score=134.90  Aligned_cols=91  Identities=14%  Similarity=0.301  Sum_probs=80.1

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC-CCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT-RASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~t-g~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      .+........++|||+|||+++++++|+++|++|| |.+|.|++|+.| ++++|||||+|.+.++|++|| .|++.. +.
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~-~~   82 (104)
T 1wi8_A            6 SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEES-LG   82 (104)
T ss_dssp             CCCCCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCE-ET
T ss_pred             CCCCCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCE-eC
Confidence            34455667889999999999999999999999999 999999999998 999999999999999999999 998876 55


Q ss_pred             CCCccceeecccccccc
Q 018554           84 GASSPLQVKYADGELER  100 (354)
Q Consensus        84 g~~~~l~v~~~~~~~~~  100 (354)
                      +  +.|+|.+++.+...
T Consensus        83 g--~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           83 N--KRIRVDVADQAQDK   97 (104)
T ss_dssp             T--EECEEEECCCCCCC
T ss_pred             C--cEEEEEEccCCCCC
Confidence            5  88999988766543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=7.5e-19  Score=137.14  Aligned_cols=89  Identities=24%  Similarity=0.305  Sum_probs=80.5

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD--------EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~--------~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      ..+..+.++|||+|||.++++++|+++|++||.|.        .|+|++|+.+++++|||||+|.+.++|++||+.||+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34667889999999999999999999999999999        6999999999999999999999999999999999887


Q ss_pred             ccCCCCCccceeeccccccc
Q 018554           80 KTLPGASSPLQVKYADGELE   99 (354)
Q Consensus        80 ~~~~g~~~~l~v~~~~~~~~   99 (354)
                      . +.+  +.|+|.+++.+..
T Consensus        89 ~-~~g--~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 D-FQG--SKLKVSLARKKPP  105 (113)
T ss_dssp             E-ETT--EECEEECSSCCCC
T ss_pred             c-cCC--CEEEEEECCCCCC
Confidence            6 555  8899999877654

>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=99.77  E-value=7.5e-19  Score=137.63  Aligned_cols=83  Identities=29%  Similarity=0.471  Sum_probs=73.4

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..+|||+||++++|+++|+++|++||.|++|+|++|.. .+||||||+|++.++|++|++.||+.. ++|  +.|.|+++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~-~~g--~~i~V~~a   80 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGML-LND--RKVFVGRF   80 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEEES
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEEC
Confidence            46899999999999999999999999999999999854 479999999999999999999999987 666  78999999


Q ss_pred             CChHHHH
Q 018554          182 DTEKERQ  188 (354)
Q Consensus       182 ~~~~~~~  188 (354)
                      +.+..+.
T Consensus        81 ~~~~~~~   87 (115)
T 4f25_A           81 KSRKERE   87 (115)
T ss_dssp             SCCCC--
T ss_pred             CCccccc
Confidence            8765543

>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=99.77  E-value=3.9e-19  Score=136.58  Aligned_cols=87  Identities=25%  Similarity=0.392  Sum_probs=78.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .+...++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l   80 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE-FSG--RAL   80 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBS-CSS--SCB
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe-eCC--cEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999998866 555  789


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.+++.+..
T Consensus        81 ~v~~a~~~~~   90 (104)
T 1p1t_A           81 RVDNAASEKN   90 (104)
T ss_dssp             EEEETTCTTH
T ss_pred             EEEeCCCccc
Confidence            9998876544

>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=1.3e-18  Score=134.00  Aligned_cols=86  Identities=48%  Similarity=0.814  Sum_probs=78.2

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||+.++++++|+++|++||.|++|.|+++.++.++|||||+|.+.++|++|++.||+..+.+|..+.|.|+|
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~   93 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKF   93 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEE
Confidence            46899999999999999999999999999999999998899999999999999999999999999886555447899999


Q ss_pred             cCChHH
Q 018554          181 ADTEKE  186 (354)
Q Consensus       181 a~~~~~  186 (354)
                      ++.+.+
T Consensus        94 a~~~~~   99 (105)
T 2dnh_A           94 ADTDKE   99 (105)
T ss_dssp             SCSSCC
T ss_pred             CccCcc
Confidence            987643

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=4.6e-19  Score=131.00  Aligned_cols=82  Identities=22%  Similarity=0.260  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~~~   78 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG-VQA--QMAK   78 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT-CCE--ESCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCe-Eee--EEEe
Confidence            3578999999999999999999999999999999999999999999999999999999999999998866 444  6666


Q ss_pred             eeccc
Q 018554           91 VKYAD   95 (354)
Q Consensus        91 v~~~~   95 (354)
                      ++++.
T Consensus        79 ~~~~~   83 (85)
T 1x4e_A           79 QSGPS   83 (85)
T ss_dssp             SSCCC
T ss_pred             ecCCC
Confidence            66543

>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=99.77  E-value=2.7e-18  Score=134.18  Aligned_cols=88  Identities=23%  Similarity=0.415  Sum_probs=77.4

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC----
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG----   84 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g----   84 (354)
                      .+..+.++|||+|||+++++++|+++|++||.|.+|+|++|+ +++++|||||+|.+.++|++|++.||+..+-..    
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            455678999999999999999999999999999999999999 899999999999999999999999998774211    


Q ss_pred             -CCccceeeccccc
Q 018554           85 -ASSPLQVKYADGE   97 (354)
Q Consensus        85 -~~~~l~v~~~~~~   97 (354)
                       ..++|.|+|+++.
T Consensus        99 ~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           99 APTEPLLCKFSGPS  112 (114)
T ss_dssp             CCSSCBEEEECCCS
T ss_pred             CCCCceeEEccCCC
Confidence             2477888888753

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1e-18  Score=133.90  Aligned_cols=84  Identities=18%  Similarity=0.279  Sum_probs=74.4

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .++....++|||+|||+++|+++|+++|++||.|.+|.|++|+. ++++|||||+|.+.++|.+||+ +++.. +.|  +
T Consensus         5 ~~~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~-~~g--r   79 (103)
T 1s79_A            5 LKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQK-YKE--T   79 (103)
T ss_dssp             CSSCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCC-CTT--T
T ss_pred             ccccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCE-ECC--E
Confidence            34566789999999999999999999999999999999999998 9999999999999999999998 76655 655  7


Q ss_pred             cceeecccc
Q 018554           88 PLQVKYADG   96 (354)
Q Consensus        88 ~l~v~~~~~   96 (354)
                      .|.|.++..
T Consensus        80 ~l~V~~~~~   88 (103)
T 1s79_A           80 DLLILFKDD   88 (103)
T ss_dssp             TCEEEEHHH
T ss_pred             EEEEEEchH
Confidence            888887653

>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=99.77  E-value=1.2e-18  Score=131.45  Aligned_cols=85  Identities=21%  Similarity=0.317  Sum_probs=75.5

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ........++|||+|||+++++++|+++|++||+|.+|+|++|+. ++++|||||+|.+.++|++|++.||+.. +.+  
T Consensus         9 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--   84 (95)
T 2ywk_A            9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIR-LYG--   84 (95)
T ss_dssp             ---CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCE-ETT--
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCE-ECC--
Confidence            345567889999999999999999999999999999999999986 9999999999999999999999998876 555  


Q ss_pred             ccceeeccc
Q 018554           87 SPLQVKYAD   95 (354)
Q Consensus        87 ~~l~v~~~~   95 (354)
                      +.|+|.+++
T Consensus        85 ~~l~V~~a~   93 (95)
T 2ywk_A           85 RPINVSGPS   93 (95)
T ss_dssp             EECEEECCC
T ss_pred             CEEEEEEcC
Confidence            888888875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.77  E-value=2.9e-19  Score=133.91  Aligned_cols=81  Identities=20%  Similarity=0.429  Sum_probs=73.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCC-CeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYG-TIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G-~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      +++|||+|||.++|+++|+++|++|| .|++|+|++| .++.+||||||+|.+.++|.+|++.+++...++|  +.|+|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g--r~i~V~   78 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILG--QKVSMH   78 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETT--EEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECC--EEEEEE
Confidence            46899999999999999999999999 8999999998 4789999999999999999999998866555776  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ||+++
T Consensus        79 ~a~~~   83 (91)
T 2lxi_A           79 YSDPK   83 (91)
T ss_dssp             CCCSC
T ss_pred             EcCCC
Confidence            99765

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.77  E-value=7.1e-19  Score=136.38  Aligned_cols=88  Identities=24%  Similarity=0.336  Sum_probs=73.8

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .++..+.++|||+|||.++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++|++.+ + ..+.|  +
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~-~~l~g--~   94 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-R-HELDS--K   94 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-C-EEETT--E
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-C-CcCCC--E
Confidence            345678899999999999999999999999999999999999999999999999999999999999986 4 44666  7


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.++..+..
T Consensus        95 ~l~V~~a~~~~~  106 (109)
T 2rs2_A           95 TIDPKVAFPRRA  106 (109)
T ss_dssp             EEEEEECCCCCC
T ss_pred             EEEEEEccCCCC
Confidence            888888876544

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.77  E-value=3.8e-18  Score=127.93  Aligned_cols=85  Identities=25%  Similarity=0.324  Sum_probs=76.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||.++++++|+++|++||.|.+|+|+++  +++++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~-~~g--~~l   78 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMK-LSG--REI   78 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCC-BTT--BCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--cEE
Confidence            4567899999999999999999999999999999999985  68999999999999999999999998876 555  788


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.+++....
T Consensus        79 ~v~~a~~~~~   88 (92)
T 2dgv_A           79 DVRIDRNASG   88 (92)
T ss_dssp             CCEECSCCSS
T ss_pred             EEEEcCCCCC
Confidence            8988876543

>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=99.76  E-value=1.5e-18  Score=128.87  Aligned_cols=84  Identities=26%  Similarity=0.417  Sum_probs=72.5

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ...+..+.++|||+|||.++++++|+++|++||.|.+|++++|+.|++++|||||+|.+.++|++|++. ++.. +.|  
T Consensus         4 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~-~~g--   79 (87)
T 3s7r_A            4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHR-LDG--   79 (87)
T ss_dssp             ---CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEE-ETT--
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCE-ECC--
Confidence            345667899999999999999999999999999999999999999999999999999999999999965 4544 555  


Q ss_pred             ccceeecc
Q 018554           87 SPLQVKYA   94 (354)
Q Consensus        87 ~~l~v~~~   94 (354)
                      +.|+|+++
T Consensus        80 ~~i~v~~A   87 (87)
T 3s7r_A           80 RVIDPKKA   87 (87)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEEEeC
Confidence            67777654

>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=99.76  E-value=2.2e-18  Score=137.19  Aligned_cols=89  Identities=24%  Similarity=0.320  Sum_probs=79.6

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++|+++|+++|++||.|.+|.|+.|+.+++++|||||+|.+.++|++||+.||+.. +.+  +
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~   92 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD-LMG--Q   92 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCB-SSS--S
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCe-eCC--e
Confidence            3455678899999999999999999999999999999999999999999999999999999999999998877 555  7


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|.|.++..+..
T Consensus        93 ~l~v~~a~~~~~  104 (126)
T 3ex7_B           93 PISVDWCFVRGP  104 (126)
T ss_dssp             BCEEEESEESSS
T ss_pred             EEEEEEecCCCC
Confidence            889998865543

>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=99.76  E-value=4.1e-18  Score=130.63  Aligned_cols=90  Identities=24%  Similarity=0.411  Sum_probs=79.1

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ........+.++|||+|||+++++++|+++|++||.|.+|+|++|+.  .++|||||+|.+.++|++|++.||+.. +.+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g   82 (103)
T 2cq3_A            6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTV-VEG   82 (103)
T ss_dssp             CCCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCE-ETT
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            34456677889999999999999999999999999999999999875  389999999999999999999998876 555


Q ss_pred             CCccceeeccccccc
Q 018554           85 ASSPLQVKYADGELE   99 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~   99 (354)
                        +.|+|.+++.+..
T Consensus        83 --~~l~v~~a~~~~~   95 (103)
T 2cq3_A           83 --RKIEVNNATARVM   95 (103)
T ss_dssp             --EECEEEECCSSCC
T ss_pred             --EEEEEEEcccCCC
Confidence              8899999876544

>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=99.76  E-value=2.5e-18  Score=142.07  Aligned_cols=88  Identities=24%  Similarity=0.378  Sum_probs=79.3

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ....+.++|||+|||.++|+++|+++|++||+|.+|.|++|+.|++++|||||+|.+.++|++||+.||+.. +.+  +.
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~  110 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR-LDD--RI  110 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSE-ETT--EE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCE-ECC--eE
Confidence            344578999999999999999999999999999999999999999999999999999999999999998866 555  88


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|.|++....
T Consensus       111 l~V~~a~~~~~  121 (156)
T 1h2v_Z          111 IRTDWDAGFKE  121 (156)
T ss_dssp             CEEEEESCCCT
T ss_pred             EEEEECCCCCC
Confidence            99999876543

>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=99.76  E-value=2.6e-18  Score=132.67  Aligned_cols=84  Identities=21%  Similarity=0.333  Sum_probs=75.9

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||+|||.++++++|+++|++||.|.+|.|++|+ +++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~   98 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVP-LDG--R   98 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCE-eCC--c
Confidence            4456778999999999999999999999999999999999999 89999999999999999999999998876 455  7


Q ss_pred             cceeeccc
Q 018554           88 PLQVKYAD   95 (354)
Q Consensus        88 ~l~v~~~~   95 (354)
                      .|+|.++.
T Consensus        99 ~l~V~~a~  106 (107)
T 3ulh_A           99 PMNIQLVT  106 (107)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEeC
Confidence            88888764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=133.33  Aligned_cols=87  Identities=23%  Similarity=0.289  Sum_probs=77.5

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||+|||.++++++|+++|++||.|.+|+|++|+ +++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~   84 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQL-LFD--R   84 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--E
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCE-eCC--C
Confidence            3456678999999999999999999999999999999999998 49999999999999999999999998876 555  7


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|+|.+++...
T Consensus        85 ~l~v~~a~~~~   95 (114)
T 2do0_A           85 PMHVKMDERAL   95 (114)
T ss_dssp             ECEEEECSCCC
T ss_pred             EEEEEEcccCC
Confidence            88998886543

>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=99.76  E-value=1.8e-18  Score=133.98  Aligned_cols=87  Identities=24%  Similarity=0.366  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEe-eCCCCCCcccEEEEEeCCHHHHHHHHHHhc-CCccCCCCCc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFAL-VDEVNII-KDKTTRASRGCCFVICPSRQEADKAVNACH-NKKTLPGASS   87 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~-v~~i~i~-~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~-~~~~~~g~~~   87 (354)
                      ..+.++|||+|||+++++++|+++|++||. |.+|.++ +|+.|++++|||||+|.+.++|++|++.|+ +...+.+  +
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g--~   82 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG--H   82 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT--B
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC--C
Confidence            457899999999999999999999999998 9999998 899999999999999999999999999995 3344665  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.|++.+..
T Consensus        83 ~l~V~~a~~~~~   94 (109)
T 2dis_A           83 QIAVDWAEPEID   94 (109)
T ss_dssp             CCEEEESCSSCS
T ss_pred             eEEEEEcCCCCC
Confidence            899999876654

>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=99.76  E-value=1.4e-18  Score=129.10  Aligned_cols=84  Identities=14%  Similarity=0.362  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC-cccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRA-SRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~-~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .+.++|||+|||.++++++|+++|++||.|.+|.+++|+.++. ++|||||+|.+.++|++|++.||+.. +.+  +.|+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~   78 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ-IDG--QEIT   78 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCe-ECC--eEEE
Confidence            3578999999999999999999999999999999999988766 99999999999999999999998876 555  7888


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |.++....
T Consensus        79 v~~a~~~~   86 (88)
T 4a8x_A           79 ATAVLAPW   86 (88)
T ss_dssp             EEEECCCC
T ss_pred             EEECCCCC
Confidence            88876543

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.3e-18  Score=131.17  Aligned_cols=89  Identities=21%  Similarity=0.425  Sum_probs=78.0

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ...+....++|||+|||+++++++|+++|++||.|.+|+|++|+.+  ++|||||+|.+.++|++|++.||+.. +.+  
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--   82 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRK-ILG--   82 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEE-ETT--
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCC-cCC--
Confidence            3456678899999999999999999999999999999999999653  78999999999999999999998866 555  


Q ss_pred             ccceeecccccccc
Q 018554           87 SPLQVKYADGELER  100 (354)
Q Consensus        87 ~~l~v~~~~~~~~~  100 (354)
                      +.|+|.+++.+..+
T Consensus        83 ~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           83 KEVKVNWATTPSSQ   96 (103)
T ss_dssp             EEEEEEECCCTTCC
T ss_pred             CeEEEEECCCCccc
Confidence            88999998765543

>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=99.76  E-value=3.1e-18  Score=130.51  Aligned_cols=88  Identities=19%  Similarity=0.312  Sum_probs=74.5

Q ss_pred             ccccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcC-CccC
Q 018554            4 SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHN-KKTL   82 (354)
Q Consensus         4 ~~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~-~~~~   82 (354)
                      +..++....+.++|||+|||+++++++|+++|++||.|.+|.++++      ||||||+|.+.++|++|++.+++ ...+
T Consensus         5 s~~~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~   78 (101)
T 2cq1_A            5 SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHL   78 (101)
T ss_dssp             CCCCCCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             CCCCCccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            3445666778899999999999999999999999999999998875      68999999999999999998853 2335


Q ss_pred             CCCCccceeeccccccc
Q 018554           83 PGASSPLQVKYADGELE   99 (354)
Q Consensus        83 ~g~~~~l~v~~~~~~~~   99 (354)
                      .|  +.|+|.|++.+..
T Consensus        79 ~G--r~l~V~~a~~~~~   93 (101)
T 2cq1_A           79 RN--QPIYIQYSNHKEL   93 (101)
T ss_dssp             TT--EECEEEECSCSSC
T ss_pred             CC--cEEEEEEcCcccC
Confidence            55  8999999876544

>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=99.76  E-value=4.4e-18  Score=130.41  Aligned_cols=88  Identities=14%  Similarity=0.149  Sum_probs=74.5

Q ss_pred             ccccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc-cC
Q 018554            4 SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK-TL   82 (354)
Q Consensus         4 ~~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~-~~   82 (354)
                      +..+.....+.++|||+|||++++|++|+++|++||.|.+|.|+++      ||||||+|.+.++|++|++.|++.. .+
T Consensus         5 ~~~~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i   78 (104)
T 1wex_A            5 SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYI   78 (104)
T ss_dssp             CCCSCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBS
T ss_pred             CCCCCCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            3445556778899999999999999999999999999999998874      5899999999999999999987543 35


Q ss_pred             CCCCccceeeccccccc
Q 018554           83 PGASSPLQVKYADGELE   99 (354)
Q Consensus        83 ~g~~~~l~v~~~~~~~~   99 (354)
                      .+  +.|+|.|++.+..
T Consensus        79 ~G--r~l~V~~a~~~~~   93 (104)
T 1wex_A           79 AG--QQAFFNYSTSKRI   93 (104)
T ss_dssp             SS--SBCEEEECSSSSC
T ss_pred             CC--EEEEEEEccCccc
Confidence            44  8899999876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.76  E-value=2.9e-18  Score=125.00  Aligned_cols=73  Identities=15%  Similarity=0.175  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      .+..|||+||++.+||++|+++|.+||+|.++++..      +||||||+|.+.++|++|++.||+.. +.+  +.|+|+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~-l~g--r~I~V~   76 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCV-LAN--TTIFAE   76 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCE-ECC--cEEEEE
Confidence            578899999999999999999999999999999865      67999999999999999999998866 555  777777


Q ss_pred             cc
Q 018554           93 YA   94 (354)
Q Consensus        93 ~~   94 (354)
                      ++
T Consensus        77 ~A   78 (89)
T 2wbr_A           77 SP   78 (89)
T ss_dssp             CC
T ss_pred             EC
Confidence            65

>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=99.75  E-value=5.2e-18  Score=130.03  Aligned_cols=88  Identities=24%  Similarity=0.275  Sum_probs=77.6

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      .+....+.++|||+|||+++++++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|++||+.  + ..+.+  
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~-~~~~g--   82 (103)
T 2cqg_A            8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--R-HMIDG--   82 (103)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--C-EEETT--
T ss_pred             CCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--C-CeeCC--
Confidence            455667889999999999999999999999999999999999999999999999999999999999984  3 34555  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|.|.++..+..
T Consensus        83 ~~l~v~~a~~~~~   95 (103)
T 2cqg_A           83 RWCDCKLPNSKQS   95 (103)
T ss_dssp             EEEEEECCCTTCC
T ss_pred             eEEEEEecCCCCc
Confidence            7889988876543

>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=99.75  E-value=3.5e-18  Score=133.55  Aligned_cols=85  Identities=15%  Similarity=0.326  Sum_probs=73.3

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-ccCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK-KTLPGA   85 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~-~~~~g~   85 (354)
                      .+....+.++|||+|||++++|++|+++|++||.|.+|+|+++      ||||||+|++.++|++|++.+++. ..+.| 
T Consensus        24 ~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G-   96 (119)
T 2ad9_A           24 SRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRG-   96 (119)
T ss_dssp             TTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTT-
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECC-
Confidence            3445667899999999999999999999999999999999876      589999999999999999998752 34555 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.+++.+..
T Consensus        97 -r~l~V~~a~~k~~  109 (119)
T 2ad9_A           97 -QPIYIQFSNHKEL  109 (119)
T ss_dssp             -BCCEEEECSSSSC
T ss_pred             -eEEEEEEccCCCC
Confidence             8999999876544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.75  E-value=1.8e-18  Score=124.66  Aligned_cols=75  Identities=29%  Similarity=0.433  Sum_probs=68.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      +|||+|||+++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++ +++.. +.+  +.|+|+++
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-IHFHE-INN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCC-SSS--CCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCE-ECC--EEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999998 77755 555  77777764

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.75  E-value=2.9e-18  Score=127.73  Aligned_cols=81  Identities=20%  Similarity=0.327  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +.++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|+ .+|+.. +.+  +.|+|.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~-~~g--~~l~V~   80 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESL-FRG--RQIKVI   80 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCE-ETT--EECEEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCE-ECC--cEEEEE
Confidence            4689999999999999999999999999999999999999999999999999999999999 898876 555  888998


Q ss_pred             ccccc
Q 018554           93 YADGE   97 (354)
Q Consensus        93 ~~~~~   97 (354)
                      +++..
T Consensus        81 ~a~~~   85 (89)
T 3ucg_A           81 PKRTN   85 (89)
T ss_dssp             ETTTT
T ss_pred             EccCC
Confidence            88754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.75  E-value=7.9e-18  Score=138.84  Aligned_cols=89  Identities=17%  Similarity=0.255  Sum_probs=79.1

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCC--CeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYG--TIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G--~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      .++|||+||++++|+++|+++|+.||  .|.+|+|++| .++.++|||||+|.+.++|++||+.|||.. ++|  +.|.|
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~-~~G--r~l~V  131 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKV-LNG--EKVDV  131 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCE-ETT--EECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC--eEeEE
Confidence            57999999999999999999999999  9999999999 589999999999999999999999999987 666  78999


Q ss_pred             EecCChHHHHHHHHH
Q 018554          179 KWADTEKERQARRAQ  193 (354)
Q Consensus       179 ~~a~~~~~~~~~~~~  193 (354)
                      ++|+.+..+..+...
T Consensus       132 ~~a~~~~~~~~e~~~  146 (156)
T 3n9u_C          132 RPATRQNLSQFEAQA  146 (156)
T ss_dssp             EECCHHHHHHHHHHH
T ss_pred             EEcCCCcchhhhhhc
Confidence            999877665544433

>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=99.75  E-value=5.1e-19  Score=138.37  Aligned_cols=85  Identities=24%  Similarity=0.375  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||.++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++|| .||+.. +.+  +.|+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g--~~l~   97 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQR-LLG--VPII   97 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEE-ETT--EEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCE-eCC--eEEE
Confidence            345689999999999999999999999999999999999999999999999999999999999 998766 555  8899


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.+++.+..
T Consensus        98 V~~a~~~~~  106 (114)
T 2cq4_A           98 VQASQAEKN  106 (114)
T ss_dssp             EEEHHHHHH
T ss_pred             EEecCCCcc
Confidence            998876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.2e-18  Score=126.23  Aligned_cols=76  Identities=28%  Similarity=0.429  Sum_probs=69.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      ++|||+|||.++++++|+++|++||+|.+|.+++|+.+++++|||||+|.+.++|++|++.++  ..+.|  +.++|+++
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--HELDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT--CCCSS--CCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC--CccCC--EEEEEEec
Confidence            589999999999999999999999999999999999999999999999999999999999987  44665  67777765

>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=99.75  E-value=3.3e-18  Score=142.76  Aligned_cols=124  Identities=24%  Similarity=0.354  Sum_probs=75.8

Q ss_pred             EEeCCHHHHHHHHHHhcCCccCCCCCccceeecc---------------------ccccccccceEEEecCCCCCCHHHH
Q 018554           61 VICPSRQEADKAVNACHNKKTLPGASSPLQVKYA---------------------DGELERLEHKLFIGMLPKNVSEAEV  119 (354)
Q Consensus        61 V~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~---------------------~~~~~~~~~~l~V~~l~~~~t~~~l  119 (354)
                      .+|++.++|+.|+..++++.. ..+.+.+...+.                     .+......++|||+||++++++++|
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~-~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L   89 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAK-HRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEI   89 (165)
T ss_dssp             --------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHH
T ss_pred             hhhhccccccccchhhccccc-cccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHH
Confidence            678888888888887765442 222222222221                     1111223568999999999999999


Q ss_pred             HHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCChHHHH
Q 018554          120 SALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQ  188 (354)
Q Consensus       120 ~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~~~~~  188 (354)
                      +++|++||.|..|.|+.+ .++.++|||||+|.+.++|.+||+.|||.. +.|  +.|.|.|+..+..+.
T Consensus        90 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           90 QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE-IMG--QTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEESEECC---
T ss_pred             HHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEecCCCCCC
Confidence            999999999999999998 588999999999999999999999999976 565  789999997665443

>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=99.75  E-value=2.5e-18  Score=132.51  Aligned_cols=86  Identities=38%  Similarity=0.678  Sum_probs=78.2

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ....++|||+||+.++|+++|+++|++||.|++|+|+++. ++.++|||||+|.+.++|.+|++.||+..++.+..+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            3446899999999999999999999999999999999984 689999999999999999999999999887766668999


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+|++.+
T Consensus        90 v~~a~~~   96 (106)
T 2dgp_A           90 VKPADSE   96 (106)
T ss_dssp             EEECCCC
T ss_pred             EEECCcc
Confidence            9999865

>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=8.7e-18  Score=128.07  Aligned_cols=82  Identities=28%  Similarity=0.465  Sum_probs=75.5

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++|+++|+++|++||.|++|+|+.+.++.++|||||+|.+.++|.+|++.||+.. ++|  +.|+|+
T Consensus        15 ~~~~~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           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMT-IKE--NIIKVA   91 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEE-SSS--CEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999976 666  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++++
T Consensus        92 ~a~~~   96 (100)
T 2do4_A           92 ISNSG   96 (100)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99765

>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=99.75  E-value=8.4e-18  Score=124.66  Aligned_cols=80  Identities=25%  Similarity=0.549  Sum_probs=73.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||+.++++++|+++|++||.|.+++++++ .++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|+|
T Consensus         6 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v~~   82 (87)
T 3bs9_A            6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW-LGG--RQIRTNW   82 (87)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEEe
Confidence            578999999999999999999999999999999999 488999999999999999999999999976 666  7899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++.+
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            8764

>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=1.1e-17  Score=122.92  Aligned_cols=79  Identities=23%  Similarity=0.535  Sum_probs=73.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .+|||+|||.++++++|+++|+.||.|.++.++++ .++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|+|+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~-~~g--~~l~v~~a   78 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD-LNG--RPLRINWA   78 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCe-eCC--cEEEEEec
Confidence            68999999999999999999999999999999998 689999999999999999999999999987 565  78999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus        79 ~~~   81 (83)
T 3md1_A           79 AKL   81 (83)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            764

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=1.4e-18  Score=140.01  Aligned_cols=92  Identities=25%  Similarity=0.355  Sum_probs=81.8

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      +...+..+.++|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+.|++.. +.+ 
T Consensus        39 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~-i~g-  116 (135)
T 2lea_A           39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV-LDG-  116 (135)
T ss_dssp             CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCC-SSS-
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC-
Confidence            334556678999999999999999999999999999999999999999999999999999999999999998877 555 


Q ss_pred             Cccceeecccccccc
Q 018554           86 SSPLQVKYADGELER  100 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~  100 (354)
                       +.|+|.+++.+...
T Consensus       117 -~~l~V~~a~~~~~~  130 (135)
T 2lea_A          117 -RELRVQMARYGRPP  130 (135)
T ss_dssp             -SCCEEEECCCCCCC
T ss_pred             -EEEEEEECCCCCCC
Confidence             88999998765543

>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=99.75  E-value=1.5e-18  Score=131.76  Aligned_cols=86  Identities=16%  Similarity=0.247  Sum_probs=77.0

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||+++++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|++|++.||+.. +.+  +.
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~   86 (98)
T 2cqp_A           10 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP-IGS--RK   86 (98)
T ss_dssp             CCCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCE-ETT--EE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCe-eCC--eE
Confidence            345667899999999999999999999999999999999999999999999999999999999999998876 555  78


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |+|.++...
T Consensus        87 l~V~~a~~~   95 (98)
T 2cqp_A           87 VKLVLGSGP   95 (98)
T ss_dssp             CEEEESSCS
T ss_pred             EEEEEcCCC
Confidence            888887643

>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=99.75  E-value=1.8e-18  Score=131.97  Aligned_cols=85  Identities=15%  Similarity=0.303  Sum_probs=71.7

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCC-CCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDK-TTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~-~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      .......++|||+|||+++++++|+++|++|| |.+|+|++|+ .+|+++|||||+|.+.++|++|+ .+++.. +.+  
T Consensus        13 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~-~~g--   87 (100)
T 2j76_E           13 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEES-LGN--   87 (100)
T ss_dssp             -------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCC-BTT--
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCE-ECC--
Confidence            34566789999999999999999999999999 9999999998 68999999999999999999999 898866 555  


Q ss_pred             ccceeeccccc
Q 018554           87 SPLQVKYADGE   97 (354)
Q Consensus        87 ~~l~v~~~~~~   97 (354)
                      +.|+|.+++.+
T Consensus        88 ~~l~V~~a~~~   98 (100)
T 2j76_E           88 RRIRVDVADQA   98 (100)
T ss_dssp             BCCCCEECCCS
T ss_pred             eEEEEEeccCC
Confidence            78888887754

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.74  E-value=1.6e-18  Score=130.92  Aligned_cols=83  Identities=16%  Similarity=0.223  Sum_probs=73.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++++++|+++|++||.|.++.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--r~l   87 (95)
T 2ek1_A           11 GKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP-IGS--RKV   87 (95)
T ss_dssp             ----CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCe-ECC--cEE
Confidence            34457999999999999999999999999999999999999999999999999999999999999998876 555  788


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      +|.++.
T Consensus        88 ~v~~a~   93 (95)
T 2ek1_A           88 KLSGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEEecc
Confidence            888764

>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=99.74  E-value=4.3e-18  Score=128.82  Aligned_cols=84  Identities=21%  Similarity=0.217  Sum_probs=74.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLL----AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~----~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ...+.++|||+|||+++++++|+    ++|++||+|.+|+|++|+.+   +|||||+|.+.++|++|++.||+.. +.+ 
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~-~~g-   79 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYK-IGS-   79 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEE-ETT-
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCE-ECC-
Confidence            44567899999999999999999    99999999999999999875   8899999999999999999998866 555 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.+++....
T Consensus        80 -r~l~V~~a~~~~~   92 (96)
T 2dgx_A           80 -KKILVSLATGASG   92 (96)
T ss_dssp             -EEEEEEECCCSSC
T ss_pred             -eEEEEEEcCCCCC
Confidence             8899999876543

>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=99.74  E-value=1e-17  Score=126.35  Aligned_cols=81  Identities=22%  Similarity=0.388  Sum_probs=74.7

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++++++|+++|++||.|++|+|+++.++.++|||||+|++.++|.+|++.||+.. ++|  +.|+|+
T Consensus        14 ~~~~~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           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIR-LYG--RPINVS   90 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCE-ECC--CEEEEE
Confidence            34689999999999999999999999999999999999889999999999999999999999999987 565  789999


Q ss_pred             ecCC
Q 018554          180 WADT  183 (354)
Q Consensus       180 ~a~~  183 (354)
                      |++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>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=99.74  E-value=1.1e-18  Score=130.48  Aligned_cols=81  Identities=23%  Similarity=0.392  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      ++|||+|||.++++++|+++|++||+|.+|.+++|+.+++++|||||+|.+.+ |.+|++.||+.. +.|  +.|+|.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~-~~g--~~l~V~~a   77 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTD-FMG--RTIRVTEA   77 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSC-CSS--SSCSEEEC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCE-ECC--eEEEEEEc
Confidence            68999999999999999999999999999999999999999999999999999 999999998866 555  88899888


Q ss_pred             ccccc
Q 018554           95 DGELE   99 (354)
Q Consensus        95 ~~~~~   99 (354)
                      .....
T Consensus        78 ~~~~~   82 (90)
T 2ki2_A           78 NPKKS   82 (90)
T ss_dssp             -----
T ss_pred             CCCCC
Confidence            76543

>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=99.74  E-value=6.3e-18  Score=129.78  Aligned_cols=89  Identities=27%  Similarity=0.536  Sum_probs=79.2

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      +...++|||+||+.++++++|+++|++||.|.++.++++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~   81 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE-FSG--RALR   81 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBS-CSS--SCBE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe-eCC--cEEE
Confidence            334689999999999999999999999999999999998 478899999999999999999999999976 566  6899


Q ss_pred             EEecCChHHHHHH
Q 018554          178 VKWADTEKERQAR  190 (354)
Q Consensus       178 v~~a~~~~~~~~~  190 (354)
                      |+|++.+..+...
T Consensus        82 v~~a~~~~~~~~~   94 (104)
T 1p1t_A           82 VDNAASEKNKEEL   94 (104)
T ss_dssp             EEETTCTTHHHHH
T ss_pred             EEeCCCccchhhh
Confidence            9999987666543

>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=99.74  E-value=1e-17  Score=129.86  Aligned_cols=86  Identities=15%  Similarity=0.364  Sum_probs=75.4

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||.|.+|+|..+   ++++|||||+|.+.++|++||+.||+.. +.+  +
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~   89 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYD-YDG--Y   89 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCE-ETT--E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCE-ECC--e
Confidence            345667899999999999999999999999999999999665   4689999999999999999999998876 555  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        90 ~l~V~~a~~~~~  101 (109)
T 1x4a_A           90 RLRVEFPRSGRG  101 (109)
T ss_dssp             ECEEECCCCCCC
T ss_pred             EEEEEEcccCCC
Confidence            899999876544

>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=7e-18  Score=133.87  Aligned_cols=86  Identities=22%  Similarity=0.373  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||.++++++|+++|++||.|.+|+|++|+ +++++|||||+|.+.++|++|++.|++.. +.+  +.|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l  106 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVP-LDG--RPM  106 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEE-SSS--CEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCE-ECC--cEE
Confidence            45677899999999999999999999999999999999999 89999999999999999999999998865 555  789


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.++.....
T Consensus       107 ~V~~a~~~~~  116 (124)
T 2kt5_A          107 DIQLVASQID  116 (124)
T ss_dssp             EEEEECCTTC
T ss_pred             EEEEeCCCCC
Confidence            9998876543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.5e-18  Score=136.07  Aligned_cols=86  Identities=27%  Similarity=0.406  Sum_probs=76.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +....++|||+|||+++++++|+++|++||.|.+|.|++|+.|++++|||||+|.+.++|++||+. ++.. +.+  +.|
T Consensus        23 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~-~~g--~~l   98 (116)
T 1x4b_A           23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHS-IDG--RVV   98 (116)
T ss_dssp             HHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEE-ETT--EEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcE-ECC--EEE
Confidence            345569999999999999999999999999999999999999999999999999999999999988 6544 555  889


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.++..+..
T Consensus        99 ~V~~a~~~~~  108 (116)
T 1x4b_A           99 EPKRAVAREE  108 (116)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEECCCCcc
Confidence            9999876654

>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=2.6e-18  Score=128.40  Aligned_cols=81  Identities=16%  Similarity=0.295  Sum_probs=68.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCC--CeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYG--TIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G--~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .+|||+||++++|+++|+++|++||  .|.+++|++| .++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~-~~g--r~i~V~   78 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE-LHG--QNPVVT   78 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSC-SSS--CCCEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCe-eCC--EEEEEE
Confidence            4799999999999999999999999  9999999999 489999999999999999999999999987 666  688999


Q ss_pred             ecCChHH
Q 018554          180 WADTEKE  186 (354)
Q Consensus       180 ~a~~~~~  186 (354)
                      ++.+...
T Consensus        79 ~~~~~~~   85 (90)
T 3p5t_L           79 PSNKLEH   85 (90)
T ss_dssp             CC-----
T ss_pred             ECCCCcc
Confidence            8876543

>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=99.74  E-value=6.2e-18  Score=139.99  Aligned_cols=87  Identities=26%  Similarity=0.374  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++++++|+++|++||.|.+|.|++|+.+|+++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l  142 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV-LDG--REL  142 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEE-SSS--SEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCE-ECC--eEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999998866 555  889


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.+++.+..
T Consensus       143 ~v~~a~~~~~  152 (158)
T 2kn4_A          143 RVQMARYGRP  152 (158)
T ss_dssp             EEEEECCSSC
T ss_pred             EEEECCCCCC
Confidence            9999876544

>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=99.74  E-value=5.9e-18  Score=130.82  Aligned_cols=88  Identities=14%  Similarity=0.295  Sum_probs=73.9

Q ss_pred             ccccccCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-cc
Q 018554            4 SKKEKKSSEERVKLFVGQVPKH-MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK-KT   81 (354)
Q Consensus         4 ~~~~~~~~~~~~~lfVg~Lp~~-~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~-~~   81 (354)
                      .++.+.+....++|||+|||++ +++++|+++|++||.|.+|+|++      +||||||+|.+.++|++|++.|++. ..
T Consensus        15 ~k~~~~~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~   88 (112)
T 1x4f_A           15 DQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALW   88 (112)
T ss_dssp             CCCCCCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCC
T ss_pred             hhhccccCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCce
Confidence            3444556778999999999998 99999999999999999999975      4689999999999999999998753 33


Q ss_pred             CCCCCccceeeccccccc
Q 018554           82 LPGASSPLQVKYADGELE   99 (354)
Q Consensus        82 ~~g~~~~l~v~~~~~~~~   99 (354)
                      +.|  +.|+|.+++.+..
T Consensus        89 l~G--r~l~V~~a~~~~~  104 (112)
T 1x4f_A           89 FQG--RCVKVDLSEKYKK  104 (112)
T ss_dssp             SSS--SCCEEEEECSCSS
T ss_pred             ECC--EEEEEEECccccc
Confidence            555  8899999876543

>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=99.74  E-value=8.3e-18  Score=129.21  Aligned_cols=85  Identities=15%  Similarity=0.253  Sum_probs=73.3

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE-VNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~-i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ..+....++|||+|||+++++++|+++|+.||.|.+ |.|++| .+++++|||||+|.+.++|++||+. ++.. +.+  
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~-~~g--   83 (104)
T 1wg5_A            9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKER-IGH--   83 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCC-SSS--
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-Ccch-hCC--
Confidence            445677899999999999999999999999999988 888888 6899999999999999999999997 6644 555  


Q ss_pred             ccceeeccccc
Q 018554           87 SPLQVKYADGE   97 (354)
Q Consensus        87 ~~l~v~~~~~~   97 (354)
                      +.|+|.++..+
T Consensus        84 r~i~v~~~~~~   94 (104)
T 1wg5_A           84 RYIEIFKSSRA   94 (104)
T ss_dssp             SCCEEEEECTT
T ss_pred             cEEEEEECCHH
Confidence            67777766543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=8e-18  Score=125.97  Aligned_cols=85  Identities=15%  Similarity=0.269  Sum_probs=75.6

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||+|||+++++++|+++|+.| .|.+|+|++| .+|+++|||||+|.+.++|++|++ +|+.. +.+  +
T Consensus         4 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~-~~g--r   77 (91)
T 2dgw_A            4 GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREY-MGG--R   77 (91)
T ss_dssp             CCCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEE-ETT--E
T ss_pred             CCCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCce-eCC--c
Confidence            3456788999999999999999999999999 9999999999 679999999999999999999999 98766 555  7


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|+|.+++.+.
T Consensus        78 ~i~v~~a~~~~   88 (91)
T 2dgw_A           78 YIEVFREKSGP   88 (91)
T ss_dssp             EEEEEEESSCC
T ss_pred             EEEEEECCcCC
Confidence            88888877653

>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=99.73  E-value=4.3e-18  Score=149.42  Aligned_cols=86  Identities=16%  Similarity=0.256  Sum_probs=76.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCC--CeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYG--TIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G--~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ..++|||+||++++|+++|+++|++||  .|++|+|++| .++++||||||+|++.++|++||+.||+.. |+|  +.|+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~-~~G--r~l~  143 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE-LHG--QNPV  143 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSC-BTT--BCCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCe-ECC--EEeE
Confidence            357899999999999999999999999  9999999999 489999999999999999999999999987 666  6899


Q ss_pred             EEecCChHHHHH
Q 018554          178 VKWADTEKERQA  189 (354)
Q Consensus       178 v~~a~~~~~~~~  189 (354)
                      |+||+.......
T Consensus       144 V~~a~~~~~~~~  155 (229)
T 3q2s_C          144 VTPVNKQFLSQF  155 (229)
T ss_dssp             EEECCHHHHHHH
T ss_pred             EEECCCCccchh
Confidence            999987655443

>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=99.73  E-value=8e-18  Score=128.00  Aligned_cols=82  Identities=29%  Similarity=0.441  Sum_probs=75.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|++||.|++|+|+++. ++.++|||||+|.+.++|.+|++.||+.. ++|  +.|+|+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V~   83 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV-FQG--RMLHVL   83 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEE-SSS--CEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEE
Confidence            36799999999999999999999999999999999996 88999999999999999999999999976 665  689999


Q ss_pred             ecCChH
Q 018554          180 WADTEK  185 (354)
Q Consensus       180 ~a~~~~  185 (354)
                      |++.+.
T Consensus        84 ~a~~~~   89 (99)
T 1whw_A           84 PSTIKK   89 (99)
T ss_dssp             ECCCCS
T ss_pred             EcCCCc
Confidence            998763

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.7e-17  Score=127.23  Aligned_cols=81  Identities=25%  Similarity=0.439  Sum_probs=74.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||++++|+++|+++|++||.|++|+|+.+ ++.+++||||+|.+.++|.+|++.||+.. ++|  +.|.|+|
T Consensus        14 ~~~~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           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRI-VAT--KPLYVAL   89 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCB-SSS--SBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCE-eCC--cEEEEEE
Confidence            4689999999999999999999999999999999999 88999999999999999999999999987 565  6899999


Q ss_pred             cCChH
Q 018554          181 ADTEK  185 (354)
Q Consensus       181 a~~~~  185 (354)
                      ++.+.
T Consensus        90 a~~~~   94 (103)
T 2d9p_A           90 AQRKE   94 (103)
T ss_dssp             CSSCC
T ss_pred             ecccc
Confidence            97653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=6.1e-18  Score=131.09  Aligned_cols=87  Identities=25%  Similarity=0.445  Sum_probs=76.7

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ....+..+.++|||+|||.++++++|+++|++||+|.+|++++|+  ++++|||||+|.+.++|++|++.|++.. +.| 
T Consensus        21 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g-   96 (109)
T 2err_A           21 MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTV-VEG-   96 (109)
T ss_dssp             -CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCE-ETT-
T ss_pred             CCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCE-ECC-
Confidence            344566788999999999999999999999999999999999986  4589999999999999999999998876 555 


Q ss_pred             Cccceeeccccc
Q 018554           86 SSPLQVKYADGE   97 (354)
Q Consensus        86 ~~~l~v~~~~~~   97 (354)
                       +.|+|.+++.+
T Consensus        97 -~~l~V~~a~~~  107 (109)
T 2err_A           97 -RKIEVNNATAR  107 (109)
T ss_dssp             -EECEEEECCCS
T ss_pred             -EEEEEEECCCC
Confidence             88999988764

>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=99.73  E-value=2e-18  Score=135.02  Aligned_cols=85  Identities=20%  Similarity=0.292  Sum_probs=75.1

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALV-DEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v-~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ....+.++|||+|||+++|+++|+++|+.||.| .+|+|++|+ +++++|||||+|.+.++|++||+. |+.. +.+  +
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~-~~g--r   84 (114)
T 2cpy_A           10 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKK-LNG--R   84 (114)
T ss_dssp             SCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEE-ETT--E
T ss_pred             CCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCc-cCC--e
Confidence            456678999999999999999999999999999 899999999 899999999999999999999987 6644 655  7


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|.|.++..+.
T Consensus        85 ~i~v~~a~~~~   95 (114)
T 2cpy_A           85 EAFVHVVTLED   95 (114)
T ss_dssp             EEEEEEECHHH
T ss_pred             EEEEEECCHHH
Confidence            88888876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-17  Score=124.94  Aligned_cols=80  Identities=29%  Similarity=0.543  Sum_probs=73.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||+.++++++|+++|++||.|++|+++++. ++.++|||||+|++.++|.+|++.||+.. ++|  +.|+|+|
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V~~   81 (95)
T 2dnz_A            5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFE-LAG--RPMRVGH   81 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCC-SSS--SCCEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCe-eCC--cEEEEEE
Confidence            5789999999999999999999999999999999984 68999999999999999999999999976 666  6899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++.+
T Consensus        82 a~~~   85 (95)
T 2dnz_A           82 VTER   85 (95)
T ss_dssp             SSCC
T ss_pred             cccc
Confidence            8764

>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=99.73  E-value=4.8e-18  Score=149.14  Aligned_cols=82  Identities=17%  Similarity=0.314  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFA--LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G--~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      +.++|||+||++++||++|+++|++||  +|++|+|++|+.|+++||||||+|.+.++|++||+.||+.. +.+  +.|+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~-~~G--r~l~  143 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE-LHG--QNPV  143 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSC-BTT--BCCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCe-ECC--EEeE
Confidence            678999999999999999999999999  99999999999999999999999999999999999998876 555  7888


Q ss_pred             eeccccc
Q 018554           91 VKYADGE   97 (354)
Q Consensus        91 v~~~~~~   97 (354)
                      |.+++..
T Consensus       144 V~~a~~~  150 (229)
T 3q2s_C          144 VTPVNKQ  150 (229)
T ss_dssp             EEECCHH
T ss_pred             EEECCCC
Confidence            8887654

>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=126.31  Aligned_cols=85  Identities=18%  Similarity=0.274  Sum_probs=71.8

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc-CCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT-LPG   84 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~-~~g   84 (354)
                      ++.....++++|||+|||.++|+++|+++|++||.|.+|++++      .||||||+|++.++|.+|++.+++..+ +.|
T Consensus        13 ~~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~G   86 (100)
T 3r27_A           13 DDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAG   86 (100)
T ss_dssp             ----CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETT
T ss_pred             cccccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCC
Confidence            4556677899999999999999999999999999999999986      357999999999999999999987652 444


Q ss_pred             CCccceeecccccc
Q 018554           85 ASSPLQVKYADGEL   98 (354)
Q Consensus        85 ~~~~l~v~~~~~~~   98 (354)
                        +.|+|.|++.+.
T Consensus        87 --r~i~V~~S~~k~   98 (100)
T 3r27_A           87 --HPAFVNYSTSQK   98 (100)
T ss_dssp             --EEEEEEECSCSC
T ss_pred             --cEEEEEeccccc
Confidence              899999987653

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.8e-17  Score=126.99  Aligned_cols=82  Identities=23%  Similarity=0.470  Sum_probs=75.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++++++|+++|++||.|++|.|+++ .++.++|||||+|.+.++|.+|++.||+.. ++|  +.|+|
T Consensus        13 ~~~~~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           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG-YDH--LILNV   89 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCE-ETT--EECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCe-eCC--cEEEE
Confidence            34689999999999999999999999999999999999 488999999999999999999999999987 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus        90 ~~a~~~   95 (103)
T 2cq0_A           90 EWAKPS   95 (103)
T ss_dssp             EESSCC
T ss_pred             EECCCC
Confidence            999765

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.4e-18  Score=129.75  Aligned_cols=78  Identities=26%  Similarity=0.457  Sum_probs=69.4

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-cccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK-HKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|++||+|++|+|+++     ||||||+|++.++|.+|++.|++. ..++|  +.|.|.
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G--r~l~V~   87 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRG--QPIYIQ   87 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETT--EECCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--EEEEEE
Confidence            3679999999999999999999999999999999986     899999999999999999998753 33666  789999


Q ss_pred             ecCChH
Q 018554          180 WADTEK  185 (354)
Q Consensus       180 ~a~~~~  185 (354)
                      ||+.+.
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            997653

>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=99.73  E-value=1.3e-17  Score=123.02  Aligned_cols=79  Identities=29%  Similarity=0.499  Sum_probs=72.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++++++|+++|++||.|.++.++++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~   82 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--RTIRVN   82 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEE
Confidence            4689999999999999999999999999999999988 688899999999999999999999999987 565  789999


Q ss_pred             ecC
Q 018554          180 WAD  182 (354)
Q Consensus       180 ~a~  182 (354)
                      ||+
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.6e-17  Score=124.12  Aligned_cols=81  Identities=27%  Similarity=0.378  Sum_probs=74.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++++++|+++|++||.|++|.++++. ++.++|||||+|.+.++|.+|++.||+.. ++|  +.|+|
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v   89 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME-LDG--RRIRV   89 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            346889999999999999999999999999999999984 68899999999999999999999999976 565  78999


Q ss_pred             EecCC
Q 018554          179 KWADT  183 (354)
Q Consensus       179 ~~a~~  183 (354)
                      +|+++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99874

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.73  E-value=8e-18  Score=136.30  Aligned_cols=84  Identities=25%  Similarity=0.389  Sum_probs=75.4

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||+|++|+|++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        57 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~  133 (140)
T 2ku7_A           57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--R  133 (140)
T ss_dssp             CSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEE-ETT--E
T ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCE-ECC--E
Confidence            3456688999999999999999999999999999999999999999999999999999999999999998865 555  7


Q ss_pred             cceeecc
Q 018554           88 PLQVKYA   94 (354)
Q Consensus        88 ~l~v~~~   94 (354)
                      .|+|.++
T Consensus       134 ~l~v~~A  140 (140)
T 2ku7_A          134 TIRVNLA  140 (140)
T ss_dssp             EEEEEC-
T ss_pred             EEEEEeC
Confidence            7887764

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.73  E-value=2.5e-17  Score=128.80  Aligned_cols=82  Identities=23%  Similarity=0.520  Sum_probs=75.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++|+++|+++|+.||.|++|+|+++ .++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V   89 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW-LGG--RQIRT   89 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCE-ETT--EECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            34689999999999999999999999999999999999 489999999999999999999999999977 666  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .|++.+
T Consensus        90 ~~a~~~   95 (115)
T 2dgo_A           90 NWATRK   95 (115)
T ss_dssp             EESSCC
T ss_pred             EEccCC
Confidence            999765

>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=99.73  E-value=2.4e-18  Score=136.63  Aligned_cols=85  Identities=15%  Similarity=0.234  Sum_probs=74.3

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ....+.++|||+|||+++|+++|+++|+.||.|.++.++.+..+|+++|||||+|.+.++|++||+ +|+.. +.+  +.
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~-~~g--r~   95 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQY-MGN--RF   95 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBC-STT--SC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCe-ECC--cE
Confidence            345677999999999999999999999999999997777777889999999999999999999999 87755 655  78


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |.|.++..+
T Consensus        96 i~V~~a~~~  104 (124)
T 1wel_A           96 IQVHPITKK  104 (124)
T ss_dssp             BEEEEECHH
T ss_pred             EEEEECCHH
Confidence            888877654

>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=99.73  E-value=1.8e-17  Score=125.33  Aligned_cols=83  Identities=20%  Similarity=0.403  Sum_probs=75.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      +++|||+||+.++++++|+++|++||.|.+|+|+++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+|
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~~   78 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ-LGS--RFLKCGY   78 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEEE
Confidence            478999999999999999999999999999999998 478999999999999999999999999977 666  7899999


Q ss_pred             cCChHHH
Q 018554          181 ADTEKER  187 (354)
Q Consensus       181 a~~~~~~  187 (354)
                      ++.+...
T Consensus        79 a~~~~~~   85 (96)
T 2x1f_A           79 SSNSDIS   85 (96)
T ss_dssp             CSCSSGG
T ss_pred             cCCCCCC
Confidence            9876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.73  E-value=2.3e-18  Score=136.64  Aligned_cols=85  Identities=21%  Similarity=0.350  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||.++++++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|++|+ .||+.. +.+  +.|+
T Consensus        33 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g--~~l~  108 (124)
T 2jwn_A           33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETV-FRG--RTIK  108 (124)
T ss_dssp             HHHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCE-ETT--EECE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCe-ECC--eEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999 788866 555  8899


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.+++....
T Consensus       109 V~~a~~~~~  117 (124)
T 2jwn_A          109 VLPKRTNMP  117 (124)
T ss_dssp             EEESSCCCS
T ss_pred             EEECCCCCC
Confidence            998875443

>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=5.3e-18  Score=131.90  Aligned_cols=87  Identities=15%  Similarity=0.289  Sum_probs=77.0

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEeeCCCCC---CcccEEEEEeCCHHHHHHHHHHhcCCccC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLL---AMFKEFALVDEVNIIKDKTTR---ASRGCCFVICPSRQEADKAVNACHNKKTL   82 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~---~~F~~~G~v~~i~i~~d~~tg---~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~   82 (354)
                      ......++|||+|||+++++++|+   ++|++||+|.+|.|++|+.++   +++|||||+|.+.++|++||+.||+.. +
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~-~   88 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV-V   88 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE-E
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCE-E
Confidence            355678899999999999999999   999999999999999998754   566999999999999999999998876 5


Q ss_pred             CCCCccceeecccccc
Q 018554           83 PGASSPLQVKYADGEL   98 (354)
Q Consensus        83 ~g~~~~l~v~~~~~~~   98 (354)
                      .+  +.|+|.++..+.
T Consensus        89 ~g--r~l~V~~a~~k~  102 (111)
T 2cpi_A           89 DG--RTLKASLGTTKY  102 (111)
T ss_dssp             TT--EEEEEESCCCCS
T ss_pred             CC--EEEEEEeccccc
Confidence            55  889999987654

>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=99.73  E-value=1.6e-17  Score=129.94  Aligned_cols=82  Identities=22%  Similarity=0.382  Sum_probs=75.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++++++|+++|++||.|++|+|+++. ++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V   99 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ-IGM--KRLKV   99 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            346899999999999999999999999999999999995 89999999999999999999999999977 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus       100 ~~a~~~  105 (115)
T 2cpz_A          100 QLKRSK  105 (115)
T ss_dssp             ECCCCS
T ss_pred             EEcCCC
Confidence            999765

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.73  E-value=1.5e-17  Score=125.51  Aligned_cols=82  Identities=18%  Similarity=0.253  Sum_probs=71.1

Q ss_pred             cccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc-cCCCce
Q 018554           96 GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK-MEGSSV  174 (354)
Q Consensus        96 ~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~-~~g~~~  174 (354)
                      ......+++|||+||++++|+++|+++|++||.|++++++++     ||+|||+|++.++|.+|++.|++..+ +.|  +
T Consensus        15 ~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~G--r   87 (100)
T 3r27_A           15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAG--H   87 (100)
T ss_dssp             --CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETT--E
T ss_pred             cccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCC--c
Confidence            334445789999999999999999999999999999999864     89999999999999999999998752 455  7


Q ss_pred             eEEEEecCCh
Q 018554          175 PLVVKWADTE  184 (354)
Q Consensus       175 ~l~v~~a~~~  184 (354)
                      +|.|.|++.+
T Consensus        88 ~i~V~~S~~k   97 (100)
T 3r27_A           88 PAFVNYSTSQ   97 (100)
T ss_dssp             EEEEEECSCS
T ss_pred             EEEEEecccc
Confidence            9999999764

>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=99.73  E-value=5.9e-18  Score=128.87  Aligned_cols=84  Identities=18%  Similarity=0.275  Sum_probs=72.3

Q ss_pred             cccCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc-cCCC
Q 018554            7 EKKSSEERVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK-TLPG   84 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~-~~~g   84 (354)
                      ++....+.++|||+|||+ ++||+||+++|++||.|.+|+|++++      |||||+|++.++|++||+.|++.. .+.|
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~G   81 (102)
T 1x4d_A            8 QKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFG   81 (102)
T ss_dssp             CCCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECC
Confidence            344566889999999999 99999999999999999999998764      699999999999999999998643 3555


Q ss_pred             CCccceeecccccc
Q 018554           85 ASSPLQVKYADGEL   98 (354)
Q Consensus        85 ~~~~l~v~~~~~~~   98 (354)
                        +.|+|.+++...
T Consensus        82 --r~l~V~~a~~~~   93 (102)
T 1x4d_A           82 --KPVRVHLSQKYK   93 (102)
T ss_dssp             --EECEEEEECCCT
T ss_pred             --cEEEEEECCCCC
Confidence              889999987543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=127.35  Aligned_cols=89  Identities=25%  Similarity=0.346  Sum_probs=77.9

Q ss_pred             cccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            5 KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         5 ~~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ..........++|||+|||.++++++|+++|+.|+   +|.+++|+.+++++|||||+|.+.++|++||+.||+.. +.+
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g   81 (102)
T 2fc8_A            6 SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGE-IDG   81 (102)
T ss_dssp             CTTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE-ETT
T ss_pred             CCCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCe-ECC
Confidence            34456678899999999999999999999999773   78889999999999999999999999999999998876 555


Q ss_pred             CCccceeeccccccc
Q 018554           85 ASSPLQVKYADGELE   99 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~   99 (354)
                        +.|+|.+++.+..
T Consensus        82 --~~l~V~~a~~~~~   94 (102)
T 2fc8_A           82 --NKVTLDWAKPKGE   94 (102)
T ss_dssp             --EECEEEECCCCCS
T ss_pred             --eEEEEEEecCCCC
Confidence              7899999887654

>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=1.2e-17  Score=127.86  Aligned_cols=80  Identities=18%  Similarity=0.352  Sum_probs=72.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+++..+.++|||||+|++.++|.+|++ +++.. ++|  +.|.|.|
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~-~~g--r~l~V~~   85 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQK-YKE--TDLLILF   85 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCC-CTT--TTCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCE-ECC--EEEEEEE
Confidence            3578999999999999999999999999999999999779999999999999999999998 88865 677  5788888


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +..-
T Consensus        86 ~~~~   89 (103)
T 1s79_A           86 KDDY   89 (103)
T ss_dssp             HHHH
T ss_pred             chHH
Confidence            7543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=1.8e-18  Score=132.17  Aligned_cols=86  Identities=20%  Similarity=0.278  Sum_probs=76.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++++++|+++|++||.|.+ .++.|+.+++++|||||+|.+.++|++||+ ||+.. +.+  +.|
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~-~~g--~~l   87 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLK-VFG--NEI   87 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCC-BTT--BCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcE-ECC--cEE
Confidence            4557889999999999999999999999999888 778888889999999999999999999998 98876 445  889


Q ss_pred             eeecccccccc
Q 018554           90 QVKYADGELER  100 (354)
Q Consensus        90 ~v~~~~~~~~~  100 (354)
                      +|.+++.+..+
T Consensus        88 ~V~~a~~~~~~   98 (101)
T 1fj7_A           88 KLEKPKGRDGT   98 (101)
T ss_dssp             EEECCSCCCCS
T ss_pred             EEEEcCCCCCC
Confidence            99998876554

>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=99.73  E-value=8.9e-18  Score=128.49  Aligned_cols=82  Identities=13%  Similarity=0.115  Sum_probs=70.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||+++||+||+++|++||.| +|+|++|+ +++++|||||+|.+.++|++||+ +|+.. +.+  +.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~-~~g--r~   83 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKAN-MQH--RY   83 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCC-SSS--SC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCe-ECC--cE
Confidence            456678999999999999999999999999955 99999998 79999999999999999999995 66644 655  67


Q ss_pred             ceeecccc
Q 018554           89 LQVKYADG   96 (354)
Q Consensus        89 l~v~~~~~   96 (354)
                      |+|.++..
T Consensus        84 i~V~~~~~   91 (102)
T 1wez_A           84 VELFLNST   91 (102)
T ss_dssp             CEEEEECC
T ss_pred             EEEEECCC
Confidence            77776654

>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=3.1e-17  Score=128.05  Aligned_cols=82  Identities=24%  Similarity=0.411  Sum_probs=75.2

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||++++++++|+++|++||.|++|+|+++.++.++|||||+|++.++|++|++.||+.. ++|  +.|+|+
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~   89 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQL-LFD--RPMHVK   89 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCE-eCC--CEEEEE
Confidence            34689999999999999999999999999999999999889999999999999999999999999987 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98753

>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=99.72  E-value=1.6e-17  Score=130.21  Aligned_cols=80  Identities=30%  Similarity=0.517  Sum_probs=74.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||+.++|+++|+++|++||.|++|.|+.+.++.++|||||+|++.++|++|++.|||.. ++|  +.|+|+|+
T Consensus         7 ~~~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            7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKS-LHG--KAIKVEQA   83 (116)
T ss_dssp             CCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCB-CSS--SBCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEC
Confidence            579999999999999999999999999999999999889999999999999999999999999987 666  68999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +..
T Consensus        84 ~~~   86 (116)
T 2fy1_A           84 KKP   86 (116)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=3.4e-17  Score=125.44  Aligned_cols=82  Identities=24%  Similarity=0.455  Sum_probs=74.1

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ....++|||+||++++|+++|+++|++||.|++|+|+++..+ +++||||+|.+.++|++|++.||+.. ++|  +.|+|
T Consensus        12 ~~~~~~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           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTV-VEG--RKIEV   87 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            344689999999999999999999999999999999998655 79999999999999999999999987 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus        88 ~~a~~~   93 (103)
T 2cq3_A           88 NNATAR   93 (103)
T ss_dssp             EECCSS
T ss_pred             EEcccC
Confidence            998765

>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=99.72  E-value=5e-18  Score=136.44  Aligned_cols=83  Identities=12%  Similarity=0.155  Sum_probs=73.4

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFAL---VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~---v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .+..+.++|||+|||+++|+++|+++|++||.   |.+|+|++|+. |+++|||||+|.+.++|++||+ +|+.. +.+ 
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~-l~g-  114 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRES-MGH-  114 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEE-SSS-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCE-ECC-
Confidence            34567899999999999999999999999999   89999999998 9999999999999999999999 87755 555 


Q ss_pred             Cccceeecccc
Q 018554           86 SSPLQVKYADG   96 (354)
Q Consensus        86 ~~~l~v~~~~~   96 (354)
                       +.|+|.++..
T Consensus       115 -r~i~V~~a~~  124 (136)
T 2hgl_A          115 -RYIEVFKSHR  124 (136)
T ss_dssp             -SEEEEEECCH
T ss_pred             -EEEEEEECCh
Confidence             7778776653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=2e-17  Score=131.41  Aligned_cols=85  Identities=12%  Similarity=0.269  Sum_probs=73.4

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLL----AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~----~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .+..+.++|||+||++++++++|+    ++|++||.|.+|.+.+   ++++||||||+|.+.++|++|++.||+.. +.|
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~-l~g   99 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYP-FQG   99 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCC-CTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCE-eCC
Confidence            345678999999999999999876    6999999999988754   57899999999999999999999999876 555


Q ss_pred             CCccceeeccccccc
Q 018554           85 ASSPLQVKYADGELE   99 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~   99 (354)
                        +.|+|.|++.+..
T Consensus       100 --r~l~V~~a~~~~~  112 (127)
T 2a3j_A          100 --NPLVITFSETPQS  112 (127)
T ss_dssp             --SCCEEEECCCCCH
T ss_pred             --CEEEEEEccCcch
Confidence              7899999876544

>2dgs_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=3.2e-17  Score=124.64  Aligned_cols=80  Identities=23%  Similarity=0.504  Sum_probs=73.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++++++|+++|++||.|++|+|+++ .++.++|||||+|++.++|.+|++ ||+.. ++|  +.|+|+
T Consensus         9 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~-~~g--~~l~V~   84 (99)
T 2dgs_A            9 KSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHD-IMG--KKVEVK   84 (99)
T ss_dssp             SCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCB-SSS--CBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCE-ECC--eEEEEE
Confidence            4689999999999999999999999999999999998 478899999999999999999998 99976 666  588999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      +++.+
T Consensus        85 ~a~~~   89 (99)
T 2dgs_A           85 RAEPR   89 (99)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            98765

>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=99.72  E-value=1.9e-17  Score=127.33  Aligned_cols=83  Identities=20%  Similarity=0.358  Sum_probs=75.6

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++|+++|+++|++||.|++|.|+++. ++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|
T Consensus        13 ~~~~~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           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK-LYG--KPIRV   89 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB-CSS--CBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEE
Confidence            346899999999999999999999999999999999985 88999999999999999999999999976 666  68999


Q ss_pred             EecCChH
Q 018554          179 KWADTEK  185 (354)
Q Consensus       179 ~~a~~~~  185 (354)
                      +|++.+.
T Consensus        90 ~~a~~~~   96 (105)
T 1x5u_A           90 NKASAHN   96 (105)
T ss_dssp             EETTTTS
T ss_pred             EECCCCC
Confidence            9997653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=6.3e-18  Score=128.90  Aligned_cols=81  Identities=16%  Similarity=0.280  Sum_probs=73.6

Q ss_pred             cceEEEecCCC------CCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554          102 EHKLFIGMLPK------NVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus       102 ~~~l~V~~l~~------~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      .++|||+|||.      ++++++|+++|++||.|.+|+|+++. ++.++|||||+|.+.++|.+|++.|||.. ++|. +
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~-~~g~-r   83 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR-LDLK-H   83 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCB-SSSS-C
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcc-cCCC-e
Confidence            57899999999      99999999999999999999999985 69999999999999999999999999987 5551 5


Q ss_pred             eEEEEecCCh
Q 018554          175 PLVVKWADTE  184 (354)
Q Consensus       175 ~l~v~~a~~~  184 (354)
                      .|+|++|++.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            8899999654

>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=3.3e-17  Score=126.39  Aligned_cols=80  Identities=29%  Similarity=0.468  Sum_probs=74.2

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++|+++|+++|+.||.|++|+|+++.++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|+
T Consensus        27 ~~~~~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           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVP-LDG--RPMNIQ  103 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCE-eCC--cEEEEE
Confidence            34689999999999999999999999999999999999999999999999999999999999999987 565  789999


Q ss_pred             ecC
Q 018554          180 WAD  182 (354)
Q Consensus       180 ~a~  182 (354)
                      |+.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.72  E-value=3.8e-17  Score=126.33  Aligned_cols=84  Identities=27%  Similarity=0.478  Sum_probs=75.6

Q ss_pred             cccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554           98 LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus        98 ~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      .....++|||+||+.++++++|+++|++||.|++|+|+++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~-i~g--~~l   98 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFE-LAG--RPM   98 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCC-SSS--SCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEE
Confidence            3445789999999999999999999999999999999998 578899999999999999999999999976 666  688


Q ss_pred             EEEecCCh
Q 018554          177 VVKWADTE  184 (354)
Q Consensus       177 ~v~~a~~~  184 (354)
                      +|++++.+
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99998764

>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=99.72  E-value=1.3e-17  Score=134.05  Aligned_cols=81  Identities=15%  Similarity=0.132  Sum_probs=73.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCC---eeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGT---IKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~---v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      ...++|||+||++++|+++|+++|+.||.   |++|+|++|..++++|||||+|++.++|++|++ +|+.. ++|  +.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~-l~g--r~i  117 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRES-MGH--RYI  117 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEE-SSS--SEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCE-ECC--EEE
Confidence            34689999999999999999999999999   899999999889999999999999999999999 99976 666  688


Q ss_pred             EEEecCCh
Q 018554          177 VVKWADTE  184 (354)
Q Consensus       177 ~v~~a~~~  184 (354)
                      +|.++..+
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99988644

>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=99.72  E-value=2.2e-18  Score=165.11  Aligned_cols=80  Identities=23%  Similarity=0.485  Sum_probs=73.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++++|+++|+++|++||.|+.|.|+.+ .++.++|||||+|.+.++|.+||+.|||.. |+|  ..|.|.|
T Consensus       102 ~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~-i~g--r~i~V~~  178 (437)
T 3pgw_S          102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK-IDG--RRVLVDV  178 (437)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE-ECC--EEEEEEE
Confidence            579999999999999999999999999999999998 588999999999999999999999999987 565  7899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +...
T Consensus       179 a~~~  182 (437)
T 3pgw_S          179 ERGR  182 (437)
T ss_pred             eCCC
Confidence            8753

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.5e-17  Score=123.98  Aligned_cols=79  Identities=25%  Similarity=0.453  Sum_probs=72.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++++++|+++|++||.|++|+|+++. ++.++|||||+|++.++|.+|++.||+.. ++|  +.|+|+
T Consensus        15 ~~~~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           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQ-LFG--RVIKAS   91 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEE-ETT--EEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCe-eCC--cEEEEE
Confidence            36799999999999999999999999999999999984 68899999999999999999999999976 565  789999


Q ss_pred             ecC
Q 018554          180 WAD  182 (354)
Q Consensus       180 ~a~  182 (354)
                      ||+
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3e-17  Score=126.42  Aligned_cols=81  Identities=28%  Similarity=0.523  Sum_probs=73.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++++++|+++|+.||.|++|.|+++. ++.++|||||+|.+.++|.+|++.|||.. ++|  +.|.|+
T Consensus        22 ~~~~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           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD-LMG--QPISVD   98 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCB-SSS--SBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCE-ECC--cEEEEE
Confidence            46789999999999999999999999999999999984 68999999999999999999999999976 666  678999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        99 ~a~~~  103 (106)
T 1p27_B           99 WCFVR  103 (106)
T ss_dssp             ESEES
T ss_pred             eecCC
Confidence            98654

>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=99.72  E-value=4e-17  Score=123.68  Aligned_cols=85  Identities=19%  Similarity=0.294  Sum_probs=73.2

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||.|++|.++++      +|||||+|.+.++|++|++.||+.. +.+..+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~-~~~~g~   83 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFP-LGGPDR   83 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCB-CSSSSC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCE-eCCCCc
Confidence            345567899999999999999999999999999999998764      6799999999999999999998876 552248


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        84 ~l~V~~a~~~~~   95 (97)
T 1why_A           84 RLRVDFAKSGPS   95 (97)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            899999887643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.72  E-value=1.1e-17  Score=128.70  Aligned_cols=84  Identities=17%  Similarity=0.218  Sum_probs=73.4

Q ss_pred             ccCCCCCCeEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 018554            8 KKSSEERVKLFVGQVPKHM------TEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT   81 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~------te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~   81 (354)
                      ..+....++|||+|||+++      ++++|+++|++||.|.+|.|+  +.+|+++|||||+|.+.++|.+|++.||+.. 
T Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~-   85 (105)
T 2nlw_A            9 QEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYK-   85 (105)
T ss_dssp             CSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEE-
T ss_pred             CCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcc-
Confidence            3445567899999999999      789999999999999999988  4679999999999999999999999998866 


Q ss_pred             CCCCCc-cceeecccc
Q 018554           82 LPGASS-PLQVKYADG   96 (354)
Q Consensus        82 ~~g~~~-~l~v~~~~~   96 (354)
                      +.|  + .|+|.++..
T Consensus        86 ~~g--~~~l~V~~a~~   99 (105)
T 2nlw_A           86 LDK--QHTFRVNLFTD   99 (105)
T ss_dssp             CST--TCEEEEECSCC
T ss_pred             cCC--CceEEEEEcch
Confidence            555  6 889988764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.72  E-value=3.7e-17  Score=124.34  Aligned_cols=79  Identities=27%  Similarity=0.433  Sum_probs=72.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeE--------EEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCC
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD--------LQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEG  171 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~--------i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g  171 (354)
                      ..++|||+||+.++++++|+++|++||.|.+        ++|+++ .++.++|||||+|.+.++|++|++.|||.. ++|
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~-~~g   90 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE-FSG   90 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB-SSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE-eCC
Confidence            3689999999999999999999999999999        999998 578999999999999999999999999986 666


Q ss_pred             CceeEEEEecC
Q 018554          172 SSVPLVVKWAD  182 (354)
Q Consensus       172 ~~~~l~v~~a~  182 (354)
                        +.|+|++|+
T Consensus        91 --~~l~V~~A~   99 (99)
T 2la6_A           91 --NPIKVSFAT   99 (99)
T ss_dssp             --SBCEEEECC
T ss_pred             --cEEEEEecC
Confidence              678888874

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=127.29  Aligned_cols=82  Identities=22%  Similarity=0.345  Sum_probs=74.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhcc-CCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSI-YGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~-~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|+. ||.|++|+|+++.++.++|||||+|.+.++|.+|++.||+...++|  +.|.|+
T Consensus         8 ~~~~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            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGS--KPVRLS   85 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS--SCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCC--EeEEEE
Confidence            4689999999999999999999999 9999999999999999999999999999999999999999763566  578999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        86 ~a~~~   90 (104)
T 2dhg_A           86 VAIPK   90 (104)
T ss_dssp             BCCCC
T ss_pred             EccCC
Confidence            88655

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=6.6e-18  Score=132.83  Aligned_cols=83  Identities=13%  Similarity=0.161  Sum_probs=73.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFAL---VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~---v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ....+.++|||+|||+++|+++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++||+ +|+.. +.+ 
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~-~~g-   87 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRES-MGH-   87 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEE-ETT-
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCe-ECC-
Confidence            34567899999999999999999999999999   89999999987 9999999999999999999999 87754 555 


Q ss_pred             Cccceeecccc
Q 018554           86 SSPLQVKYADG   96 (354)
Q Consensus        86 ~~~l~v~~~~~   96 (354)
                       +.|+|.++..
T Consensus        88 -r~i~V~~a~~   97 (118)
T 2db1_A           88 -RYIEVFKSHR   97 (118)
T ss_dssp             -EEEEEEEECH
T ss_pred             -eEEEEEECCH
Confidence             7777776643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3e-17  Score=126.66  Aligned_cols=83  Identities=28%  Similarity=0.590  Sum_probs=74.9

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC--CCCcceEEEEEeCCHHHHHHHHHHh-CCCcccCCCcee
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS--QQTSKGCAFLKYETKEQALAALEAI-NGKHKMEGSSVP  175 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~--~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~~g~~~~  175 (354)
                      ....++|||+||+.++|+++|+++|++||.|++|+|+++.  ++.++|||||+|.+.++|.+|++.| |+.. ++|  +.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~-~~g--~~   88 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH-LYG--RR   88 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCB-SSS--CB
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCe-ECC--CE
Confidence            3446899999999999999999999999999999999984  7889999999999999999999999 8876 666  68


Q ss_pred             EEEEecCCh
Q 018554          176 LVVKWADTE  184 (354)
Q Consensus       176 l~v~~a~~~  184 (354)
                      |+|+|++.+
T Consensus        89 l~v~~a~~~   97 (107)
T 2cph_A           89 LVLEWADSE   97 (107)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEeCCCC
Confidence            999999765

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.72  E-value=1.2e-17  Score=122.17  Aligned_cols=73  Identities=19%  Similarity=0.253  Sum_probs=64.3

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554           14 RVKLFVGQVPKHM------TEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus        14 ~~~lfVg~Lp~~~------te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      +++|||+|||.++      ++++|+++|++||.|.+|.+.  +.+|+++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~-~~g--~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYK-LDK--Q   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCC-CSS--S
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcc-cCC--c
Confidence            4799999999999      789999999999999999987  4578999999999999999999999998877 444  4


Q ss_pred             -ccee
Q 018554           88 -PLQV   91 (354)
Q Consensus        88 -~l~v   91 (354)
                       .|+|
T Consensus        76 ~~l~V   80 (81)
T 2krb_A           76 HTFRV   80 (81)
T ss_dssp             SCCCC
T ss_pred             eeEEe
Confidence             4544

>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=99.72  E-value=6.7e-18  Score=130.41  Aligned_cols=85  Identities=15%  Similarity=0.258  Sum_probs=74.6

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFAL---VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~---v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ..+..+.++|||+|||+++|+++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++||+ +|+.. +.+
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~-~~g   81 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMY-MGQ   81 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCC-SSS
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcce-eCC
Confidence            445678899999999999999999999999998   89999999998 9999999999999999999999 87754 555


Q ss_pred             CCccceeeccccc
Q 018554           85 ASSPLQVKYADGE   97 (354)
Q Consensus        85 ~~~~l~v~~~~~~   97 (354)
                        +.|+|.++..+
T Consensus        82 --r~i~V~~a~~~   92 (107)
T 2lmi_A           82 --RYVEVYEINNE   92 (107)
T ss_dssp             --SCCCCEECCHH
T ss_pred             --eEEEEEECCHH
Confidence              67788776543

>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=99.72  E-value=5e-17  Score=126.89  Aligned_cols=84  Identities=29%  Similarity=0.529  Sum_probs=75.6

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCC------Cc
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEG------SS  173 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g------~~  173 (354)
                      ...++|||+||+.++|+++|+++|+.||.|++|+|+++.++.++|||||+|.+.++|.+|++.|||.. +++      ..
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF-IKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC-CCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCE-EcCCccccCCC
Confidence            34689999999999999999999999999999999999989999999999999999999999999987 532      23


Q ss_pred             eeEEEEecCCh
Q 018554          174 VPLVVKWADTE  184 (354)
Q Consensus       174 ~~l~v~~a~~~  184 (354)
                      +.|.|+|+++.
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            68999999753

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.4e-17  Score=121.16  Aligned_cols=80  Identities=29%  Similarity=0.513  Sum_probs=71.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ....+.++|||+|||.++++++|+++|++||.|.+|.++        +|||||+|.+.++|++|++.||+.. +.+  +.
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~   71 (90)
T 2dnq_A            3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYK-LHG--VN   71 (90)
T ss_dssp             SCSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCB-CSS--CB
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCc-cCC--cE
Confidence            456788999999999999999999999999999999987        5799999999999999999998866 555  88


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|.+++.+..
T Consensus        72 l~v~~a~~~~~   82 (90)
T 2dnq_A           72 INVEASKNKSK   82 (90)
T ss_dssp             CEEECSSCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999876654

>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=99.71  E-value=6.5e-18  Score=121.64  Aligned_cols=75  Identities=24%  Similarity=0.439  Sum_probs=66.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      +|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|++|++. ++.. +.|  +.++|+++
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-KYHN-VGL--SKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCC-BTT--BCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCe-ECC--EEEEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999985 4544 655  66666653

>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=4e-17  Score=125.08  Aligned_cols=82  Identities=28%  Similarity=0.505  Sum_probs=73.8

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||++++++++|+++|++||.|++|+|+++... ++|||||+|.+.++|.+|++.||+.. ++|  +.|+|+
T Consensus        13 ~~~~~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           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRK-ILG--KEVKVN   88 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCC-cCC--CeEEEE
Confidence            34689999999999999999999999999999999998544 68999999999999999999999977 565  789999


Q ss_pred             ecCChH
Q 018554          180 WADTEK  185 (354)
Q Consensus       180 ~a~~~~  185 (354)
                      |++...
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            998753

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3e-17  Score=124.82  Aligned_cols=83  Identities=23%  Similarity=0.419  Sum_probs=74.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCee-EEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc--eeE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIK-DLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS--VPL  176 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~-~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~--~~l  176 (354)
                      ..++|||+||+.++++++|+++|++||.|. +|+|++++ ++.++|||||+|.+.++|++|++.|||.. ++|+.  ++|
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g~~~~~~l   86 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKP-LPGATPAKRF   86 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSE-ESSCSSCEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCc-cCCCCcceeE
Confidence            468999999999999999999999999999 99999995 88999999999999999999999999976 66654  238


Q ss_pred             EEEecCCh
Q 018554          177 VVKWADTE  184 (354)
Q Consensus       177 ~v~~a~~~  184 (354)
                      +|.||+..
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            99998754

>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=99.71  E-value=2.9e-17  Score=136.99  Aligned_cols=87  Identities=21%  Similarity=0.282  Sum_probs=77.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|++++.||+++|||||+|.+.++|.+||+.||+.. +.+  +.|
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l  144 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE-IMG--QTI  144 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            34556789999999999999999999999999999999999999999999999999999999999998866 555  888


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      .|.|+..+..
T Consensus       145 ~V~~a~~~~~  154 (165)
T 1rk8_A          145 QVDWCFVKGP  154 (165)
T ss_dssp             EEEESEECC-
T ss_pred             EEEEecCCCC
Confidence            9998865543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.7e-17  Score=127.10  Aligned_cols=81  Identities=25%  Similarity=0.386  Sum_probs=74.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++++++|+++|++||.|++|.|+++. ++.++|||||+|.+.++|++|++.||+.. ++|  +.|.|+
T Consensus        12 ~~~~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           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAE-LDG--RELRVQ   88 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCC-BTT--BCCEEE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCE-ECC--cEEEEE
Confidence            46899999999999999999999999999999999984 68899999999999999999999999977 666  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus        89 ~a~~~   93 (103)
T 2dnm_A           89 VARYG   93 (103)
T ss_dssp             ECSSC
T ss_pred             ECCcC
Confidence            98764

>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=2.8e-17  Score=119.81  Aligned_cols=73  Identities=19%  Similarity=0.256  Sum_probs=67.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +..|||+||++.+||++|+++|.+||+|.++++..     +||||||+|.++++|.+|++.||+.. ++|  +.|+|++|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~-l~g--r~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCV-LAN--TTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCE-ECC--cEEEEEEC
Confidence            46799999999999999999999999999999986     49999999999999999999999976 666  78999999


Q ss_pred             C
Q 018554          182 D  182 (354)
Q Consensus       182 ~  182 (354)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.1e-17  Score=126.37  Aligned_cols=82  Identities=28%  Similarity=0.484  Sum_probs=75.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|++||.|++|+|+++ .++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|+
T Consensus        11 ~~~~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           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--RTIRVN   87 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE-ETT--EEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEE
Confidence            4689999999999999999999999999999999998 578899999999999999999999999976 565  789999


Q ss_pred             ecCChH
Q 018554          180 WADTEK  185 (354)
Q Consensus       180 ~a~~~~  185 (354)
                      |++.+.
T Consensus        88 ~a~~~~   93 (102)
T 2cqb_A           88 LAKPMR   93 (102)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            997653

>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=99.71  E-value=1.3e-17  Score=127.03  Aligned_cols=77  Identities=21%  Similarity=0.230  Sum_probs=69.0

Q ss_pred             ccceEEEecCCC-CCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-ccCCCceeEEE
Q 018554          101 LEHKLFIGMLPK-NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH-KMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~-~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~~g~~~~l~v  178 (354)
                      ..++|||+||++ ++|++||+++|++||.|.+|.|+++     ++||||+|++.++|.+|++.||+.. .++|  ++|.|
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G--r~l~V   86 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFG--KPVRV   86 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETT--EECEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECC--cEEEE
Confidence            468999999999 9999999999999999999999976     6899999999999999999998753 3566  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .||+..
T Consensus        87 ~~a~~~   92 (102)
T 1x4d_A           87 HLSQKY   92 (102)
T ss_dssp             EEECCC
T ss_pred             EECCCC
Confidence            999754

>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=99.71  E-value=3.7e-17  Score=124.34  Aligned_cols=84  Identities=31%  Similarity=0.481  Sum_probs=73.9

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .......+.++|||+|||.++++++|+++|++||+|.+|+++++      +|||||+|.+.++|++|++.||+.. +.+ 
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~-~~g-   78 (99)
T 2cpj_A            7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMP-LRG-   78 (99)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCC-BTT-
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCE-eCC-
Confidence            34456678899999999999999999999999999999999865      5799999999999999999998877 555 


Q ss_pred             Cccceeecccccc
Q 018554           86 SSPLQVKYADGEL   98 (354)
Q Consensus        86 ~~~l~v~~~~~~~   98 (354)
                       +.|+|.+++.+.
T Consensus        79 -~~l~v~~a~~~~   90 (99)
T 2cpj_A           79 -KQLRVRFACHSA   90 (99)
T ss_dssp             -BCCEEEESSCCS
T ss_pred             -ceEEEEEcCCCC
Confidence             889999987654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.2e-17  Score=124.79  Aligned_cols=80  Identities=31%  Similarity=0.527  Sum_probs=74.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEE-EEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i-~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .++|||+||+.++++++|+++|++||.|.++ +|+++ .++.++|||||+|++.++|++|++.||+.. ++|  +.|+|+
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v~   81 (96)
T 1x5t_A            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY-LCN--RPITVS   81 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCE-ETT--EECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEE
Confidence            5799999999999999999999999999999 99998 688999999999999999999999999987 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        82 ~a~~~   86 (96)
T 1x5t_A           82 YAFKK   86 (96)
T ss_dssp             ESCCC
T ss_pred             Eeccc
Confidence            99765

>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=99.71  E-value=2e-17  Score=128.35  Aligned_cols=82  Identities=34%  Similarity=0.523  Sum_probs=74.9

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++|+++|+++|+.||.|++|.|+.+ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|.|
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V  100 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE-IMG--QTIQV  100 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE-ECC--cEEEE
Confidence            34689999999999999999999999999999999998 578999999999999999999999999987 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus       101 ~~a~~~  106 (110)
T 1oo0_B          101 DWCFVK  106 (110)
T ss_dssp             EESEES
T ss_pred             EEcccC
Confidence            998754

>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=99.71  E-value=7e-18  Score=132.01  Aligned_cols=88  Identities=23%  Similarity=0.347  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||.++|+++|+++|++||.|.+|.+..+..+++++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~l   97 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYK-LYG--KIL   97 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCB-CSS--CBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCE-eCC--cEE
Confidence            44567999999999999999999999999998544333333378999999999999999999999998866 444  889


Q ss_pred             eeecccccccc
Q 018554           90 QVKYADGELER  100 (354)
Q Consensus        90 ~v~~~~~~~~~  100 (354)
                      +|.+++.+..+
T Consensus        98 ~v~~a~~~~~~  108 (115)
T 2cpx_A           98 VIEFGKNKKQR  108 (115)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEEccCCCCC
Confidence            99998776543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.1e-17  Score=126.20  Aligned_cols=85  Identities=19%  Similarity=0.380  Sum_probs=73.5

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .....+.++|||+|||.++++++|+++|++||.|   +++++ .+++++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~   81 (101)
T 2fc9_A            9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKRE-IEG--R   81 (101)
T ss_dssp             CCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEE-ETT--E
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCE-eCC--e
Confidence            3456788999999999999999999999999977   56677 579999999999999999999999998866 555  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++.+..
T Consensus        82 ~l~v~~a~~~~~   93 (101)
T 2fc9_A           82 AIRLELQGPRGS   93 (101)
T ss_dssp             EEEEEECSSCCC
T ss_pred             EEEEEEcCCCCC
Confidence            899999876543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.71  E-value=3.4e-17  Score=125.00  Aligned_cols=79  Identities=22%  Similarity=0.529  Sum_probs=69.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||.++++++|+++|++||.|.+|+++      +++|||||+|.+.++|++|++.||+.. +.+  +.
T Consensus        22 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~   92 (101)
T 2la4_A           22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFP-FQG--RN   92 (101)
T ss_dssp             TSCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCE-ETT--EE
T ss_pred             cCCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCe-ECC--eE
Confidence            345567999999999999999999999999999999997      357899999999999999999998876 555  88


Q ss_pred             ceeecccc
Q 018554           89 LQVKYADG   96 (354)
Q Consensus        89 l~v~~~~~   96 (354)
                      |+|.|++.
T Consensus        93 l~V~~a~~  100 (101)
T 2la4_A           93 LRTGWGKE  100 (101)
T ss_dssp             CCCCBCCC
T ss_pred             EEEEeccC
Confidence            89988865

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.3e-17  Score=126.18  Aligned_cols=81  Identities=32%  Similarity=0.555  Sum_probs=73.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++++++|+++|++||.|++|+|+++ .++.++|||||+|.+.++|.+|++.||+.. ++|  +.|+|+
T Consensus        11 ~~~~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           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS-VDG--RQIRVD   87 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCC-TTS--CCCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEEEE
Confidence            4689999999999999999999999999999999998 478889999999999999999999999987 666  678888


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus        88 ~a~~~   92 (102)
T 1x5s_A           88 QAGKS   92 (102)
T ss_dssp             EEECC
T ss_pred             ECCCC
Confidence            88654

>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=99.70  E-value=2.5e-17  Score=128.66  Aligned_cols=85  Identities=14%  Similarity=0.209  Sum_probs=76.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCe-eEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTI-KDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v-~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++|+++|+++|+.||.| .+|+|++|.++.++|||||+|++.++|.+||+. |+.. ++|  +.|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~-~~g--r~i~v   88 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKK-LNG--REAFV   88 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEE-ETT--EEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCc-cCC--eEEEE
Confidence            346899999999999999999999999999 899999999999999999999999999999987 8865 666  78999


Q ss_pred             EecCChHHHH
Q 018554          179 KWADTEKERQ  188 (354)
Q Consensus       179 ~~a~~~~~~~  188 (354)
                      .++..+..+.
T Consensus        89 ~~a~~~~~~~   98 (114)
T 2cpy_A           89 HVVTLEDMRE   98 (114)
T ss_dssp             EEECHHHHHH
T ss_pred             EECCHHHHHH
Confidence            9998765544

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.70  E-value=3e-17  Score=129.02  Aligned_cols=80  Identities=21%  Similarity=0.393  Sum_probs=72.7

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++++++|+++|++||.|++|+|+++ .++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|
T Consensus        38 ~~~~~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           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQ-VGT--KRLKV  114 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCE-ETT--EECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            34689999999999999999999999999999999998 578999999999999999999999999987 665  68899


Q ss_pred             EecC
Q 018554          179 KWAD  182 (354)
Q Consensus       179 ~~a~  182 (354)
                      +|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            8874

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6.1e-17  Score=122.66  Aligned_cols=82  Identities=20%  Similarity=0.338  Sum_probs=71.0

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .+....++|||+|||+++++++|+++|++||.|. +.++.+    +++|||||+|.+.++|++|++.||+.. +.+  +.
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~   85 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLR-LGT--DT   85 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCC-SSS--SC
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCE-ECC--cE
Confidence            3456689999999999999999999999999997 677654    688999999999999999999998876 555  78


Q ss_pred             ceeecccccc
Q 018554           89 LQVKYADGEL   98 (354)
Q Consensus        89 l~v~~~~~~~   98 (354)
                      |+|.+++.+.
T Consensus        86 l~V~~a~~~~   95 (97)
T 2e5j_A           86 LRVALARQQR   95 (97)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEcCCCC
Confidence            9999887654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=4.1e-17  Score=123.82  Aligned_cols=80  Identities=30%  Similarity=0.449  Sum_probs=72.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC----CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS----QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~----~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      .++|||+||++++++++|+++|++||.|++|.|+++.    ++.++|||||+|.+.++|++|++.||+.. ++|  +.|.
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~   81 (98)
T 2cpf_A            5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT-VDG--HKLE   81 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE-ETT--EECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCe-eCC--eEEE
Confidence            5789999999999999999999999999999999874    33789999999999999999999999987 665  7899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+|++.+
T Consensus        82 V~~a~~~   88 (98)
T 2cpf_A           82 VRISERA   88 (98)
T ss_dssp             EECSSCS
T ss_pred             EEEccCC
Confidence            9999765

>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=3.9e-17  Score=123.51  Aligned_cols=78  Identities=14%  Similarity=0.233  Sum_probs=71.4

Q ss_pred             cceEEEecCCCCCCHHHHH----HhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          102 EHKLFIGMLPKNVSEAEVS----ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~----~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      .++|||+||++++++++|+    ++|++||.|++|+|+++..+  ++||||+|++.++|++|++.|||.. ++|  +.|+
T Consensus         9 ~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~-~~g--r~l~   83 (96)
T 2dgx_A            9 GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYK-IGS--KKIL   83 (96)
T ss_dssp             CEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEE-ETT--EEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEE
Confidence            5789999999999999999    99999999999999998655  8999999999999999999999976 565  7899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |++|+..
T Consensus        84 V~~a~~~   90 (96)
T 2dgx_A           84 VSLATGA   90 (96)
T ss_dssp             EEECCCS
T ss_pred             EEEcCCC
Confidence            9999754

>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=99.70  E-value=5.8e-17  Score=125.86  Aligned_cols=82  Identities=28%  Similarity=0.458  Sum_probs=74.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhC------CCcccCCC
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAIN------GKHKMEGS  172 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~------g~~~~~g~  172 (354)
                      ...++|||+||++++|+++|+++|++||.|++|+|+++ .++.++|||||+|.+.++|.+|++.||      +.. ++| 
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~-~~g-   90 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK-LDG-   90 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE-SSS-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE-EcC-
Confidence            34678999999999999999999999999999999998 478899999999999999999999999      765 666 


Q ss_pred             ceeEEEEecCCh
Q 018554          173 SVPLVVKWADTE  184 (354)
Q Consensus       173 ~~~l~v~~a~~~  184 (354)
                       +.|+|+|+..+
T Consensus        91 -~~l~v~~a~~~  101 (111)
T 1x4h_A           91 -RQLKVDLAVTR  101 (111)
T ss_dssp             -CEEEEECCCCC
T ss_pred             -EEEEEEECCCC
Confidence             68999999765

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.70  E-value=4.9e-17  Score=121.85  Aligned_cols=80  Identities=24%  Similarity=0.344  Sum_probs=72.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||+.++++++|+++|++||.|++++|.++ ++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|+|
T Consensus         7 ~~~~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            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMK-LSG--REIDVRI   82 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCC-BTT--BCCCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEEE
Confidence            3679999999999999999999999999999999985 77889999999999999999999999977 666  6889999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++..
T Consensus        83 a~~~   86 (92)
T 2dgv_A           83 DRNA   86 (92)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            8764

>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=99.70  E-value=2.6e-17  Score=128.59  Aligned_cols=79  Identities=25%  Similarity=0.443  Sum_probs=69.7

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-cccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK-HKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++|+++|+++|++||.|++|+|+++     ||||||+|++.++|.+|++.|++. ..++|  +.|.|
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G--r~l~V  101 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRG--QPIYI  101 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTT--BCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--eEEEE
Confidence            34689999999999999999999999999999999986     899999999999999999999853 33666  68999


Q ss_pred             EecCChH
Q 018554          179 KWADTEK  185 (354)
Q Consensus       179 ~~a~~~~  185 (354)
                      .|++.+.
T Consensus       102 ~~a~~k~  108 (119)
T 2ad9_A          102 QFSNHKE  108 (119)
T ss_dssp             EECSSSS
T ss_pred             EEccCCC
Confidence            9997653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.54  E-value=9.6e-19  Score=137.23  Aligned_cols=88  Identities=19%  Similarity=0.394  Sum_probs=79.0

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDE--------VNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~--------i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      ++..+.++|||+|||.++++++|+++|++||.|.+        |.|++|+.+++++|||||+|.+.++|++|++.||+..
T Consensus         2 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   81 (116)
T 2lcw_A            2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   81 (116)
Confidence            34567899999999999999999999999999999        9999999999999999999999999999999998866


Q ss_pred             cCCCCCccceeeccccccc
Q 018554           81 TLPGASSPLQVKYADGELE   99 (354)
Q Consensus        81 ~~~g~~~~l~v~~~~~~~~   99 (354)
                       +.+  +.|+|.+++.+..
T Consensus        82 -~~g--~~l~V~~a~~~~~   97 (116)
T 2lcw_A           82 -FSG--NPIKVSFATRRAD   97 (116)
Confidence             555  7888988876544

>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=99.70  E-value=6.3e-17  Score=120.40  Aligned_cols=79  Identities=22%  Similarity=0.387  Sum_probs=72.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||+.++++++|+++|+.||.|.+++++++. ++.++|||||+|.+.++|++|+ .||+.. ++|  +.|+|++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~-~~g--~~l~V~~   81 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESL-FRG--RQIKVIP   81 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCE-ETT--EECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCE-ECC--cEEEEEE
Confidence            5799999999999999999999999999999999984 8899999999999999999999 999987 565  7899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +++.
T Consensus        82 a~~~   85 (89)
T 3ucg_A           82 KRTN   85 (89)
T ss_dssp             TTTT
T ss_pred             ccCC
Confidence            8753

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.4e-17  Score=126.88  Aligned_cols=82  Identities=24%  Similarity=0.454  Sum_probs=73.7

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ....++|||+||+.++|+++|+++|++||.|++|+++++..+ ++|||||+|++.++|++|++.|||.. ++|  +.|+|
T Consensus        26 ~~~~~~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           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTV-VEG--RKIEV  101 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTB-CTTEEEEECCCSHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCC-CceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            344789999999999999999999999999999999988643 79999999999999999999999987 666  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      ++++.+
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            998764

>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=99.70  E-value=3e-17  Score=131.06  Aligned_cols=82  Identities=28%  Similarity=0.400  Sum_probs=74.8

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++|+++|+++|++||.|++|+|+++ .++.++|||||+|++.++|++|++.|||.. ++|  +.|+|
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~-i~g--~~l~V  120 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME-LDG--RRIRV  120 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCC-SSS--SCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            34689999999999999999999999999999999998 478899999999999999999999999976 666  68899


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus       121 ~~a~~~  126 (129)
T 2kxn_B          121 DFSITK  126 (129)
T ss_dssp             SCCSSS
T ss_pred             EEecCC
Confidence            998765

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.9e-17  Score=126.91  Aligned_cols=83  Identities=22%  Similarity=0.344  Sum_probs=74.5

Q ss_pred             cccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554           98 LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus        98 ~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      .+...++|||+||++++|+++|+++|++||.|++|+|+++ .++.++|||||+|.+.++|++|++.+++ . ++|  +.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~-~~g--~~l   88 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-I-IDG--RKA   88 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-E-ETT--EEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-c-CCC--EEE
Confidence            3445789999999999999999999999999999999998 4789999999999999999999999998 4 666  789


Q ss_pred             EEEecCCh
Q 018554          177 VVKWADTE  184 (354)
Q Consensus       177 ~v~~a~~~  184 (354)
                      +|+|+...
T Consensus        89 ~V~~a~~~   96 (116)
T 2cqd_A           89 NVNLAYLG   96 (116)
T ss_dssp             EEEESTTT
T ss_pred             EEEEcccC
Confidence            99998644

>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=99.70  E-value=6e-17  Score=119.48  Aligned_cols=81  Identities=22%  Similarity=0.441  Sum_probs=69.9

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHh-cCCccCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC-HNKKTLPG   84 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l-~~~~~~~g   84 (354)
                      ....+....++|||+|||.++++++|+++|++||.|.+|+++++      +|||||+|.+.++|++|++.| ++.. +.+
T Consensus         4 ~~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~-~~g   76 (85)
T 2ytc_A            4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLI-VNG   76 (85)
T ss_dssp             CCCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCE-ETT
T ss_pred             CCCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCee-ECC
Confidence            34455678899999999999999999999999999999999874      689999999999999999998 5544 655


Q ss_pred             CCccceeeccc
Q 018554           85 ASSPLQVKYAD   95 (354)
Q Consensus        85 ~~~~l~v~~~~   95 (354)
                        +.|+|.|++
T Consensus        77 --~~l~v~~ak   85 (85)
T 2ytc_A           77 --RRLNVKWGR   85 (85)
T ss_dssp             --EECCEEECC
T ss_pred             --CEEEEEecC
Confidence              788888764

>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=99.70  E-value=1.1e-16  Score=118.73  Aligned_cols=79  Identities=22%  Similarity=0.375  Sum_probs=70.4

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      +...++|||+||+.++++++|+++|++||.|.+++++++. ++.++|||||+|.+.++|.+|++. ++.. ++|  +.|+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~-~~g--~~i~   83 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHR-LDG--RVID   83 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEE-ETT--EEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCE-ECC--EEEE
Confidence            3446899999999999999999999999999999999984 799999999999999999999965 7755 676  6888


Q ss_pred             EEec
Q 018554          178 VKWA  181 (354)
Q Consensus       178 v~~a  181 (354)
                      |++|
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8876

>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=99.70  E-value=8.1e-17  Score=122.60  Aligned_cols=77  Identities=27%  Similarity=0.477  Sum_probs=68.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-cccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK-HKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|++||.|++|.|+++     ||||||+|++.++|.+|++.|++. ..++|  ++|.|.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G--r~l~V~   86 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRN--QPIYIQ   86 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETT--EECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--cEEEEE
Confidence            4679999999999999999999999999999999976     899999999999999999987532 23565  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        87 ~a~~~   91 (101)
T 2cq1_A           87 YSNHK   91 (101)
T ss_dssp             ECSCS
T ss_pred             EcCcc
Confidence            99765

>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=99.70  E-value=4.4e-17  Score=126.68  Aligned_cols=80  Identities=24%  Similarity=0.417  Sum_probs=72.1

Q ss_pred             cceEEEecCCCCCCHHHHH---HhhccCCCeeEEEEeeCC-C---CCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554          102 EHKLFIGMLPKNVSEAEVS---ALFSIYGTIKDLQILRGS-Q---QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~---~~F~~~G~v~~i~i~~~~-~---~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      .++|||+||++++++++|+   ++|++||.|++|.|+++. +   +.++|||||+|++.++|++|++.|||.. ++|  +
T Consensus        15 ~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~-~~g--r   91 (111)
T 2cpi_A           15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV-VDG--R   91 (111)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE-ETT--E
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCE-ECC--E
Confidence            5789999999999999999   999999999999999885 2   3566999999999999999999999987 666  7


Q ss_pred             eEEEEecCCh
Q 018554          175 PLVVKWADTE  184 (354)
Q Consensus       175 ~l~v~~a~~~  184 (354)
                      .|+|+||.++
T Consensus        92 ~l~V~~a~~k  101 (111)
T 2cpi_A           92 TLKASLGTTK  101 (111)
T ss_dssp             EEEEESCCCC
T ss_pred             EEEEEecccc
Confidence            8999999765

>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=99.69  E-value=3.6e-17  Score=127.73  Aligned_cols=83  Identities=24%  Similarity=0.504  Sum_probs=74.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++++++|+++|+.||.|++|+|+.+. ++.++|||||+|.+.++|.+|+ .||+.. ++|  +.|.|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g--~~l~V   98 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQR-LLG--VPIIV   98 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEE-ETT--EEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCE-eCC--eEEEE
Confidence            346899999999999999999999999999999999985 5889999999999999999999 999976 565  78999


Q ss_pred             EecCChHH
Q 018554          179 KWADTEKE  186 (354)
Q Consensus       179 ~~a~~~~~  186 (354)
                      +|++.+..
T Consensus        99 ~~a~~~~~  106 (114)
T 2cq4_A           99 QASQAEKN  106 (114)
T ss_dssp             EEHHHHHH
T ss_pred             EecCCCcc
Confidence            99865543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.69  E-value=7.8e-17  Score=127.79  Aligned_cols=82  Identities=26%  Similarity=0.445  Sum_probs=75.2

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++++++|+++|++||.|++|+|.++.++.++|||||+|++.++|.+|++.|||.. ++|  +.|+|+
T Consensus        33 ~~~~~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           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVP-LDG--RPMDIQ  109 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEE-SSS--CEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCE-ECC--cEEEEE
Confidence            34689999999999999999999999999999999999888999999999999999999999999976 666  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ||...
T Consensus       110 ~a~~~  114 (124)
T 2kt5_A          110 LVASQ  114 (124)
T ss_dssp             EECCT
T ss_pred             EeCCC
Confidence            98754

>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=99.69  E-value=2.7e-17  Score=130.08  Aligned_cols=83  Identities=18%  Similarity=0.225  Sum_probs=71.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD--EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~--~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      .+....++|||+|||+++||++|+++|+.| .|.  +|+|++|+. |+++|||||+|.+.++|++||+. ++ ..+.+  
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~-~~l~g--  110 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HK-ERIGH--  110 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TT-CCBTT--
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CC-CEECC--
Confidence            455678999999999999999999999999 666  999999987 99999999999999999999986 45 44666  


Q ss_pred             ccceeeccccc
Q 018554           87 SPLQVKYADGE   97 (354)
Q Consensus        87 ~~l~v~~~~~~   97 (354)
                      +.|+|..+..+
T Consensus       111 R~I~V~~a~~~  121 (126)
T 2hgm_A          111 RYIEVFKSSQE  121 (126)
T ss_dssp             BCCCCEEECHH
T ss_pred             EEEEEEECCHH
Confidence            67777766543

>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=99.69  E-value=1.7e-17  Score=128.37  Aligned_cols=83  Identities=19%  Similarity=0.287  Sum_probs=69.3

Q ss_pred             ccCCCCCCeEEE--cCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc--CC
Q 018554            8 KKSSEERVKLFV--GQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT--LP   83 (354)
Q Consensus         8 ~~~~~~~~~lfV--g~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~--~~   83 (354)
                      +....+.++|||  |||+++++|++|+++|++||+|.+|.|+.      .||||||+|.+.++|++|++.||++.+  ..
T Consensus        19 ~~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~l   92 (114)
T 2cq2_A           19 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDL   92 (114)
T ss_dssp             CCCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             cCCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEcccc
Confidence            345667889999  88999999999999999999999998764      368999999999999999999999864  23


Q ss_pred             CCCccceeecccc
Q 018554           84 GASSPLQVKYADG   96 (354)
Q Consensus        84 g~~~~l~v~~~~~   96 (354)
                      +..++|.|.+++.
T Consensus        93 g~g~~l~v~~a~~  105 (114)
T 2cq2_A           93 GQKITLYLNFVEK  105 (114)
T ss_dssp             SCEEECEEEEESC
T ss_pred             CCCcEEEEEeccc
Confidence            3357788776653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.1e-17  Score=126.20  Aligned_cols=83  Identities=25%  Similarity=0.384  Sum_probs=75.4

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCee--------EEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCccc
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIK--------DLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKM  169 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~--------~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  169 (354)
                      ....++|||+||++++|+++|+++|++||.|.        .|+|+.+ .++.++|||||+|.+.++|.+|++.||+.. +
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~   90 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD-F   90 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE-E
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc-c
Confidence            34468999999999999999999999999999        6999998 689999999999999999999999999987 5


Q ss_pred             CCCceeEEEEecCCh
Q 018554          170 EGSSVPLVVKWADTE  184 (354)
Q Consensus       170 ~g~~~~l~v~~a~~~  184 (354)
                      +|  +.|+|+|++.+
T Consensus        91 ~g--~~l~V~~a~~~  103 (113)
T 2cpe_A           91 QG--SKLKVSLARKK  103 (113)
T ss_dssp             TT--EECEEECSSCC
T ss_pred             CC--CEEEEEECCCC
Confidence            55  78999998765

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.9e-17  Score=127.97  Aligned_cols=80  Identities=20%  Similarity=0.223  Sum_probs=69.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+.++|||+|||+++|++||+++|+.| .|.+|+|++|+. |+++|||||+|.+.++|++|| .+|+.. +.+  +.|.
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~-~~g--r~i~   86 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRML-MIQ--RYVE   86 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEE-ETT--EEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCe-ECC--eEEE
Confidence            3456799999999999999999999999 899999999986 999999999999999999999 676644 655  6777


Q ss_pred             eecccc
Q 018554           91 VKYADG   96 (354)
Q Consensus        91 v~~~~~   96 (354)
                      |..+..
T Consensus        87 V~~a~~   92 (109)
T 2dnn_A           87 VSPATE   92 (109)
T ss_dssp             EEECCH
T ss_pred             EEECCc
Confidence            766543

>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=99.69  E-value=7.1e-17  Score=123.67  Aligned_cols=78  Identities=15%  Similarity=0.225  Sum_probs=68.9

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-ccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH-KMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~~g~~~~l~v  178 (354)
                      ...++|||+||++++++++|+++|++||.|++|.|+++     ||||||+|++.++|.+|++.|++.. .++|  ++|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G--r~l~V   85 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAG--QQAFF   85 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSS--SBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--EEEEE
Confidence            34689999999999999999999999999999999875     8999999999999999999997653 3566  68999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .|++.+
T Consensus        86 ~~a~~~   91 (104)
T 1wex_A           86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEccCc
Confidence            999764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-16  Score=119.34  Aligned_cols=79  Identities=22%  Similarity=0.298  Sum_probs=72.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||++++++++|+++|+.| .|.+|+|+++.++.++|||||+|++.++|.+|++ ||+.. ++|  +.|.|.+
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~-~~g--r~i~v~~   83 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREY-MGG--RYIEVFR   83 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEE-ETT--EEEEEEE
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCce-eCC--cEEEEEE
Confidence            36899999999999999999999999 9999999999889999999999999999999999 99976 666  6899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++.+
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            8754

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.69  E-value=6.5e-17  Score=130.89  Aligned_cols=81  Identities=26%  Similarity=0.502  Sum_probs=74.4

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++|+++|+++|+.||.|++|+|+++. ++.++|||||+|++.++|.+|++.||+.. ++|  +.|+|+
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~  117 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN-ILN--KRLKVA  117 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEE-CSS--CEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEEEE
Confidence            36899999999999999999999999999999999984 68899999999999999999999999976 666  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus       118 ~a~~~  122 (139)
T 1u6f_A          118 LAASG  122 (139)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            99765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.69  E-value=1.4e-16  Score=122.07  Aligned_cols=79  Identities=20%  Similarity=0.416  Sum_probs=72.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++++++|+++|+.|| |++|+|+++. ++.++|||||+|++.++|++|+ .||+.. ++|  +.|+|+
T Consensus        14 ~~~~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           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGAL-LGD--RSLRVD   88 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCE-ETT--EECEEE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCe-ECC--eEEEEE
Confidence            368999999999999999999999997 9999999995 6899999999999999999999 899976 565  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        89 ~a~~~   93 (103)
T 2dng_A           89 IAEGR   93 (103)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            98765

>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=99.69  E-value=7.6e-17  Score=124.67  Aligned_cols=83  Identities=18%  Similarity=0.173  Sum_probs=71.5

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC---
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA---   85 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~---   85 (354)
                      ......++|||+|||+++++++|+++|++||+|.+|.|++|       |||||+|.+.++|++||+.||+..+ .+.   
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~-~g~~~~   81 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKF-RSHEGE   81 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEE-ECTTSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCc-cCCcCc
Confidence            34567899999999999999999999999999999999887       7999999999999999999988764 332   


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                      .+.|+|.+++.+..
T Consensus        82 ~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           82 TAYIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEEEESSCCSC
T ss_pred             ceEEEEEeCCCCCC
Confidence            27788888876543

>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=99.69  E-value=2.6e-17  Score=122.18  Aligned_cols=80  Identities=28%  Similarity=0.505  Sum_probs=71.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCC-cceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQT-SKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .++|||+||+.++|+++|+++|++||.|.++.++.+. ++. ++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~   80 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ-IDG--QEITAT   80 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCe-ECC--eEEEEE
Confidence            5789999999999999999999999999999999885 333 79999999999999999999999987 665  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ++.+.
T Consensus        81 ~a~~~   85 (88)
T 4a8x_A           81 AVLAP   85 (88)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            98654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=7.6e-17  Score=124.62  Aligned_cols=82  Identities=28%  Similarity=0.490  Sum_probs=70.4

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ........++|||+|||.++++++|+++|++||.|.+|.++        +|||||+|.+.++|++|++.||+.. +.+  
T Consensus        24 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--   92 (108)
T 2jvo_A           24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKS-FAN--   92 (108)
T ss_dssp             ----CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCE-ETT--
T ss_pred             ccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCE-ECC--
Confidence            34456788999999999999999999999999999999997        6899999999999999999998877 444  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|+|.+++.+..
T Consensus        93 ~~l~V~~a~~~~~  105 (108)
T 2jvo_A           93 QPLEVVYSKLPAK  105 (108)
T ss_dssp             EECEEESCSCCC-
T ss_pred             eEEEEEEecCCCC
Confidence            8899999876544

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=9.1e-17  Score=124.42  Aligned_cols=82  Identities=16%  Similarity=0.391  Sum_probs=73.1

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .+....++|||+|||.++++++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.|++.. +.+  +.
T Consensus        20 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~   90 (109)
T 1x4g_A           20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTT-IEG--HV   90 (109)
T ss_dssp             HSCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCE-ETT--EE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCE-ECC--cE
Confidence            35667899999999999999999999999999999999887      6799999999999999999998866 555  88


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|.|++.+..
T Consensus        91 l~v~~a~~~~~  101 (109)
T 1x4g_A           91 VKCYWGKESPD  101 (109)
T ss_dssp             CEEECCCCCCS
T ss_pred             EEEEecCCCCC
Confidence            99999876544

>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=7e-17  Score=126.92  Aligned_cols=80  Identities=16%  Similarity=0.158  Sum_probs=73.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCC---eeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGT---IKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~---v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ..++|||+||++++|+++|+++|+.||.   |.+|+|+++..++++|||||+|++.++|++||+ +|+.. ++|  +.|+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~-~~g--r~i~   91 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRES-MGH--RYIE   91 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEE-ETT--EEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCe-ECC--eEEE
Confidence            4678999999999999999999999999   899999999889999999999999999999999 89966 666  6899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |.++..+
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998644

>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=99.69  E-value=1.2e-16  Score=133.81  Aligned_cols=87  Identities=39%  Similarity=0.681  Sum_probs=78.9

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||+|||.++|+++|+++|++||.|.+|.+++|.. |+++|||||+|.+.++|.+|++.||+..+..+..+
T Consensus        89 ~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~-g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~  167 (175)
T 3nmr_A           89 KNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSS  167 (175)
T ss_dssp             CCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSS
T ss_pred             ccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC-CCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCC
Confidence            33455789999999999999999999999999999999999974 89999999999999999999999999887776678


Q ss_pred             cceeeccc
Q 018554           88 PLQVKYAD   95 (354)
Q Consensus        88 ~l~v~~~~   95 (354)
                      .|.|+|++
T Consensus       168 ~l~V~~ad  175 (175)
T 3nmr_A          168 PMVVKFAD  175 (175)
T ss_dssp             CCEEEECC
T ss_pred             CeEEEecC
Confidence            99999874

>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=4.1e-17  Score=117.42  Aligned_cols=74  Identities=22%  Similarity=0.401  Sum_probs=67.7

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +|||+|||+++++++|+++|++||.|.++.++++. ++.++|||||+|++.++|++|++ +|+.. ++|  +.|+|+||
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-IHFHE-INN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCC-SSS--CCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCE-ECC--EEEEEEeC
Confidence            59999999999999999999999999999999985 78999999999999999999997 89976 666  57888875

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.69  E-value=9.7e-17  Score=135.16  Aligned_cols=86  Identities=22%  Similarity=0.373  Sum_probs=77.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++++++|+++|++||.|++|.|+.|+ +++++|||||+|.+.++|++|++.|++.. +.+  +.|
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~-l~G--r~l  159 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVP-LDG--RPM  159 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCB-CSS--SBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            34557899999999999999999999999999999999999 89999999999999999999999998876 555  888


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.++.....
T Consensus       160 ~V~~a~~~~~  169 (177)
T 2f3j_A          160 DIQLVASQID  169 (177)
T ss_dssp             EEEEESSGGG
T ss_pred             EEEEecCCCC
Confidence            9988876543

>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=99.68  E-value=5.4e-17  Score=122.36  Aligned_cols=79  Identities=19%  Similarity=0.263  Sum_probs=71.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|++||.|+++.++.+ .++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--r~l~v~~   91 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP-IGS--RKVKLSG   91 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCe-ECC--cEEEEEe
Confidence            578999999999999999999999999998888876 578899999999999999999999999987 565  7899988


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      +..
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            753

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.9e-17  Score=129.61  Aligned_cols=80  Identities=16%  Similarity=0.265  Sum_probs=68.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCe----eEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALV----DEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v----~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ..+.++|||+|||+++|++||+++|++||.|    .+|+|++|+ +|+++|||||+|.+.++|++||+. |+ ..+.+  
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~-~~l~g--   94 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HK-DLLGK--   94 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TT-EESSS--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CC-CeeCC--
Confidence            4678999999999999999999999999975    689999995 799999999999999999999986 55 44655  


Q ss_pred             ccceeeccc
Q 018554           87 SPLQVKYAD   95 (354)
Q Consensus        87 ~~l~v~~~~   95 (354)
                      +.|.|..+.
T Consensus        95 R~i~V~~a~  103 (123)
T 2dha_A           95 RYIELFRST  103 (123)
T ss_dssp             CEECCEEEC
T ss_pred             eEEEEEECC
Confidence            566665543

>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=99.68  E-value=5.4e-17  Score=123.14  Aligned_cols=79  Identities=19%  Similarity=0.258  Sum_probs=71.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++++++|+++|++||.|+++.++.+ .++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|++
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~l~V~~   91 (98)
T 2cqp_A           15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP-IGS--RKVKLVL   91 (98)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCE-ETT--EECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCe-eCC--eEEEEEE
Confidence            578999999999999999999999999998877776 678999999999999999999999999986 666  7899999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            864

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.68  E-value=3.6e-17  Score=123.83  Aligned_cols=84  Identities=17%  Similarity=0.393  Sum_probs=73.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLL----AMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~----~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      +..+.++|||+|||.++++++|+    ++|++||.|.+|.+++   +++++|||||+|.+.++|++|++.||+.. +.+ 
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g-   78 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFP-FYD-   78 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCE-ETT-
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCE-ECC-
Confidence            45678999999999999999999    9999999999998874   47889999999999999999999999876 444 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.+++.+..
T Consensus        79 -~~l~v~~a~~~~~   91 (97)
T 1nu4_A           79 -KPMRIQYAKTDSD   91 (97)
T ss_dssp             -EECEEEECSSCCT
T ss_pred             -cEEEEEEccCCCc
Confidence             8899999876544

>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=2.3e-16  Score=130.23  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=74.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|++||.|++|.|+++. ++.+++||||+|++.++|++||+.||+.. ++|  +.|+|+
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~  114 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR-LDD--RIIRTD  114 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSE-ETT--EECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCE-ECC--eEEEEE
Confidence            46899999999999999999999999999999999995 68899999999999999999999999987 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus       115 ~a~~~  119 (156)
T 1h2v_Z          115 WDAGF  119 (156)
T ss_dssp             EESCC
T ss_pred             ECCCC
Confidence            99764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.2e-17  Score=129.05  Aligned_cols=68  Identities=22%  Similarity=0.455  Sum_probs=62.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC---CCcccEEEEEeCCHHHHHHHHHHhc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT---RASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~t---g~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      ......++|||+|||+++++++|+++|++||+|. +.++.++.+   |+++|||||+|.+.++|++||+.++
T Consensus         3 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~   73 (114)
T 2dnl_A            3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL   73 (114)
T ss_dssp             CSSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE
T ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh
Confidence            3456789999999999999999999999999999 888888887   7999999999999999999999984

>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=99.68  E-value=4.7e-17  Score=124.04  Aligned_cols=79  Identities=24%  Similarity=0.417  Sum_probs=71.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC--CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS--QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~--~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++|||+||+.++++++|+++|+.|| |.+|+|+++.  ++.++|||||+|.+.++|.+|+ .|||.. ++|  +.|+|
T Consensus        18 ~~~~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           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEES-LGN--RRIRV   92 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCC-BTT--BCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCE-ECC--eEEEE
Confidence            368999999999999999999999999 9999999985  7899999999999999999999 899977 666  67889


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      ++++.+
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            988764

>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=99.68  E-value=1.5e-16  Score=122.13  Aligned_cols=79  Identities=24%  Similarity=0.422  Sum_probs=72.2

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-C-CCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-Q-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++|||+||++++|+++|+++|+.|| |++|.|+++. + +.++|||||+|.+.++|++|+ .||+.. ++|  +.|+|
T Consensus        14 ~~~~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           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEES-LGN--KRIRV   88 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCE-ETT--EECEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCE-eCC--cEEEE
Confidence            368999999999999999999999999 9999999985 4 899999999999999999999 999987 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      ++++.+
T Consensus        89 ~~a~~~   94 (104)
T 1wi8_A           89 DVADQA   94 (104)
T ss_dssp             EECCCC
T ss_pred             EEccCC
Confidence            999765

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.68  E-value=2.2e-17  Score=126.31  Aligned_cols=82  Identities=27%  Similarity=0.391  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++++++|+++|++||.|.+|.|++|+ +++++|||||+|.+.++|++|++  ++.. +.|  +.|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~-~~g--~~l   78 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQIN-FHG--KKL   78 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCE-ETT--EEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCe-ECC--EEE
Confidence            34567899999999999999999999999999999999999 89999999999999999999998  4544 555  677


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      .|.++..+
T Consensus        79 ~v~~a~~~   86 (102)
T 2xs2_A           79 KLGPAIRK   86 (102)
T ss_dssp             EEEEEEEC
T ss_pred             EEEECCcC
Confidence            77766543

>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=99.68  E-value=1.1e-16  Score=127.35  Aligned_cols=82  Identities=28%  Similarity=0.508  Sum_probs=74.3

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++|+++|+++|++||.|++|.|+.+. ++.++|||||+|.+.++|++|++.||+.. ++|  +.|.|
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v   96 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD-LMG--QPISV   96 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCB-SSS--SBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCe-eCC--eEEEE
Confidence            346799999999999999999999999999999999984 88999999999999999999999999987 666  67899


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|+..+
T Consensus        97 ~~a~~~  102 (126)
T 3ex7_B           97 DWCFVR  102 (126)
T ss_dssp             EESEES
T ss_pred             EEecCC
Confidence            998644

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=1.5e-16  Score=123.23  Aligned_cols=82  Identities=20%  Similarity=0.352  Sum_probs=71.0

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ....++|||+||+.++|+++|+++|+.||.|++|+|+++. ++.++|||||+|++.++|.+|++.++  ..++|  +.|+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~--~~l~g--~~l~   97 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR--HELDS--KTID   97 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC--EEETT--EEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC--CcCCC--EEEE
Confidence            3446899999999999999999999999999999999984 68999999999999999999999864  44776  6899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+++..+
T Consensus        98 V~~a~~~  104 (109)
T 2rs2_A           98 PKVAFPR  104 (109)
T ss_dssp             EEECCCC
T ss_pred             EEEccCC
Confidence            9998764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.68  E-value=2.8e-17  Score=124.23  Aligned_cols=86  Identities=16%  Similarity=0.266  Sum_probs=73.0

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .......+.++|||+|||.++++++|+++|++||.|..+     ..+++++|||||+|.+.++|++|++.|++.. +.+ 
T Consensus         8 ~~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g-   80 (96)
T 1fjc_A            8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAE-IDG-   80 (96)
T ss_dssp             TTTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEE-ETT-
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC-
Confidence            344556678999999999999999999999999988766     3468899999999999999999999998865 555 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.++..+..
T Consensus        81 -~~l~v~~a~~~~~   93 (96)
T 1fjc_A           81 -RSVSLYYTGEKGG   93 (96)
T ss_dssp             -EEEEEEECSSSCC
T ss_pred             -eEEEEEEcCCCCC
Confidence             7899998876543

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.5e-16  Score=123.09  Aligned_cols=80  Identities=21%  Similarity=0.487  Sum_probs=71.5

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++|+++|+++|++||.|++|+|..+  +.+++||||+|++.++|++|++.||+.. ++|  +.|+|+
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~V~   94 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYD-YDG--YRLRVE   94 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEE
Confidence            34689999999999999999999999999999999764  4478999999999999999999999986 565  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus        95 ~a~~~   99 (109)
T 1x4a_A           95 FPRSG   99 (109)
T ss_dssp             CCCCC
T ss_pred             EcccC
Confidence            98764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=118.61  Aligned_cols=81  Identities=26%  Similarity=0.392  Sum_probs=71.4

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      +....+.++|||+|||.++++++|+++|++||.|.+|+++++        ||||+|.+.++|++|++.||+.. +.+  +
T Consensus         3 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~-~~g--~   71 (90)
T 2dnp_A            3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKE-VKG--K   71 (90)
T ss_dssp             CCSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCE-ETT--E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCE-ECC--c
Confidence            345678899999999999999999999999999999999743        99999999999999999998866 555  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|+|.+++....
T Consensus        72 ~l~v~~a~~~~~   83 (90)
T 2dnp_A           72 RINVELSTKGQK   83 (90)
T ss_dssp             ECEEEESCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            899999876544

>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=99.68  E-value=1.6e-17  Score=133.88  Aligned_cols=119  Identities=16%  Similarity=0.125  Sum_probs=70.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec---cccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEE
Q 018554           57 GCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY---ADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQ  133 (354)
Q Consensus        57 G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~---~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~  133 (354)
                      |+||.+|...+.+..++.......  .+.  ...-..   .........++|||+||++++|++||+++|++|| |++|+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~--gg~--~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~   76 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMT--GGQ--QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVH   76 (139)
T ss_dssp             -----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEE
T ss_pred             CcccccccCccccchhcccchhcc--CCC--CCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEE
Confidence            578888887777766665432211  110  000010   1112233467999999999999999999999999 77999


Q ss_pred             EeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          134 ILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       134 i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      |++|.+++++|||||+|++.++|++|| .+|+.. +++  +.|+|.++...
T Consensus        77 i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~-l~g--R~i~V~~a~~~  123 (139)
T 2hgn_A           77 IEIGPDGRVTGEADVEFATHEEAVAAM-SKDRAN-MQH--RYIELFLNSTT  123 (139)
T ss_dssp             CCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCS-SSS--CCCCCEECCCS
T ss_pred             EEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCE-ECC--EEEEEEECCCC
Confidence            999988999999999999999999999 788865 676  46777777554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.68  E-value=4.8e-17  Score=125.94  Aligned_cols=81  Identities=16%  Similarity=0.173  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .....++|||+|||+++++++|+++|++|| +|..|.|..+    +++|||||+|.+.++|++||+.||+.. +.+  +.
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~-l~G--r~   96 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIE-FRG--SV   96 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEE-ETT--EE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCE-ECC--eE
Confidence            455678999999999999999999999999 8999988643    488999999999999999999998866 555  78


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |+|.+++..
T Consensus        97 i~V~~a~~~  105 (111)
T 2jvr_A           97 ITVERDDNP  105 (111)
T ss_dssp             EEEEESCC-
T ss_pred             EEEEECCCC
Confidence            888887643

>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=99.68  E-value=1.5e-16  Score=120.45  Aligned_cols=78  Identities=27%  Similarity=0.479  Sum_probs=69.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||+.++|+++|+++|++||.|++|++.++     ++||||+|++.++|++|++.||+.. +++..+.|+|+|
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~-~~~~g~~l~V~~   89 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFP-LGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCB-CSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCE-eCCCCcEEEEEE
Confidence            3578999999999999999999999999999999875     7899999999999999999999986 562237899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++++
T Consensus        90 a~~~   93 (97)
T 1why_A           90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9765

>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=99.68  E-value=2.5e-17  Score=132.74  Aligned_cols=82  Identities=15%  Similarity=0.123  Sum_probs=69.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++||+||+++|++|| |.+|+|++|+. ++++|||||+|.+.++|++|| .+|+.. +.+  +.|
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~-l~g--R~i  115 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRAN-MQH--RYI  115 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCS-SSS--CCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCE-ECC--EEE
Confidence            456778999999999999999999999999 67999999987 999999999999999999999 676644 655  677


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      +|..+...
T Consensus       116 ~V~~a~~~  123 (139)
T 2hgn_A          116 ELFLNSTT  123 (139)
T ss_dssp             CCEECCCS
T ss_pred             EEEECCCC
Confidence            77766543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=5.6e-17  Score=117.24  Aligned_cols=75  Identities=20%  Similarity=0.392  Sum_probs=68.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++|||+|||.++++++|+++|++||.|.++.+.++. ++.++|||||+|.+.++|.+|++.++ .. ++|  +.|.|++|
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-HE-LDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CC-CSS--CCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-Cc-cCC--EEEEEEec
Confidence            479999999999999999999999999999999984 78999999999999999999999988 44 777  57888876

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=3e-17  Score=131.55  Aligned_cols=82  Identities=16%  Similarity=0.360  Sum_probs=73.8

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeE--EEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCC----cccCC
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD--LQILRGS-QQTSKGCAFLKYETKEQALAALEAINGK----HKMEG  171 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~--i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~----~~~~g  171 (354)
                      ....++|||+||++++|+++|+++|++||.|..  |+|++|+ ++.+||||||+|++. +|.+|++.|||.    . ++|
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~-~~g   97 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT-IDG   97 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC-GGG
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc-CCC
Confidence            344689999999999999999999999999976  9999996 899999999999999 999999999997    5 555


Q ss_pred             CceeEEEEecCCh
Q 018554          172 SSVPLVVKWADTE  184 (354)
Q Consensus       172 ~~~~l~v~~a~~~  184 (354)
                        +.|+|+|++..
T Consensus        98 --r~l~V~~a~~~  108 (131)
T 2m2b_A           98 --KTINVEFAKGS  108 (131)
T ss_dssp             --CCCCCEECCCS
T ss_pred             --EEEEEEECCCC
Confidence              68899998764

>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=1.2e-16  Score=122.26  Aligned_cols=78  Identities=22%  Similarity=0.270  Sum_probs=68.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+|||+++|++||+++|+.||. ++|+|++|++++++|||||+|++.++|++||+ +|+.. +++  +.|+|.+
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~-~~g--r~i~V~~   88 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKAN-MQH--RYVELFL   88 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCC-SSS--SCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCe-ECC--cEEEEEE
Confidence            3679999999999999999999999995 59999999999999999999999999999995 78865 666  4677777


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      +..
T Consensus        89 ~~~   91 (102)
T 1wez_A           89 NST   91 (102)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.3e-17  Score=120.28  Aligned_cols=78  Identities=17%  Similarity=0.295  Sum_probs=70.1

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++++++++|+++|++||.|.+++|+++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+|
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~~~~~~   81 (85)
T 1x4e_A            5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG-VQA--QMAKQSG   81 (85)
T ss_dssp             CCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT-CCE--ESCCSSC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCe-Eee--EEEeecC
Confidence            578999999999999999999999999999999998 578999999999999999999999999976 555  5666666


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.67  E-value=2.8e-17  Score=122.66  Aligned_cols=80  Identities=19%  Similarity=0.432  Sum_probs=69.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++|||+||+.++++++|+++|++||.|+++++.++. ++.++|||||+|++.+ |.+|++.|||.. ++|  +.|+|++|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~-~~g--~~l~V~~a   77 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTD-FMG--RTIRVTEA   77 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSC-CSS--SSCSEEEC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCE-ECC--eEEEEEEc
Confidence            589999999999999999999999999999999984 6899999999999999 999999999987 666  67899998


Q ss_pred             CChHH
Q 018554          182 DTEKE  186 (354)
Q Consensus       182 ~~~~~  186 (354)
                      +....
T Consensus        78 ~~~~~   82 (90)
T 2ki2_A           78 NPKKS   82 (90)
T ss_dssp             -----
T ss_pred             CCCCC
Confidence            76533

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.5e-16  Score=119.19  Aligned_cols=82  Identities=28%  Similarity=0.447  Sum_probs=72.1

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      +.......++|||+|||.++++++|+++|++||.|.+|.++++        ||||+|.+.++|++|++.||+.. +.+  
T Consensus         3 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~-~~g--   71 (92)
T 2dgt_A            3 SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTE-FQG--   71 (92)
T ss_dssp             CSCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEE-ETT--
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCe-eCC--
Confidence            3456778899999999999999999999999999999999743        99999999999999999998876 555  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|+|.+++.+..
T Consensus        72 ~~l~V~~a~~~~~   84 (92)
T 2dgt_A           72 KRMHVQLSTSRLR   84 (92)
T ss_dssp             EEEEEEESSCCCS
T ss_pred             cEEEEEEccCCCC
Confidence            8899999876544

>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=99.67  E-value=2.1e-16  Score=129.58  Aligned_cols=83  Identities=22%  Similarity=0.376  Sum_probs=73.7

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .......++|||+|||+++|+++|+++|++||.|.+|+|++|     ++|||||+|.+.++|++|++.||+.. +.+  +
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~  138 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRT-LCG--C  138 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSC-SSS--S
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCE-ECC--e
Confidence            345667899999999999999999999999999999999887     57899999999999999999999866 555  8


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|+|.+++.+.
T Consensus       139 ~l~v~~a~~~~  149 (150)
T 2i2y_A          139 RVRVELSNGEK  149 (150)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEEcCCCC
Confidence            89999987653

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.4e-16  Score=126.34  Aligned_cols=84  Identities=17%  Similarity=0.214  Sum_probs=72.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|+.||.|.+ +.+..+.++.++|||||+|.+.++|.+||+ ||+.. ++|  +.|.|.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~-~~g--r~i~V~   99 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQY-MGN--RFIQVH   99 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBC-STT--SCBEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCe-ECC--cEEEEE
Confidence            3589999999999999999999999999988 455555789999999999999999999999 99976 666  578999


Q ss_pred             ecCChHHHH
Q 018554          180 WADTEKERQ  188 (354)
Q Consensus       180 ~a~~~~~~~  188 (354)
                      ++..+....
T Consensus       100 ~a~~~~~~~  108 (124)
T 1wel_A          100 PITKKGMLE  108 (124)
T ss_dssp             EECHHHHHH
T ss_pred             ECCHHHHHH
Confidence            987765433

>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=99.67  E-value=1e-16  Score=124.51  Aligned_cols=79  Identities=19%  Similarity=0.212  Sum_probs=69.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||.++++++|+++|++||.|.+|.|++      ++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         6 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l   76 (111)
T 1whx_A            6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSK-FHH--VPL   76 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCB-SSS--SBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCE-ECC--eEE
Confidence            344578999999999999999999999999999998864      56799999999999999999999877 444  789


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      .|.|+...
T Consensus        77 ~V~~a~~~   84 (111)
T 1whx_A           77 YLEWAPIG   84 (111)
T ss_dssp             EEEEEETT
T ss_pred             EEEECCCC
Confidence            99988653

>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=2.5e-16  Score=121.60  Aligned_cols=77  Identities=17%  Similarity=0.220  Sum_probs=70.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||++++|++||+++|+.| .|.+|.|++|.+++++|||||+|.+.++|++|+ .+|+.. ++|  +.|+|..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~-~~g--r~i~V~~a   90 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRML-MIQ--RYVEVSPA   90 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEE-ETT--EEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCe-ECC--eEEEEEEC
Confidence            5789999999999999999999999 899999999988999999999999999999999 689876 666  68899888


Q ss_pred             CC
Q 018554          182 DT  183 (354)
Q Consensus       182 ~~  183 (354)
                      ..
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            54

>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=1.3e-16  Score=122.43  Aligned_cols=79  Identities=19%  Similarity=0.213  Sum_probs=70.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|+.||.|.+ |.|+.+.+++++|||||+|++.++|++|++. |+.. ++|  +.|+|.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~-~~g--r~i~v~   89 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKER-IGH--RYIEIF   89 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCC-SSS--SCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-Ccch-hCC--cEEEEE
Confidence            3689999999999999999999999999988 8999988899999999999999999999997 8865 676  467887


Q ss_pred             ecCC
Q 018554          180 WADT  183 (354)
Q Consensus       180 ~a~~  183 (354)
                      ++..
T Consensus        90 ~~~~   93 (104)
T 1wg5_A           90 KSSR   93 (104)
T ss_dssp             EECT
T ss_pred             ECCH
Confidence            7754

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=8e-17  Score=120.97  Aligned_cols=83  Identities=24%  Similarity=0.372  Sum_probs=69.6

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFAL-VDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~-v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ......++|||+|||.++|+++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||++..+.+  +
T Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~   73 (93)
T 2cqh_A            3 SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHG--K   73 (93)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETT--E
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECC--E
Confidence            34567899999999999999999999999999 6666552       578999999999999999999998333555  8


Q ss_pred             cceeecccccccc
Q 018554           88 PLQVKYADGELER  100 (354)
Q Consensus        88 ~l~v~~~~~~~~~  100 (354)
                      .|+|.+++.+..+
T Consensus        74 ~l~v~~a~~~~~~   86 (93)
T 2cqh_A           74 IMEVDYSVSKKLR   86 (93)
T ss_dssp             ECEEEECCCCCCC
T ss_pred             EEEEEEccCcccc
Confidence            8999998766543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.67  E-value=5.5e-17  Score=126.15  Aligned_cols=78  Identities=13%  Similarity=0.188  Sum_probs=66.5

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCC----HHH----HHHHHH--HhcCCc
Q 018554           15 VKLFVGQV----PKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS----RQE----ADKAVN--ACHNKK   80 (354)
Q Consensus        15 ~~lfVg~L----p~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~----~~~----A~~Ai~--~l~~~~   80 (354)
                      ++|||+||    |++++|++|+++|+.||+|.+|.++.|+.||+++|||||+|.|    .++    |.+|++  .+++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999996    333    788888  566655


Q ss_pred             cCCCCCccceeeccc
Q 018554           81 TLPGASSPLQVKYAD   95 (354)
Q Consensus        81 ~~~g~~~~l~v~~~~   95 (354)
                       +.|  +.|+|.+.+
T Consensus        83 -I~G--r~irV~ln~   94 (136)
T 2j8a_A           83 -IMG--FKFEVILNK   94 (136)
T ss_dssp             -ETT--EEEEEEECC
T ss_pred             -ecC--cEEEEEECc
Confidence             555  777777654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=1.6e-16  Score=126.19  Aligned_cols=83  Identities=27%  Similarity=0.422  Sum_probs=72.3

Q ss_pred             ccceEEEecCCCCCCHHHHH----HhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          101 LEHKLFIGMLPKNVSEAEVS----ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~----~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      ..++|||+||++++++++|+    ++|++||.|++|.+.+  ++.+||||||+|.+.++|.+|++.|||.. +.|  +.|
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~-l~g--r~l  102 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYP-FQG--NPL  102 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCC-CTT--SCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCE-eCC--CEE
Confidence            36789999999999999876    6999999999988764  57789999999999999999999999987 666  589


Q ss_pred             EEEecCChHHHH
Q 018554          177 VVKWADTEKERQ  188 (354)
Q Consensus       177 ~v~~a~~~~~~~  188 (354)
                      +|.||+.+....
T Consensus       103 ~V~~a~~~~~~~  114 (127)
T 2a3j_A          103 VITFSETPQSQV  114 (127)
T ss_dssp             EEEECCCCCHHH
T ss_pred             EEEEccCcchhc
Confidence            999998765544

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.67  E-value=1.1e-16  Score=123.84  Aligned_cols=91  Identities=16%  Similarity=0.183  Sum_probs=69.9

Q ss_pred             ccceeeccccccccccceEEEecCCCCCCHHHHHHhhccCC-CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554           87 SPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYG-TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus        87 ~~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G-~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      ..+.+.+...  ....++|||+||++++++++|+++|++|| +|..+.|..+   .++|||||+|++.++|++||+.|||
T Consensus        15 ~~~~~~~~~~--p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng   89 (111)
T 2jvr_A           15 VPRGSHMSKL--PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNN   89 (111)
T ss_dssp             ------------CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTT
T ss_pred             eecchhcCCC--CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCC
Confidence            3444555443  22357999999999999999999999999 9999998643   3689999999999999999999999


Q ss_pred             CcccCCCceeEEEEecCChH
Q 018554          166 KHKMEGSSVPLVVKWADTEK  185 (354)
Q Consensus       166 ~~~~~g~~~~l~v~~a~~~~  185 (354)
                      .. ++|  +.|+|++++...
T Consensus        90 ~~-l~G--r~i~V~~a~~~p  106 (111)
T 2jvr_A           90 IE-FRG--SVITVERDDNPP  106 (111)
T ss_dssp             EE-ETT--EEEEEEESCC--
T ss_pred             CE-ECC--eEEEEEECCCCC
Confidence            87 666  789999997653

>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=2e-16  Score=120.30  Aligned_cols=77  Identities=30%  Similarity=0.529  Sum_probs=70.1

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++|+++|+++|++||.|++|++.++     ++||||+|.+.++|.+|++.||+.. ++|  +.|+|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~-~~g--~~l~v~   84 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMP-LRG--KQLRVR   84 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCC-BTT--BCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCE-eCC--ceEEEE
Confidence            34679999999999999999999999999999999975     8999999999999999999999987 666  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        85 ~a~~~   89 (99)
T 2cpj_A           85 FACHS   89 (99)
T ss_dssp             ESSCC
T ss_pred             EcCCC
Confidence            98764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=9.6e-17  Score=123.37  Aligned_cols=81  Identities=22%  Similarity=0.374  Sum_probs=73.5

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++++++|+++|++||.|++|+|+++ .++.++|||||+|++.++|.+|++. ++.. ++|  +.|+|
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~-~~g--~~l~V   89 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHT-LDG--RNIDP   89 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEE-ETT--EEEBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCe-ECC--EEEEE
Confidence            34689999999999999999999999999999999999 5789999999999999999999998 8865 666  68999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      ++++.+
T Consensus        90 ~~a~~~   95 (105)
T 2dh8_A           90 KPCTPR   95 (105)
T ss_dssp             CCSCCS
T ss_pred             EEccCC
Confidence            998765

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=116.22  Aligned_cols=75  Identities=27%  Similarity=0.556  Sum_probs=68.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHh-CCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI-NGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++++++|+++|++||.|+++++.++     +|||||+|++.++|.+|++.| ++.. ++|  +.|+|
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~-~~g--~~l~v   81 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLI-VNG--RRLNV   81 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCE-ETT--EECCE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCee-ECC--CEEEE
Confidence            34689999999999999999999999999999999975     899999999999999999999 8765 666  78999


Q ss_pred             EecC
Q 018554          179 KWAD  182 (354)
Q Consensus       179 ~~a~  182 (354)
                      +||+
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>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=1.3e-16  Score=122.74  Aligned_cols=80  Identities=18%  Similarity=0.326  Sum_probs=71.8

Q ss_pred             ccceEEEecCCCCC------CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554          101 LEHKLFIGMLPKNV------SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus       101 ~~~~l~V~~l~~~~------t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      ..++|||+|||+.+      |+++|+++|++||.|.+|.|. ..++.++|||||+|.+.++|.+|++.|||.. ++|  +
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~-~~g--~   89 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYK-LDK--Q   89 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEE-CST--T
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcc-cCC--C
Confidence            36799999999999      789999999999999999998 4678899999999999999999999999976 666  5


Q ss_pred             -eEEEEecCCh
Q 018554          175 -PLVVKWADTE  184 (354)
Q Consensus       175 -~l~v~~a~~~  184 (354)
                       .|+|+|++..
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             7999998653

>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=99.67  E-value=2.7e-16  Score=129.05  Aligned_cols=83  Identities=12%  Similarity=0.145  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .....+|||+||++++|+++|+++|++||+|++|+|+.+    +++|||||+|.+.++|++|++.||+..+. +..+.|+
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~-g~g~~L~  117 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIY-NACCTLR  117 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSS-SSCSCEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEec-CCCcEEE
Confidence            445567999999999999999999999999999998754    36789999999999999999999998754 3358899


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |.|++.+.
T Consensus       118 V~~Ak~~~  125 (164)
T 1sjr_A          118 IDFSKLTS  125 (164)
T ss_dssp             EEECSSSS
T ss_pred             EEEecCCc
Confidence            99987653

>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=2.3e-16  Score=120.37  Aligned_cols=79  Identities=22%  Similarity=0.350  Sum_probs=70.7

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||++++|+++|+++|++||.|   +++++.++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v~   86 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKRE-IEG--RAIRLE   86 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEE-ETT--EEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCE-eCC--eEEEEE
Confidence            346899999999999999999999999977   67777788899999999999999999999999976 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        87 ~a~~~   91 (101)
T 2fc9_A           87 LQGPR   91 (101)
T ss_dssp             ECSSC
T ss_pred             EcCCC
Confidence            99765

>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=99.67  E-value=2.3e-16  Score=122.33  Aligned_cols=78  Identities=18%  Similarity=0.380  Sum_probs=68.4

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           10 SSEERVKLFVGQVPKH-MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~-~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .....++|||+|||++ +++++|+++|++||.|.+|.+        ++|||||+|.+.++|++|++.|++.. +.+  +.
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~   91 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRV-LAG--QT   91 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCE-ETT--EE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCE-ECC--eE
Confidence            3445689999999999 999999999999999999988        57899999999999999999998866 555  78


Q ss_pred             ceeecccccc
Q 018554           89 LQVKYADGEL   98 (354)
Q Consensus        89 l~v~~~~~~~   98 (354)
                      |+|.+++...
T Consensus        92 l~V~~a~~~~  101 (110)
T 1wf1_A           92 LDINMAGEPK  101 (110)
T ss_dssp             CCEEESCCCC
T ss_pred             EEEEECCCCC
Confidence            8999887443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=2.1e-16  Score=119.47  Aligned_cols=79  Identities=16%  Similarity=0.356  Sum_probs=66.7

Q ss_pred             cCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            9 KSSEERVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      .+..+.++|||+|||. ++++++|+++|++||.|.+|.+.        +|||||+|.+.++|++|++.|++.. +.+  +
T Consensus         5 ~~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~   73 (96)
T 2kvi_A            5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEM-NFG--K   73 (96)
T ss_dssp             ----CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSS-CBT--T
T ss_pred             ccCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCe-eCC--c
Confidence            3566889999999998 99999999999999999999884        6899999999999999999998876 445  7


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|+|.+++.+.
T Consensus        74 ~l~V~~a~~~~   84 (96)
T 2kvi_A           74 KLILEVSSSNA   84 (96)
T ss_dssp             TBCEEEEECCC
T ss_pred             EEEEEEcCcCC
Confidence            78888876543

>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=99.66  E-value=1.3e-16  Score=123.44  Aligned_cols=83  Identities=25%  Similarity=0.450  Sum_probs=72.4

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCC-eeEEEEe-eC-CCCCcceEEEEEeCCHHHHHHHHHHhC-CCcccCCCceeE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGT-IKDLQIL-RG-SQQTSKGCAFLKYETKEQALAALEAIN-GKHKMEGSSVPL  176 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~-v~~i~i~-~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~~g~~~~l  176 (354)
                      ..++|||+||++++|+++|+++|++||. |.++.++ .+ .++.++|||||+|.+.++|.+|++.|+ |...++|  +.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g--~~l   84 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG--HQI   84 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT--BCC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC--CeE
Confidence            3578999999999999999999999998 9999998 56 467899999999999999999999995 4234666  689


Q ss_pred             EEEecCChH
Q 018554          177 VVKWADTEK  185 (354)
Q Consensus       177 ~v~~a~~~~  185 (354)
                      +|+||+++.
T Consensus        85 ~V~~a~~~~   93 (109)
T 2dis_A           85 AVDWAEPEI   93 (109)
T ss_dssp             EEEESCSSC
T ss_pred             EEEEcCCCC
Confidence            999997653

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=2.5e-16  Score=121.70  Aligned_cols=78  Identities=17%  Similarity=0.258  Sum_probs=69.8

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc---eeE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS---VPL  176 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~---~~l  176 (354)
                      ...++|||+||++++|+++|+++|++||.|++|+|+.+      |||||+|++.++|++||+.||+.. ++|..   +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~-~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTK-FRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEE-EECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCC-ccCCcCcceEE
Confidence            34689999999999999999999999999999999976      899999999999999999999987 55422   789


Q ss_pred             EEEecCCh
Q 018554          177 VVKWADTE  184 (354)
Q Consensus       177 ~v~~a~~~  184 (354)
                      +|++|+.+
T Consensus        86 ~V~~a~~~   93 (108)
T 1x4c_A           86 RVKVDGPR   93 (108)
T ss_dssp             EEEESSCC
T ss_pred             EEEeCCCC
Confidence            99999874

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2e-16  Score=123.85  Aligned_cols=81  Identities=23%  Similarity=0.405  Sum_probs=73.3

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++|+++|+++|+.||.|++|.|+++ .++.++|||||+|.+.++|.+|++. ++.. ++|  +.|+|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~-~~g--~~l~V  100 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHS-IDG--RVVEP  100 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEE-ETT--EEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcE-ECC--EEEEE
Confidence            34689999999999999999999999999999999998 5789999999999999999999987 8865 666  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +++..+
T Consensus       101 ~~a~~~  106 (116)
T 1x4b_A          101 KRAVAR  106 (116)
T ss_dssp             ECCSSC
T ss_pred             EECCCC
Confidence            998765

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.66  E-value=2e-16  Score=121.15  Aligned_cols=80  Identities=24%  Similarity=0.364  Sum_probs=70.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||.++|+++|+++|++||.|.+|.+++        |||||+|.+.++|++|++.||+.. +.+  +.
T Consensus         6 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~-~~g--~~   74 (103)
T 2dgu_A            6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKD-LEG--EN   74 (103)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEE-ETT--EE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCc-cCC--CE
Confidence            4456789999999999999999999999999999999873        499999999999999999998876 555  88


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|.+++.+..
T Consensus        75 l~v~~a~~~~~   85 (103)
T 2dgu_A           75 IEIVFAKPPDQ   85 (103)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEcCCCcc
Confidence            99999876544

>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=99.66  E-value=2.4e-16  Score=129.37  Aligned_cols=79  Identities=16%  Similarity=0.260  Sum_probs=69.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..+|||+||++.+|+++|+++|++||+|++|.|+.++   +++||||+|++.++|++|++.|||..+.+ ..+.|+|.|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g-~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYN-ACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSS-SCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecC-CCcEEEEEEe
Confidence            4579999999999999999999999999999998653   47899999999999999999999988543 3378999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus       122 k~~  124 (164)
T 1sjr_A          122 KLT  124 (164)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            765

>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=99.66  E-value=5.5e-16  Score=118.68  Aligned_cols=80  Identities=19%  Similarity=0.349  Sum_probs=71.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++++++++|+++|++||.|++|.|+++ .++.++|||||+|++.++|.+|++.  +. .++|  +.|.|
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~-~~~g--~~l~v   87 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RH-MIDG--RWCDC   87 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CE-EETT--EEEEE
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CC-eeCC--eEEEE
Confidence            34678999999999999999999999999999999999 4799999999999999999999983  43 4666  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus        88 ~~a~~~   93 (103)
T 2cqg_A           88 KLPNSK   93 (103)
T ss_dssp             ECCCTT
T ss_pred             EecCCC
Confidence            998765

>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=99.66  E-value=7.3e-17  Score=124.64  Aligned_cols=78  Identities=28%  Similarity=0.405  Sum_probs=68.1

Q ss_pred             cccceEEEecCCCC-CCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-ccCCCceeEE
Q 018554          100 RLEHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH-KMEGSSVPLV  177 (354)
Q Consensus       100 ~~~~~l~V~~l~~~-~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~~g~~~~l~  177 (354)
                      ...++|||+||+++ +|+++|+++|++||.|.+|.|++.     ||||||+|++.++|.+|++.|++.. .++|  +.|.
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G--r~l~   95 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQG--RCVK   95 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSS--SCCE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--EEEE
Confidence            34789999999998 999999999999999999999864     8999999999999999999987532 3566  6889


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |.|++.+
T Consensus        96 V~~a~~~  102 (112)
T 1x4f_A           96 VDLSEKY  102 (112)
T ss_dssp             EEEECSC
T ss_pred             EEECccc
Confidence            9998654

>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=99.66  E-value=3.4e-16  Score=118.54  Aligned_cols=79  Identities=18%  Similarity=0.375  Sum_probs=68.1

Q ss_pred             ccCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            8 KKSSEERVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      .....+.++|||+|||. ++++++|+++|++||.|.+|.+.        +|||||+|.+.++|++|++.+++.. +.+  
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--   84 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEM-NFG--   84 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSE-ETT--
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCE-ECC--
Confidence            34566889999999998 99999999999999999999883        6899999999999999999998866 445  


Q ss_pred             ccceeeccccc
Q 018554           87 SPLQVKYADGE   97 (354)
Q Consensus        87 ~~l~v~~~~~~   97 (354)
                      +.|+|.+++.+
T Consensus        85 ~~l~V~~a~~~   95 (97)
T 2xnq_A           85 KKLILEVSSSN   95 (97)
T ss_dssp             EECEEEECCCC
T ss_pred             EEEEEEecCCC
Confidence            78899888654

>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=2.9e-16  Score=124.49  Aligned_cols=80  Identities=21%  Similarity=0.357  Sum_probs=73.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++|+++|+++|++||.|++|.|+++ .++.++|||||+|.+.++|.+|+ .|||.. ++|  +.|+|+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g--~~l~V~  110 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETV-FRG--RTIKVL  110 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCE-ETT--EECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCe-ECC--eEEEEE
Confidence            3689999999999999999999999999999999998 58899999999999999999999 799977 666  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus       111 ~a~~~  115 (124)
T 2jwn_A          111 PKRTN  115 (124)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            98753

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.4e-16  Score=118.35  Aligned_cols=83  Identities=25%  Similarity=0.348  Sum_probs=71.6

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEF--ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~--G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      .+.......++|||+|||+++++++|+++|++|  |.|.+|.+.        +|||||+|.+.++|++|++.||+.. +.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~-~~   77 (99)
T 2cpd_A            7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKV-LD   77 (99)
T ss_dssp             CCCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEE-ET
T ss_pred             ccccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCE-eC
Confidence            444556778999999999999999999999999  899998764        5699999999999999999998876 55


Q ss_pred             CCCccceeeccccccc
Q 018554           84 GASSPLQVKYADGELE   99 (354)
Q Consensus        84 g~~~~l~v~~~~~~~~   99 (354)
                      +  +.|+|.+++.+..
T Consensus        78 g--~~l~v~~a~~~~~   91 (99)
T 2cpd_A           78 G--SPIEVTLAKPVDK   91 (99)
T ss_dssp             T--EEEEEECCCCCCC
T ss_pred             C--cEEEEEECCCCCC
Confidence            5  8899999876543

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.66  E-value=5.6e-16  Score=128.62  Aligned_cols=84  Identities=32%  Similarity=0.550  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||.++++++|+++|++||.|.++++++|+.+|+++|||||+|.+.++|.+|++.||+.. +.+....|
T Consensus        84 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g~~~~i  162 (167)
T 1fxl_A           84 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK-PSGATEPI  162 (167)
T ss_dssp             GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CTTCSSCC
T ss_pred             ccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCc-cCCCccce
Confidence            44567899999999999999999999999999999999999899999999999999999999999999876 67766778


Q ss_pred             eeecc
Q 018554           90 QVKYA   94 (354)
Q Consensus        90 ~v~~~   94 (354)
                      +|+||
T Consensus       163 ~v~~A  167 (167)
T 1fxl_A          163 TVKFA  167 (167)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            88875

>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=99.66  E-value=2.1e-16  Score=122.77  Aligned_cols=76  Identities=22%  Similarity=0.377  Sum_probs=68.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      +..++|||+||++++++++|+++|++||.|.+|.|.+.     ++||||+|.+.++|.+|++.|||.. ++|  +.|.|.
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~   79 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSK-FHH--VPLYLE   79 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-----SSCEEEEESCHHHHHHHHHHHTTCB-SSS--SBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEeCCHHHHHHHHHHhCCCE-ECC--eEEEEE
Confidence            34679999999999999999999999999999998853     8899999999999999999999987 665  678999


Q ss_pred             ecCC
Q 018554          180 WADT  183 (354)
Q Consensus       180 ~a~~  183 (354)
                      ||..
T Consensus        80 ~a~~   83 (111)
T 1whx_A           80 WAPI   83 (111)
T ss_dssp             EEET
T ss_pred             ECCC
Confidence            9864

>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=1.5e-16  Score=118.49  Aligned_cols=81  Identities=22%  Similarity=0.292  Sum_probs=62.6

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||+++||++|+++|++||.|.+|+|++|     +||||||+|.+.++|++    +++.. +.+..+.
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~-~~~~g~~   75 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGED-LIIKGIS   75 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCE-EEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCC-cccCCEE
Confidence            34567899999999999999999999999999999999875     78999999999999984    44543 3444588


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      +.|+++.++..
T Consensus        76 v~v~~a~~k~~   86 (89)
T 3d2w_A           76 VHISNAEPKHN   86 (89)
T ss_dssp             EEEEECC----
T ss_pred             EEEEEcCCCCc
Confidence            88888876544

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.7e-16  Score=117.62  Aligned_cols=81  Identities=22%  Similarity=0.283  Sum_probs=69.0

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      +.....++|||+|||+++++++|+++|++||.|.+|  +.|+.+++   ||||+|.+.++|++|++ |++.. +.+  +.
T Consensus         3 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~-~~g--~~   73 (94)
T 2e5g_A            3 SGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHS-LGG--HR   73 (94)
T ss_dssp             SCCTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCE-ETT--EE
T ss_pred             CccCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeE-ECC--EE
Confidence            345567899999999999999999999999999987  77776666   99999999999999999 98866 555  78


Q ss_pred             ceeecccccc
Q 018554           89 LQVKYADGEL   98 (354)
Q Consensus        89 l~v~~~~~~~   98 (354)
                      |.|.++..+.
T Consensus        74 l~V~~a~~~~   83 (94)
T 2e5g_A           74 LRVRPREQKE   83 (94)
T ss_dssp             CCCBCSCCSC
T ss_pred             EEEEECCcCC
Confidence            8888776543

>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=99.66  E-value=1.1e-16  Score=123.55  Aligned_cols=81  Identities=19%  Similarity=0.145  Sum_probs=72.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCC---eeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGT---IKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~---v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ..++|||+||++++|+++|+++|+.||.   |.+|+|+++..++++|||||+|.+.++|.+|++ +|+.. ++|  +.|+
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~-~~g--r~i~   85 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMY-MGQ--RYVE   85 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCC-SSS--SCCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcce-eCC--eEEE
Confidence            4678999999999999999999999998   899999999779999999999999999999999 89966 666  5788


Q ss_pred             EEecCChH
Q 018554          178 VKWADTEK  185 (354)
Q Consensus       178 v~~a~~~~  185 (354)
                      |.++..+.
T Consensus        86 V~~a~~~~   93 (107)
T 2lmi_A           86 VYEINNED   93 (107)
T ss_dssp             CEECCHHH
T ss_pred             EEECCHHH
Confidence            88887543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.4e-16  Score=118.22  Aligned_cols=82  Identities=21%  Similarity=0.325  Sum_probs=71.5

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEV-NIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i-~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ......++|||+|||+++++++|+++|++||.|.+| .|++|+.+++    |||+|.+.++|++|++.||+.. +.+  +
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~-~~g--~   82 (96)
T 2e44_A           10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQ-LEN--F   82 (96)
T ss_dssp             CCCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCB-CSS--C
T ss_pred             CCCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCE-ECC--c
Confidence            344567999999999999999999999999999999 5888876543    9999999999999999998876 444  8


Q ss_pred             cceeeccccc
Q 018554           88 PLQVKYADGE   97 (354)
Q Consensus        88 ~l~v~~~~~~   97 (354)
                      .|+|.++..+
T Consensus        83 ~l~V~~a~~~   92 (96)
T 2e44_A           83 TLKVAYIPDE   92 (96)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEEcCcc
Confidence            8999988765

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.6e-16  Score=121.18  Aligned_cols=74  Identities=32%  Similarity=0.609  Sum_probs=68.1

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||+.++++++|+++|++||.|+++++.+     ++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+|+
T Consensus        27 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~~a   98 (101)
T 2la4_A           27 VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFP-FQG--RNLRTGWG   98 (101)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCE-ETT--EECCCCBC
T ss_pred             CCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEEec
Confidence            57999999999999999999999999999999984     38999999999999999999999987 565  78999998


Q ss_pred             CC
Q 018554          182 DT  183 (354)
Q Consensus       182 ~~  183 (354)
                      ++
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=4.9e-16  Score=128.86  Aligned_cols=84  Identities=30%  Similarity=0.517  Sum_probs=77.4

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||.++++++|+++|++||.|.++.+++|+.+++++|||||+|.+.++|.+|++.||+.. +.+  +.
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~  158 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD-LNG--RP  158 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EE
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-cCC--cE
Confidence            455678899999999999999999999999999999999999999999999999999999999999998877 555  88


Q ss_pred             ceeeccc
Q 018554           89 LQVKYAD   95 (354)
Q Consensus        89 l~v~~~~   95 (354)
                      |+|.|++
T Consensus       159 i~v~~a~  165 (166)
T 3md3_A          159 LRINWAA  165 (166)
T ss_dssp             CEEEESC
T ss_pred             EEEEecC
Confidence            9998875

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.66  E-value=7.9e-16  Score=128.01  Aligned_cols=85  Identities=34%  Similarity=0.541  Sum_probs=77.6

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||.++++++|+++|++||.|.++.+++|+.+++++|||||+|.+.++|.+|++.||+.. +.+..+.
T Consensus        84 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g~~~~  162 (168)
T 1b7f_A           84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI-PEGGSQP  162 (168)
T ss_dssp             SSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CTTCSSC
T ss_pred             cccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCE-ecCCCeE
Confidence            345678999999999999999999999999999999999999889999999999999999999999999876 5666788


Q ss_pred             ceeecc
Q 018554           89 LQVKYA   94 (354)
Q Consensus        89 l~v~~~   94 (354)
                      |+|+|+
T Consensus       163 l~V~~A  168 (168)
T 1b7f_A          163 LSVRLA  168 (168)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            888875

>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=5.2e-16  Score=116.27  Aligned_cols=75  Identities=24%  Similarity=0.481  Sum_probs=68.1

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||++++|+++|+++|++||.|++|.++       ++||||+|++.++|.+|++.||+.. ++|  +.|+|+
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V~   77 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTE-FQG--KRMHVQ   77 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEE-ETT--EEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCe-eCC--cEEEEE
Confidence            346899999999999999999999999999999998       4499999999999999999999987 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        78 ~a~~~   82 (92)
T 2dgt_A           78 LSTSR   82 (92)
T ss_dssp             ESSCC
T ss_pred             EccCC
Confidence            99765

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.65  E-value=3.2e-16  Score=121.13  Aligned_cols=79  Identities=33%  Similarity=0.644  Sum_probs=70.3

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ....++|||+||+.++|+++|+++|++||.|++|.++       +|||||+|.+.++|++|++.|||.. ++|  +.|.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V   97 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKS-FAN--QPLEV   97 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEE
Confidence            3447899999999999999999999999999999998       7899999999999999999999987 565  78999


Q ss_pred             EecCChHHH
Q 018554          179 KWADTEKER  187 (354)
Q Consensus       179 ~~a~~~~~~  187 (354)
                      +|++....+
T Consensus        98 ~~a~~~~~r  106 (108)
T 2jvo_A           98 VYSKLPAKR  106 (108)
T ss_dssp             ESCSCCC--
T ss_pred             EEecCCCCC
Confidence            999876443

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=5e-16  Score=115.85  Aligned_cols=74  Identities=31%  Similarity=0.530  Sum_probs=67.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||+.++|+++|+++|++||.|++|++.       ++||||+|++.++|++|++.||+.. ++|  +.|+|+|
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v~~   76 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYK-LHG--VNINVEA   76 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCB-CSS--CBCEEEC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCc-cCC--cEEEEEE
Confidence            36799999999999999999999999999999998       6799999999999999999999976 666  6899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++.+
T Consensus        77 a~~~   80 (90)
T 2dnq_A           77 SKNK   80 (90)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8765

>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=99.65  E-value=2.3e-16  Score=121.96  Aligned_cols=78  Identities=23%  Similarity=0.391  Sum_probs=68.6

Q ss_pred             ccceEEE--ecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc--cCCCceeE
Q 018554          101 LEHKLFI--GMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK--MEGSSVPL  176 (354)
Q Consensus       101 ~~~~l~V--~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~~g~~~~l  176 (354)
                      ..++|||  +||++++|+++|+++|++||+|++|.|..+     ||||||+|++.++|++|++.|||+.+  ..+..+.|
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l   98 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL   98 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEEC
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEE
Confidence            4678999  779999999999999999999999988754     89999999999999999999999864  23346899


Q ss_pred             EEEecCC
Q 018554          177 VVKWADT  183 (354)
Q Consensus       177 ~v~~a~~  183 (354)
                      .|.|++.
T Consensus        99 ~v~~a~~  105 (114)
T 2cq2_A           99 YLNFVEK  105 (114)
T ss_dssp             EEEEESC
T ss_pred             EEEeccc
Confidence            9999864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=1.6e-16  Score=125.30  Aligned_cols=79  Identities=18%  Similarity=0.184  Sum_probs=70.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCe----eEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTI----KDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v----~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      .++|||+|||+++|++||+++|+.||.|    .+|.|+++.+++++|||||+|++.++|++|++. |+.. +++  +.|+
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~-l~g--R~i~   98 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDL-LGK--RYIE   98 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEE-SSS--CEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCe-eCC--eEEE
Confidence            5789999999999999999999999975    689999998999999999999999999999986 8755 776  5788


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |..+..+
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            8877544

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=2.1e-16  Score=115.48  Aligned_cols=69  Identities=19%  Similarity=0.385  Sum_probs=62.9

Q ss_pred             cceEEEecCCCCC------CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC
Q 018554          102 EHKLFIGMLPKNV------SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS  172 (354)
Q Consensus       102 ~~~l~V~~l~~~~------t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  172 (354)
                      +++|||+|||..+      ++++|+++|++||.|.++.+. ..++.++|||||+|.+.++|.+|++.|||.. ++|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~-~~g~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYK-LDKQ   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCC-CSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcc-cCCc
Confidence            3689999999999      779999999999999999988 4678889999999999999999999999987 6664

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.65  E-value=7.4e-16  Score=121.31  Aligned_cols=76  Identities=18%  Similarity=0.248  Sum_probs=67.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceE-EEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC-AFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..|||+||++.+|+++|+++|++||.|++|.|+..     +|| |||+|++.++|.+|++.|||.. +.|..+.|+|.||
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-----NGIQAMVEFESVLCAQKAKAALNGAD-IYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCC-CBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCE-ecCCCeEEEEEEe
Confidence            45789999999999999999999999999999763     376 9999999999999999999988 5555578999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus       100 k~~  102 (124)
T 2e5i_A          100 RPT  102 (124)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            765

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.65  E-value=6.8e-16  Score=122.06  Aligned_cols=77  Identities=17%  Similarity=0.293  Sum_probs=68.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceE-EEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC-AFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      -+|||+||++.+|+++|+++|++||.|++|+|+.+.    +|+ |||+|++.++|.+|++.|||..+.+ ..+.|+|.|+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g-~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYN-ACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHTTCEEET-TEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC----CCcEEEEEECCHHHHHHHHHHcCCCeecC-CCcEEEEEec
Confidence            468999999999999999999999999999988642    677 9999999999999999999998554 4589999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +..
T Consensus       104 k~~  106 (130)
T 3zzy_A          104 KLT  106 (130)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            765

>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=99.65  E-value=4.1e-16  Score=116.09  Aligned_cols=77  Identities=18%  Similarity=0.397  Sum_probs=63.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...+|||+||++++|+++|+++|++||.|++|+|+++    +||||||+|++.++|++    +++.. +.++.+.|.|++
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~-~~~~g~~v~v~~   80 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGED-LIIKGISVHISN   80 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCE-EEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCC-cccCCEEEEEEE
Confidence            3689999999999999999999999999999999985    68999999999999883    56654 444568999999


Q ss_pred             cCChHH
Q 018554          181 ADTEKE  186 (354)
Q Consensus       181 a~~~~~  186 (354)
                      |.++..
T Consensus        81 a~~k~~   86 (89)
T 3d2w_A           81 AEPKHN   86 (89)
T ss_dssp             CC----
T ss_pred             cCCCCc
Confidence            987654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=2e-16  Score=119.45  Aligned_cols=82  Identities=21%  Similarity=0.352  Sum_probs=70.9

Q ss_pred             cccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCcee
Q 018554           96 GELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP  175 (354)
Q Consensus        96 ~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~  175 (354)
                      .......++|||+||+.++++++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|++.|||.. ++|  +.
T Consensus        10 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~   82 (96)
T 1fjc_A           10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAE-IDG--RS   82 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEE-ETT--EE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCE-ECC--eE
Confidence            3344557899999999999999999999999988766    4567789999999999999999999999976 666  78


Q ss_pred             EEEEecCCh
Q 018554          176 LVVKWADTE  184 (354)
Q Consensus       176 l~v~~a~~~  184 (354)
                      |.|.|+..+
T Consensus        83 l~v~~a~~~   91 (96)
T 1fjc_A           83 VSLYYTGEK   91 (96)
T ss_dssp             EEEEECSSS
T ss_pred             EEEEEcCCC
Confidence            999998764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.65  E-value=4.8e-16  Score=125.75  Aligned_cols=79  Identities=29%  Similarity=0.496  Sum_probs=71.9

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++++++|+++|++||.|++++|+++ .++.++|||||+|++.++|++|++.||+.. ++|  +.|+|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v  137 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--RTIRV  137 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEE-ETT--EEEEE
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            34789999999999999999999999999999999998 578999999999999999999999999976 666  68899


Q ss_pred             Eec
Q 018554          179 KWA  181 (354)
Q Consensus       179 ~~a  181 (354)
                      +||
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>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=99.65  E-value=4e-16  Score=120.75  Aligned_cols=77  Identities=22%  Similarity=0.511  Sum_probs=70.8

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+++     +|||||+|.+.++|.+|++.|||.. ++|  +.|+|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~   94 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTT-IEG--HVVKCY   94 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCE-ECC--cEEEEE
Confidence            34689999999999999999999999999999999987     8999999999999999999999976 666  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus        95 ~a~~~   99 (109)
T 1x4g_A           95 WGKES   99 (109)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            99765

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=2.2e-16  Score=120.44  Aligned_cols=75  Identities=27%  Similarity=0.495  Sum_probs=69.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      ++|||+||++++|+++|+++|++||.|++|.++++    ++|||||+|++.++|++|++.||+.. ++|  +.|+|+|++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKV-ICG--SRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSC-SSS--CCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCe-ECC--cEEEEEEcc
Confidence            47999999999999999999999999999999987    68999999999999999999999986 666  579999987


Q ss_pred             Ch
Q 018554          183 TE  184 (354)
Q Consensus       183 ~~  184 (354)
                      .+
T Consensus        74 ~~   75 (101)
T 2hvz_A           74 GM   75 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=6.5e-16  Score=116.94  Aligned_cols=83  Identities=23%  Similarity=0.346  Sum_probs=71.0

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ..++...+.++|||+||  ++++++|+++|++||+|.+|.|.      +++|||||+|.+.++|++||+.||+.. +.+ 
T Consensus         7 ~~~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g-   76 (97)
T 1x5p_A            7 GERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQ-VES-   76 (97)
T ss_dssp             SCCCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEE-ETT-
T ss_pred             CccCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCe-ECC-
Confidence            33455667899999996  99999999999999999999984      477899999999999999999998876 444 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.+++.+..
T Consensus        77 -~~l~v~~a~~~~~   89 (97)
T 1x5p_A           77 -VQLKVNIARKQPM   89 (97)
T ss_dssp             -EEEEEECCSSCCC
T ss_pred             -eEEEEEECCCCCC
Confidence             8899999876544

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=1.6e-15  Score=119.35  Aligned_cols=76  Identities=21%  Similarity=0.175  Sum_probs=66.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccE-EEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGC-CFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~-aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .|||+||++.+++++|+++|++||.|.+|+|+..      .|| |||+|.+.++|++|++.|||..+ .+..+.|+|.++
T Consensus        27 ~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           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADI-YAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCC-BTTBSEEEEECC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEe-cCCCeEEEEEEe
Confidence            4679999999999999999999999999999752      276 99999999999999999999884 444568999998


Q ss_pred             cccc
Q 018554           95 DGEL   98 (354)
Q Consensus        95 ~~~~   98 (354)
                      +.+.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7653

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6e-16  Score=115.44  Aligned_cols=75  Identities=25%  Similarity=0.457  Sum_probs=68.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||++++|+++|+++|++||.|++|+++       ++||||+|.+.++|++|++.||+.. ++|  +.|+|+
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------~~~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~   76 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKE-VKG--KRINVE   76 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEE
Confidence            346899999999999999999999999999999998       4499999999999999999999977 565  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus        77 ~a~~~   81 (90)
T 2dnp_A           77 LSTKG   81 (90)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            98765

>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=99.64  E-value=1.7e-16  Score=120.15  Aligned_cols=83  Identities=25%  Similarity=0.483  Sum_probs=73.3

Q ss_pred             ccceEEEecCCCCCCHHHHH----HhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          101 LEHKLFIGMLPKNVSEAEVS----ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~----~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      ..++|||+||+.++++++|+    ++|++||.|.+|.+.+  ++.++|||||+|.+.++|.+|++.|||.. ++|  +.|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l   81 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFP-FYD--KPM   81 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCE-ECC--cEE
Confidence            46799999999999999999    9999999999999884  46678999999999999999999999977 555  789


Q ss_pred             EEEecCChHHHH
Q 018554          177 VVKWADTEKERQ  188 (354)
Q Consensus       177 ~v~~a~~~~~~~  188 (354)
                      .|+|++.+....
T Consensus        82 ~v~~a~~~~~~~   93 (97)
T 1nu4_A           82 RIQYAKTDSDII   93 (97)
T ss_dssp             EEEECSSCCTHH
T ss_pred             EEEEccCCCccc
Confidence            999998765443

>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=99.64  E-value=8.5e-16  Score=116.32  Aligned_cols=74  Identities=27%  Similarity=0.514  Sum_probs=67.6

Q ss_pred             ccceEEEecCCC-CCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPK-NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~-~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++ ++++++|+++|++||.|.++++.       +|||||+|++.++|.+|++.|||.. ++|  +.|+|+
T Consensus        21 ~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~   90 (97)
T 2xnq_A           21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEM-NFG--KKLILE   90 (97)
T ss_dssp             TTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSE-ETT--EECEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEE
Confidence            468999999998 99999999999999999999994       7899999999999999999999986 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            98764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.64  E-value=1.1e-15  Score=132.51  Aligned_cols=85  Identities=20%  Similarity=0.331  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||.++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+|++.||+.. +.+  +.|+
T Consensus       122 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~-~~g--~~i~  198 (216)
T 2qfj_A          122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFD-LGG--QYLR  198 (216)
T ss_dssp             HTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCB-CSS--SBCE
T ss_pred             cCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCE-eCC--cEEE
Confidence            3567899999999999999999999999999999999999999999999999999999999999999876 555  8899


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |.++....
T Consensus       199 V~~a~~~~  206 (216)
T 2qfj_A          199 VGKAVTPP  206 (216)
T ss_dssp             EEECSSCS
T ss_pred             EEEecCCC
Confidence            99887653

>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=99.63  E-value=4.1e-16  Score=121.93  Aligned_cols=66  Identities=18%  Similarity=0.207  Sum_probs=58.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ....++|||+|||+++++++|+++|++||+|.+|.|+.|       |||||+|.+.++|++||+.||+.. +.+
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~-~~g   78 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTK-FRS   78 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCB-CCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            356799999999999999999999999999999999876       799999999999999999998877 555

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.3e-15  Score=115.66  Aligned_cols=75  Identities=25%  Similarity=0.468  Sum_probs=68.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccC--CCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIY--GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~--G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ...++|||+||++++|+++|+++|++|  |.|.++++.       ++||||+|.+.++|.+|++.||+.. ++|  +.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~   82 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKV-LDG--SPIE   82 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEE-ETT--EEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCE-eCC--cEEE
Confidence            346899999999999999999999999  999999886       6799999999999999999999986 565  7899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+|++.+
T Consensus        83 v~~a~~~   89 (99)
T 2cpd_A           83 VTLAKPV   89 (99)
T ss_dssp             EECCCCC
T ss_pred             EEECCCC
Confidence            9999765

>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=8.9e-17  Score=130.76  Aligned_cols=88  Identities=23%  Similarity=0.393  Sum_probs=72.5

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEE--E---eeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVN--I---IKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~--i---~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ......++|||+|||+++|+++|+++|++||.|..|.  +   ++...+++++|||||+|.+.++|.+|++.||+.. +.
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~-~~  118 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYV-LF  118 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBE-ET
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCE-eC
Confidence            3456789999999999999999999999999987741  1   1112368999999999999999999999998877 55


Q ss_pred             CCCccceeeccccccc
Q 018554           84 GASSPLQVKYADGELE   99 (354)
Q Consensus        84 g~~~~l~v~~~~~~~~   99 (354)
                      +  +.|.|.+++....
T Consensus       119 g--~~l~V~~a~~~~~  132 (143)
T 3egn_A          119 G--KPMVVQFARSARP  132 (143)
T ss_dssp             T--EECEEEECCCSCC
T ss_pred             C--cEEEEEECCCCCC
Confidence            5  8899999876443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.63  E-value=3.9e-16  Score=117.97  Aligned_cols=75  Identities=27%  Similarity=0.486  Sum_probs=66.1

Q ss_pred             cccceEEEecCCC-CCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPK-NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~-~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||++ ++++++|+++|++||.|++|.|.       +|||||+|++.++|.+|++.||+.. ++|  +.|.|
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~V   77 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEM-NFG--KKLIL   77 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSS-CBT--TTBCE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCe-eCC--cEEEE
Confidence            3468999999998 99999999999999999999995       7899999999999999999999986 566  46777


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .|++..
T Consensus        78 ~~a~~~   83 (96)
T 2kvi_A           78 EVSSSN   83 (96)
T ss_dssp             EEEECC
T ss_pred             EEcCcC
Confidence            777654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=5.1e-16  Score=117.52  Aligned_cols=78  Identities=21%  Similarity=0.386  Sum_probs=68.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||++++|+++|+++|++||.|. +.++.+   .++|||||+|.+.++|++|++.|||.. ++|  +.|+|+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~V~   89 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLR-LGT--DTLRVA   89 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCC-SSS--SCCEEE
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEE
Confidence            3468999999999999999999999999997 666654   568999999999999999999999987 666  579999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        90 ~a~~~   94 (97)
T 2e5j_A           90 LARQQ   94 (97)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            98765

>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=99.63  E-value=1.3e-15  Score=118.98  Aligned_cols=79  Identities=24%  Similarity=0.473  Sum_probs=70.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||+.++|+++|+++|+.||.|.+|.|+++  +.++|||||+|.+.++|.+|++.|||.. ++|  +.|.|.|+
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~v~~a   82 (115)
T 3lqv_A            8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFN-VSN--RYLVVLYY   82 (115)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCB-SSS--CBCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEEEe
Confidence            578999999999999999999999999999999975  3458999999999999999999999987 666  68999999


Q ss_pred             CChH
Q 018554          182 DTEK  185 (354)
Q Consensus       182 ~~~~  185 (354)
                      +...
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            8643

>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=99.63  E-value=9.6e-16  Score=128.08  Aligned_cols=82  Identities=24%  Similarity=0.398  Sum_probs=75.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|.+|++.||+.. +.+  +.|
T Consensus        90 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l  166 (172)
T 2g4b_A           90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ-LGD--KKL  166 (172)
T ss_dssp             CCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCE-ECC--eEE
Confidence            34557999999999999999999999999999999999999899999999999999999999999998876 555  788


Q ss_pred             eeecc
Q 018554           90 QVKYA   94 (354)
Q Consensus        90 ~v~~~   94 (354)
                      .|+|+
T Consensus       167 ~V~~A  171 (172)
T 2g4b_A          167 LVQRA  171 (172)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            88876

>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=99.63  E-value=7.7e-16  Score=117.89  Aligned_cols=75  Identities=28%  Similarity=0.541  Sum_probs=68.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||++++|+++|+++|++||.|++|+|+       ++||||+|++.++|.+|++.||+.. ++|  +.|.|+|
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~v~~   79 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKD-LEG--ENIEIVF   79 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCc-cCC--CEEEEEE
Confidence            35789999999999999999999999999999998       5699999999999999999999986 665  7899999


Q ss_pred             cCChH
Q 018554          181 ADTEK  185 (354)
Q Consensus       181 a~~~~  185 (354)
                      ++.+.
T Consensus        80 a~~~~   84 (103)
T 2dgu_A           80 AKPPD   84 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCc
Confidence            97653

>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=99.63  E-value=4.3e-16  Score=115.72  Aligned_cols=77  Identities=14%  Similarity=0.266  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||+++++++|+++|++| .|.+|++.      +++|||||+|.+.++|++|++.+|+.. +.+  +.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~l~V   72 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYS-FRG--KDLIV   72 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEE-ETT--EEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCe-ECC--cEEEE
Confidence            467899999999999999999999999 99999884      588999999999999999999998876 555  88999


Q ss_pred             ecccccc
Q 018554           92 KYADGEL   98 (354)
Q Consensus        92 ~~~~~~~   98 (354)
                      .++..+.
T Consensus        73 ~~a~~~~   79 (88)
T 1wg1_A           73 QLQPTDA   79 (88)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCc
Confidence            9886543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.63  E-value=7.4e-16  Score=129.72  Aligned_cols=81  Identities=26%  Similarity=0.449  Sum_probs=74.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||++++++++|+++|++||.|++|.|+.+.++.++|||||+|++.++|.+|++.||+.. ++|  +.|+|+|
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~-l~G--r~l~V~~  163 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVP-LDG--RPMDIQL  163 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCB-CSS--SBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            3689999999999999999999999999999999999889999999999999999999999999976 666  6789999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |...
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8765

>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=99.63  E-value=8.8e-16  Score=119.93  Aligned_cols=80  Identities=25%  Similarity=0.466  Sum_probs=69.4

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCe----eEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCcee
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTI----KDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP  175 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v----~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~  175 (354)
                      ...++|||+||++++|+++|+++|+.||.|    ..+++.   ++.++|||||+|.+.++|.+|++.||+.. ++|  +.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~   96 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYK-LYG--KI   96 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCB-CSS--CB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCE-eCC--cE
Confidence            346899999999999999999999999998    445544   67789999999999999999999999977 565  68


Q ss_pred             EEEEecCChH
Q 018554          176 LVVKWADTEK  185 (354)
Q Consensus       176 l~v~~a~~~~  185 (354)
                      |.|+|++.+.
T Consensus        97 l~v~~a~~~~  106 (115)
T 2cpx_A           97 LVIEFGKNKK  106 (115)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEEccCCC
Confidence            9999997653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.63  E-value=2.3e-16  Score=120.57  Aligned_cols=79  Identities=22%  Similarity=0.438  Sum_probs=71.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||++++++++|+++|+.||.|++|+|+++.++.++|||||+|++.++|.+|++  ++.. ++|  +.|.|.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~-~~g--~~l~v~~   82 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQIN-FHG--KKLKLGP   82 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCE-ETT--EECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCe-ECC--EEEEEEE
Confidence            4689999999999999999999999999999999999989999999999999999999998  7755 666  6788888


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +..+
T Consensus        83 a~~~   86 (102)
T 2xs2_A           83 AIRK   86 (102)
T ss_dssp             EEEC
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=99.63  E-value=8e-16  Score=121.65  Aligned_cols=81  Identities=12%  Similarity=0.162  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccE-EEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGC-CFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~-aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..--+|||+||++.+|+++|+++|++||+|.+|+++.+     .+|| |||+|.+.++|++|++.|||..+.. ..+.|+
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g-~~~~Lr   99 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYN-ACCTLR   99 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEET-TEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecC-CCcEEE
Confidence            44567889999999999999999999999999998764     3578 9999999999999999999988544 357899


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |.|++.+.
T Consensus       100 I~~ak~~~  107 (130)
T 3zzy_A          100 IDFSKLTS  107 (130)
T ss_dssp             EEECSCSS
T ss_pred             EEecCCCc
Confidence            99987653

>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=99.62  E-value=8.5e-16  Score=119.10  Aligned_cols=73  Identities=32%  Similarity=0.570  Sum_probs=67.0

Q ss_pred             cceEEEecCCCC-CCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~-~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||+++ +++++|+++|++||.|++|.|       +++||||+|++.++|++|++.||+.. ++|  +.|+|+|
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~V~~   96 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRV-LAG--QTLDINM   96 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCE-ETT--EECCEEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCE-ECC--eEEEEEE
Confidence            579999999999 999999999999999999999       38999999999999999999999977 565  7899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++..
T Consensus        97 a~~~  100 (110)
T 1wf1_A           97 AGEP  100 (110)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.62  E-value=1.4e-15  Score=130.06  Aligned_cols=86  Identities=23%  Similarity=0.390  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|.+|++.||+.. +.+  +.|+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~l~  187 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ-LGD--KKLL  187 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCE-ETT--EECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE-ECC--EEEE
Confidence            3677999999999999999999999999999999999999899999999999999999999999998876 555  8899


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.+++.+..
T Consensus       188 v~~a~~~~~  196 (198)
T 2yh0_A          188 VQRASVGAK  196 (198)
T ss_dssp             EEESCCCCC
T ss_pred             EEECCCCCC
Confidence            999876543

>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=99.62  E-value=2.2e-16  Score=113.47  Aligned_cols=74  Identities=18%  Similarity=0.385  Sum_probs=65.9

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +|||+|||.++++++|+++|++||.|.++.+.++ .++.++|||||+|++.++|.+|++. ++.. ++|  +.|.|++|
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-KYHN-VGL--SKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCC-BTT--BCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCe-ECC--EEEEEEEC
Confidence            5999999999999999999999999999999988 4688999999999999999999985 7755 676  56777764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=2.3e-15  Score=114.95  Aligned_cols=79  Identities=24%  Similarity=0.446  Sum_probs=69.9

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+.++|+++|+++|+.|   .+|.++.+ .++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~l~V   86 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGE-IDG--NKVTL   86 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE-ETT--EECEE
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEE
Confidence            346899999999999999999999987   36778887 588899999999999999999999999987 665  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus        87 ~~a~~~   92 (102)
T 2fc8_A           87 DWAKPK   92 (102)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999765

>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=99.62  E-value=1.1e-15  Score=146.28  Aligned_cols=84  Identities=21%  Similarity=0.384  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||.++|+++|+++|++||.|..|.|+.|+.|++++|||||+|.+.++|.+||+.||+.. |.+  +.|.
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~-i~g--r~i~  175 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK-IDG--RRVL  175 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE-ECC--EEEE
Confidence            3456899999999999999999999999999999999999999999999999999999999999998876 555  7888


Q ss_pred             eeccccc
Q 018554           91 VKYADGE   97 (354)
Q Consensus        91 v~~~~~~   97 (354)
                      |.++...
T Consensus       176 V~~a~~~  182 (437)
T 3pgw_S          176 VDVERGR  182 (437)
T ss_pred             EEEeCCC
Confidence            8888654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.2e-15  Score=109.94  Aligned_cols=77  Identities=17%  Similarity=0.188  Sum_probs=65.3

Q ss_pred             CCCCCe-EEEcCCCCCCCHHH----HHHHHhhc-CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           11 SEERVK-LFVGQVPKHMTEAQ----LLAMFKEF-ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        11 ~~~~~~-lfVg~Lp~~~te~~----L~~~F~~~-G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ..++.+ |||+|||.++++++    |+++|++| |+|.+|       |+   |+|||+|.+.++|.+|++.|++..+ .+
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l-~g   73 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDV-FG   73 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCS-SS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCcc-CC
Confidence            345566 99999999999998    55899999 599998       34   9999999999999999999999884 45


Q ss_pred             CCccceeecccccccc
Q 018554           85 ASSPLQVKYADGELER  100 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~~  100 (354)
                        +.++|++++.+.+.
T Consensus        74 --r~i~v~~A~~~sd~   87 (96)
T 2diu_A           74 --NRIIVSFTPKNREL   87 (96)
T ss_dssp             --SCCEEESSCCSCCC
T ss_pred             --ceEEEEecCCCcce
Confidence              89999999876553

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.61  E-value=1.7e-15  Score=112.54  Aligned_cols=74  Identities=24%  Similarity=0.340  Sum_probs=66.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+|||+++++++|+++|++| .|+++++.     .++|||||+|.+.++|++|++.|||.. ++|  +.|+|+|+
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~l~V~~a   75 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYS-FRG--KDLIVQLQ   75 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEE-ETT--EEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCe-ECC--cEEEEEEc
Confidence            5789999999999999999999999 99999985     468999999999999999999999987 565  78999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.40  E-value=4.9e-17  Score=127.41  Aligned_cols=84  Identities=25%  Similarity=0.416  Sum_probs=75.0

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeE--------EEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD--------LQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~--------i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ...++|||+||+.++++++|+++|++||.|.+        |+|+.+ .++.++|||||+|.+.++|.+|++.||+.. ++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~   83 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE-FS   83 (116)
Confidence            34678999999999999999999999999999        899988 578899999999999999999999999976 66


Q ss_pred             CCceeEEEEecCChHH
Q 018554          171 GSSVPLVVKWADTEKE  186 (354)
Q Consensus       171 g~~~~l~v~~a~~~~~  186 (354)
                      |  +.|+|+|++.+..
T Consensus        84 g--~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 G--NPIKVSFATRRAD   97 (116)
Confidence            5  6899999876543

>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=6.7e-16  Score=122.08  Aligned_cols=78  Identities=18%  Similarity=0.197  Sum_probs=68.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCee--EEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIK--DLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~--~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++|||+|||+++|+++|+++|+.| .|+  +|+|++|+.++++|||||+|++.++|++||+. ++.. ++|  +.|+|
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~-l~g--R~I~V  115 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKER-IGH--RYIEV  115 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCC-BTT--BCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCE-ECC--EEEEE
Confidence            35789999999999999999999999 676  89999998899999999999999999999985 6644 777  56777


Q ss_pred             EecCC
Q 018554          179 KWADT  183 (354)
Q Consensus       179 ~~a~~  183 (354)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            77753

>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=99.60  E-value=1.9e-15  Score=129.07  Aligned_cols=85  Identities=25%  Similarity=0.402  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|.+|++. ++. .+.|  +.|.
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~-~~~G--~~i~  176 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYH-TVNG--HNCE  176 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCC-EETT--EECE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCc-EECC--EEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999987 454 4666  7889


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.++..+.+
T Consensus       177 v~~a~~k~~  185 (196)
T 1l3k_A          177 VRKALSKQE  185 (196)
T ss_dssp             EEECC----
T ss_pred             EEecCChhH
Confidence            988876654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.60  E-value=4.5e-15  Score=128.88  Aligned_cols=83  Identities=25%  Similarity=0.456  Sum_probs=74.4

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||++++|+++|+++|++||+|++|+|++| .++.++|||||+|.+.++|.+|++.+|+.. +.|  +.|++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~-~~g--~~i~~~   90 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDV-IKG--KPVRIM   90 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhh-cCC--cccccc
Confidence            3578999999999999999999999999999999998 479999999999999999999999999976 555  688888


Q ss_pred             ecCChHH
Q 018554          180 WADTEKE  186 (354)
Q Consensus       180 ~a~~~~~  186 (354)
                      ++.....
T Consensus        91 ~~~~~~~   97 (213)
T 4f02_A           91 WSQRDPS   97 (213)
T ss_dssp             ECCCCTH
T ss_pred             ccccccc
Confidence            8876543

>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=99.60  E-value=6.6e-16  Score=125.58  Aligned_cols=85  Identities=25%  Similarity=0.403  Sum_probs=70.9

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEE------EEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDL------QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS  173 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i------~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  173 (354)
                      ...++|||+||++++|+++|+++|+.||.|..+      .+....++.++|||||+|.+.++|.+|++.|||.. ++|  
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~-~~g--  119 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYV-LFG--  119 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBE-ETT--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCE-eCC--
Confidence            346899999999999999999999999998764      22222467889999999999999999999999987 555  


Q ss_pred             eeEEEEecCChHHH
Q 018554          174 VPLVVKWADTEKER  187 (354)
Q Consensus       174 ~~l~v~~a~~~~~~  187 (354)
                      +.|.|.||+....+
T Consensus       120 ~~l~V~~a~~~~~~  133 (143)
T 3egn_A          120 KPMVVQFARSARPK  133 (143)
T ss_dssp             EECEEEECCCSCC-
T ss_pred             cEEEEEECCCCCCc
Confidence            78999999765433

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.60  E-value=9.6e-16  Score=127.45  Aligned_cols=82  Identities=21%  Similarity=0.372  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||.++++++|+++|++||.|.+|.+++|+.+++++|||||+|.+.++|.+|++ +++.. +.|  +.|+|
T Consensus        85 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~-~~g--~~i~V  160 (167)
T 2cjk_A           85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFID-FKD--RKIEI  160 (167)
T ss_dssp             HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEEC-SSS--SCEEE
T ss_pred             cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEE-eCC--eEEEE
Confidence            356799999999999999999999999999999999999999999999999999999999998 65544 555  88999


Q ss_pred             eccccc
Q 018554           92 KYADGE   97 (354)
Q Consensus        92 ~~~~~~   97 (354)
                      .+++++
T Consensus       161 ~~a~pk  166 (167)
T 2cjk_A          161 KRAEPR  166 (167)
T ss_dssp             EECCCC
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=99.60  E-value=4.8e-15  Score=112.09  Aligned_cols=75  Identities=31%  Similarity=0.495  Sum_probs=66.8

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+||  ++|+++|+++|++||.|++|.|.     .++|||||+|++.++|.+|++.||+.. ++|  +.|+|+
T Consensus        13 ~~~~~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           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQ-VES--VQLKVN   82 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEE-ETT--EEEEEE
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEE
Confidence            34689999996  89999999999999999999996     348999999999999999999999987 555  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++.+
T Consensus        83 ~a~~~   87 (97)
T 1x5p_A           83 IARKQ   87 (97)
T ss_dssp             CCSSC
T ss_pred             ECCCC
Confidence            99765

>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=99.60  E-value=1.4e-15  Score=114.08  Aligned_cols=75  Identities=25%  Similarity=0.448  Sum_probs=65.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCC-eeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC-CcccCCCceeEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGT-IKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING-KHKMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~-v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~~g~~~~l~v  178 (354)
                      ..++|||+||++++|+++|+++|++||. |..+.+.      ++|||||+|.+.++|++|++.||+ .. ++|  +.|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~-~~g--~~l~v   77 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVE-LHG--KIMEV   77 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCE-ETT--EECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCee-ECC--EEEEE
Confidence            3578999999999999999999999999 6666664      389999999999999999999999 65 666  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++.+
T Consensus        78 ~~a~~~   83 (93)
T 2cqh_A           78 DYSVSK   83 (93)
T ss_dssp             EECCCC
T ss_pred             EEccCc
Confidence            999765

>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=99.60  E-value=2.8e-15  Score=117.16  Aligned_cols=76  Identities=16%  Similarity=0.242  Sum_probs=65.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc---eeEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS---VPLV  177 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~---~~l~  177 (354)
                      ..++|||+||++++|+++|+++|++||+|++|.|+.+      |||||+|++.++|++||+.||+.. ++|+.   ..|+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~-~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTK-FRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCB-CCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCE-ECCcEeeeEEEE
Confidence            3689999999999999999999999999999999875      899999999999999999999987 67754   1267


Q ss_pred             EEecCC
Q 018554          178 VKWADT  183 (354)
Q Consensus       178 v~~a~~  183 (354)
                      |+.+..
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            776654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.59  E-value=1.9e-16  Score=120.82  Aligned_cols=79  Identities=24%  Similarity=0.290  Sum_probs=69.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++|+++|+++|++||.|.. .++.+ .++.++|||||+|++.++|.+|++ ||+.. ++|  +.|+|+
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~-~~g--~~l~V~   90 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLK-VFG--NEIKLE   90 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCC-BTT--BCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcE-ECC--cEEEEE
Confidence            4679999999999999999999999999888 55555 578889999999999999999998 99977 565  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      +++.+
T Consensus        91 ~a~~~   95 (101)
T 1fj7_A           91 KPKGR   95 (101)
T ss_dssp             CCSCC
T ss_pred             EcCCC
Confidence            98765

>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=99.59  E-value=4.8e-16  Score=115.46  Aligned_cols=79  Identities=25%  Similarity=0.305  Sum_probs=65.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++|+    +.. +....+.|+
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~----~~~-~~~~g~~l~   71 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC----GED-LIIKGISVH   71 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTT----TCE-EEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHh----cCC-ceeCCEEEE
Confidence            346799999999999999999999999999999999875     7899999999999997643    333 333458888


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.++..+..
T Consensus        72 v~~a~~~~~   80 (88)
T 1wf0_A           72 ISNAEPKHN   80 (88)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            888876544

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.59  E-value=5.1e-15  Score=113.48  Aligned_cols=83  Identities=11%  Similarity=0.047  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCC-----CCCHHHHHHHHhhcCCeeEEEEeeCCCC-CCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           11 SEERVKLFVGQVPK-----HMTEAQLLAMFKEFALVDEVNIIKDKTT-RASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~-----~~te~~L~~~F~~~G~v~~i~i~~d~~t-g~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      ...+++|+|.||-.     +.++++|+++|++||+|.+|.|++|+.+ ++++|||||+|.+.++|.+|++.||++. +.|
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~-~~G   83 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRY-FGG   83 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCE-ETT
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCE-ECC
Confidence            45789999999952     3478999999999999999999999764 6899999999999999999999999977 555


Q ss_pred             CCccceeecccc
Q 018554           85 ASSPLQVKYADG   96 (354)
Q Consensus        85 ~~~~l~v~~~~~   96 (354)
                        +.|.|.+++.
T Consensus        84 --r~i~v~~a~~   93 (105)
T 2pe8_A           84 --RVVKACFYNL   93 (105)
T ss_dssp             --EECEEEECCH
T ss_pred             --cEEEEEEcCH
Confidence              8899988864

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.59  E-value=3.9e-15  Score=115.75  Aligned_cols=81  Identities=15%  Similarity=0.275  Sum_probs=69.5

Q ss_pred             ceEEEecC----CCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCC----HHH----HHHHHH--HhCCCc
Q 018554          103 HKLFIGML----PKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYET----KEQ----ALAALE--AINGKH  167 (354)
Q Consensus       103 ~~l~V~~l----~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~----~~~----A~~Ai~--~l~g~~  167 (354)
                      .+|||+||    ++.+++++|+++|+.||+|.++.++.| .+|.++|||||+|.+    .++    |.+|++  .|||..
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            58999999    999999999999999999999999999 489999999999996    333    788888  789976


Q ss_pred             ccCCCceeEEEEecCChHH
Q 018554          168 KMEGSSVPLVVKWADTEKE  186 (354)
Q Consensus       168 ~~~g~~~~l~v~~a~~~~~  186 (354)
                       ++|  +.|+|.+.+....
T Consensus        83 -I~G--r~irV~ln~~g~~   98 (136)
T 2j8a_A           83 -IMG--FKFEVILNKHSIL   98 (136)
T ss_dssp             -ETT--EEEEEEECCTTHH
T ss_pred             -ecC--cEEEEEECcccHH
Confidence             777  7888888775543

>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=99.58  E-value=2.8e-15  Score=110.85  Aligned_cols=73  Identities=25%  Similarity=0.401  Sum_probs=63.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEF----A-------LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~----G-------~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      ..+.++|||+|||+++++++|+++|++|    |       .|.++++.++      +|||||+|.+.++|++|+ .||+.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            4568999999999999999999999999    8       9999998765      689999999999999999 99886


Q ss_pred             ccCCCCCccceeec
Q 018554           80 KTLPGASSPLQVKY   93 (354)
Q Consensus        80 ~~~~g~~~~l~v~~   93 (354)
                      . +.+  +.|+|..
T Consensus        76 ~-~~g--~~l~V~r   86 (87)
T 2hzc_A           76 I-FQG--QSLKIRR   86 (87)
T ss_dssp             E-ETT--EECEEEC
T ss_pred             E-ECC--eEEEEeC
Confidence            6 555  6666653

>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=1.6e-14  Score=123.35  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=72.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|.++.++.++|||||+|++.++|.+|++.++.  .++|  +.|.|+|
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~--~~~G--r~l~V~~  183 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQ--KYKE--TDLLILF  183 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTC--EETT--EECEEEE
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCC--eECC--EEEEEEE
Confidence            36899999999999999999999999999999999998899999999999999999999987654  3776  6889999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++.-
T Consensus       184 ~~~y  187 (193)
T 2voo_A          184 KDDY  187 (193)
T ss_dssp             TTTC
T ss_pred             hHHH
Confidence            8653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=4.5e-15  Score=111.94  Aligned_cols=77  Identities=27%  Similarity=0.420  Sum_probs=67.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEE-EEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i-~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++++++++|+++|+.||.|+++ .|+.+..   .+.|||+|.+.++|.+|++.|||.. ++|  +.|.|++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~l~V~~   88 (96)
T 2e44_A           15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQ-LEN--FTLKVAY   88 (96)
T ss_dssp             CCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCB-CSS--CBCEEEE
T ss_pred             CCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCE-ECC--cEEEEEE
Confidence            5789999999999999999999999999999 4777643   2349999999999999999999987 666  6899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9765

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=6.6e-15  Score=110.66  Aligned_cols=75  Identities=17%  Similarity=0.329  Sum_probs=63.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||++++|+++|+++|++||.|.+| +....++.   ||||+|.+.++|.+|++ ||+.. ++|  +.|.|+++
T Consensus         8 ~~~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            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHS-LGG--HRLRVRPR   79 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCE-ETT--EECCCBCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeE-ECC--EEEEEEEC
Confidence            5789999999999999999999999999997 33223443   99999999999999999 99977 666  68888887


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ..+
T Consensus        80 ~~~   82 (94)
T 2e5g_A           80 EQK   82 (94)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            644

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.56  E-value=5e-15  Score=129.54  Aligned_cols=83  Identities=24%  Similarity=0.496  Sum_probs=68.9

Q ss_pred             cccceEEEecCCCCC---------CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554          100 RLEHKLFIGMLPKNV---------SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~---------t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      ...++|||+||+..+         ++++|+++|++||+|++|+|+.+     ||||||+|.++++|+.|+++|+|..++.
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 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            347899999999998         79999999999999999999964     8999999999999999999999987521


Q ss_pred             ---------CCceeEEEEecCChHHH
Q 018554          171 ---------GSSVPLVVKWADTEKER  187 (354)
Q Consensus       171 ---------g~~~~l~v~~a~~~~~~  187 (354)
                               +..+.|.|+||+.....
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC-----
T ss_pred             cccccccccCCCCEEEEEEccCCCCH
Confidence                     12368999999866443

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.55  E-value=1e-14  Score=127.57  Aligned_cols=83  Identities=23%  Similarity=0.384  Sum_probs=69.9

Q ss_pred             CCCCCCeEEEcCCCCCC---------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554           10 SSEERVKLFVGQVPKHM---------TEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~---------te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      .....++||||||+.++         +|++|+++|++||+|++|+|+.      ++|||||+|.+.++|++|+++|++..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35578999999999998         7999999999999999999986      46899999999999999999999987


Q ss_pred             cCC---------CCCccceeecccccc
Q 018554           81 TLP---------GASSPLQVKYADGEL   98 (354)
Q Consensus        81 ~~~---------g~~~~l~v~~~~~~~   98 (354)
                      ++.         +..+.|.|+|++.+.
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EeccccccccccCCCCEEEEEEccCCC
Confidence            631         134889999997654

>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=99.55  E-value=1.2e-14  Score=124.09  Aligned_cols=79  Identities=16%  Similarity=0.269  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ..++|||+|||+++++++|+++|++||.|.+|+|.++.. ++++|||||+|.+.++|.+|++.++ . .+.|  +.|.|.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~-~-~~~G--r~l~V~  182 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPG-Q-KYKE--TDLLIL  182 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTT-C-EETT--EECEEE
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCC-C-eECC--EEEEEE
Confidence            358999999999999999999999999999999999875 9999999999999999999998764 3 4655  788888


Q ss_pred             cccc
Q 018554           93 YADG   96 (354)
Q Consensus        93 ~~~~   96 (354)
                      +++.
T Consensus       183 ~~~~  186 (193)
T 2voo_A          183 FKDD  186 (193)
T ss_dssp             ETTT
T ss_pred             EhHH
Confidence            7654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.54  E-value=3.5e-14  Score=108.77  Aligned_cols=81  Identities=17%  Similarity=0.238  Sum_probs=69.8

Q ss_pred             ccceEEEecCCC-----CCCHHHHHHhhccCCCeeEEEEeeCC--CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCc
Q 018554          101 LEHKLFIGMLPK-----NVSEAEVSALFSIYGTIKDLQILRGS--QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSS  173 (354)
Q Consensus       101 ~~~~l~V~~l~~-----~~t~~~l~~~F~~~G~v~~i~i~~~~--~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~  173 (354)
                      .+++|+|.||-.     +-++++|+++|++||.|++|.|+++.  ++.++||+||+|++.++|.+|++.|||+. ++|  
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~-~~G--   83 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRY-FGG--   83 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCE-ETT--
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCE-ECC--
Confidence            367899999952     23789999999999999999999984  36789999999999999999999999987 666  


Q ss_pred             eeEEEEecCCh
Q 018554          174 VPLVVKWADTE  184 (354)
Q Consensus       174 ~~l~v~~a~~~  184 (354)
                      +.|.|.+++..
T Consensus        84 r~i~v~~a~~~   94 (105)
T 2pe8_A           84 RVVKACFYNLD   94 (105)
T ss_dssp             EECEEEECCHH
T ss_pred             cEEEEEEcCHH
Confidence            78999999754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=9e-15  Score=114.06  Aligned_cols=75  Identities=24%  Similarity=0.404  Sum_probs=62.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-C---CCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-Q---QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~---~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      ..++|||+||++++|+++|+++|++||.|. +.++.+. +   +.++|||||+|++.++|++|++.|++   ++|  +.+
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~---~~G--~~~   80 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE---EDG--KLY   80 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE---ETT--EEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh---cCC--cEE
Confidence            368899999999999999999999999999 8887764 4   68999999999999999999999843   444  344


Q ss_pred             EEEec
Q 018554          177 VVKWA  181 (354)
Q Consensus       177 ~v~~a  181 (354)
                      .+..+
T Consensus        81 ~~~~~   85 (114)
T 2dnl_A           81 LCVSS   85 (114)
T ss_dssp             EEECC
T ss_pred             EeccC
Confidence            44433

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.54  E-value=1.7e-14  Score=124.41  Aligned_cols=76  Identities=17%  Similarity=0.290  Sum_probs=69.0

Q ss_pred             cceEEEecCC-CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~-~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||+ +++|+++|+++|++||.|.+|+|++++    +|||||+|++.++|++|++.|||.. +.|  +.|+|.+
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~----~g~afV~f~~~~~A~~Ai~~lng~~-~~g--~~l~v~~   76 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNF-MFG--QKMNVCV   76 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS----TTCEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC----CCEEEEEECCHHHHHHHHHHhCCCE-ECC--ceEEEEE
Confidence            5789999999 899999999999999999999999763    7999999999999999999999987 565  7899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      ++.+
T Consensus        77 s~~~   80 (205)
T 3tyt_A           77 SKQP   80 (205)
T ss_dssp             CSCS
T ss_pred             ccCC
Confidence            8643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.7e-14  Score=106.11  Aligned_cols=69  Identities=17%  Similarity=0.303  Sum_probs=60.8

Q ss_pred             eEEEecCCCCCCHHH----HHHhhccC-CCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          104 KLFIGMLPKNVSEAE----VSALFSIY-GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~----l~~~F~~~-G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      .|||+||++++++++    |+++|++| |+|.+|      +   .|+|||+|.+.++|.+|++.|+|.. +.|  ++|+|
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------t---gG~AfV~F~~~esA~~A~~~l~G~~-l~g--r~i~v   78 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------T---GCSAILRFINQDSAERAQKRMENED-VFG--NRIIV   78 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------C---TTCEEEEESSHHHHHHHHHHHTTCC-SSS--SCCEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------e---cCEEEEEECCHHHHHHHHHHhcCCc-cCC--ceEEE
Confidence            399999999999988    55899999 599998      2   3999999999999999999999988 555  68999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .+|+.+
T Consensus        79 ~~A~~~   84 (96)
T 2diu_A           79 SFTPKN   84 (96)
T ss_dssp             ESSCCS
T ss_pred             EecCCC
Confidence            999765

>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=99.53  E-value=3.3e-13  Score=121.95  Aligned_cols=81  Identities=27%  Similarity=0.523  Sum_probs=71.8

Q ss_pred             cccceEEEecCCCCCCHHHHH----HhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCcee
Q 018554          100 RLEHKLFIGMLPKNVSEAEVS----ALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVP  175 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~----~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~  175 (354)
                      +..++|||+||++++|+++|+    ++|+.||.|++|+|++  ++.++|||||+|.+.++|.+|++.|||.. +.|  +.
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--~~   81 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFP-FYD--KP   81 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCe-eCC--cE
Confidence            346899999999999999977    8999999999999986  67789999999999999999999999976 565  68


Q ss_pred             EEEEecCChH
Q 018554          176 LVVKWADTEK  185 (354)
Q Consensus       176 l~v~~a~~~~  185 (354)
                      |+|.|++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            8999986544

>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=99.53  E-value=2.4e-14  Score=105.75  Aligned_cols=71  Identities=24%  Similarity=0.517  Sum_probs=63.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccC----C-------CeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccc
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIY----G-------TIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKM  169 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~----G-------~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  169 (354)
                      ..++|||+||++++++++|+++|++|    |       .|.++++.++     +|||||+|.+.++|.+|+ .||+.. +
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~-~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGII-F   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCE-E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCE-E
Confidence            36799999999999999999999999    8       8999999876     899999999999999999 999987 6


Q ss_pred             CCCceeEEEEe
Q 018554          170 EGSSVPLVVKW  180 (354)
Q Consensus       170 ~g~~~~l~v~~  180 (354)
                      +|  +.|+|+.
T Consensus        78 ~g--~~l~V~r   86 (87)
T 2hzc_A           78 QG--QSLKIRR   86 (87)
T ss_dssp             TT--EECEEEC
T ss_pred             CC--eEEEEeC
Confidence            66  5777763

>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=99.52  E-value=1.3e-14  Score=107.70  Aligned_cols=74  Identities=20%  Similarity=0.397  Sum_probs=63.1

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||++++|+++|+++|++||.|++|+|+++    ++|||||+|++.++|++|    ++.. +....+.|.|+++
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~----~~~~-~~~~g~~l~v~~a   75 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL----CGED-LIIKGISVHISNA   75 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHT----TTCE-EEETTEEEEEECC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHH----hcCC-ceeCCEEEEEEec
Confidence            579999999999999999999999999999999875    589999999999999754    4443 3334488999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +++
T Consensus        76 ~~~   78 (88)
T 1wf0_A           76 EPK   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.52  E-value=4.3e-14  Score=126.53  Aligned_cols=87  Identities=20%  Similarity=0.280  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCccce
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT-LPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~-~~g~~~~l~   90 (354)
                      .+.++|||+|||.++|+++|+++|+.||.|.+|.|++| .+|+++|||||+|.+.++|.+|++.|++..+ +.+..+.+.
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            35789999999999999999999999999999999999 4799999999999999999999999955444 444568999


Q ss_pred             eeccccccc
Q 018554           91 VKYADGELE   99 (354)
Q Consensus        91 v~~~~~~~~   99 (354)
                      |.+++....
T Consensus       173 v~~~~~~~~  181 (261)
T 3sde_A          173 VEPMEQFDD  181 (261)
T ss_dssp             EEECCCEES
T ss_pred             EeeccccCc
Confidence            998876543

>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=99.51  E-value=2.2e-14  Score=120.22  Aligned_cols=81  Identities=17%  Similarity=0.315  Sum_probs=70.5

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||.++++++|+++|++||.|..+     ..+++++|||||+|.+.++|.+|++.||+.. +.+  +.
T Consensus        94 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g--~~  165 (175)
T 1fje_B           94 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAE-IDG--RS  165 (175)
T ss_dssp             STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEE-ETT--EE
T ss_pred             cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCE-ECC--eE
Confidence            345577899999999999999999999999988765     4568999999999999999999999998866 555  78


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |+|.|+.++
T Consensus       166 i~v~~a~~k  174 (175)
T 1fje_B          166 VSLYYTGEK  174 (175)
T ss_dssp             EEEEECSSC
T ss_pred             EEEEecCCC
Confidence            999988754

>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=99.47  E-value=1.8e-13  Score=106.26  Aligned_cols=86  Identities=14%  Similarity=0.195  Sum_probs=70.2

Q ss_pred             ccccCCCCCCeEEEcCCCCCCC-----------HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHH
Q 018554            6 KEKKSSEERVKLFVGQVPKHMT-----------EAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN   74 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~t-----------e~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~   74 (354)
                      +.......+++|+|.||-...+           +++|+++|++||.|.+|.| .|+   .++|||||+|.+.++|++|++
T Consensus         7 ~~~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~   82 (112)
T 2dit_A            7 GGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQ   82 (112)
T ss_dssp             SCCCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHH
Confidence            3344667899999999943332           6899999999999999955 665   389999999999999999999


Q ss_pred             HhcCCccCCCCCccceeecccccc
Q 018554           75 ACHNKKTLPGASSPLQVKYADGEL   98 (354)
Q Consensus        75 ~l~~~~~~~g~~~~l~v~~~~~~~   98 (354)
                      .||+.. +.+  +.|+|.+++.+.
T Consensus        83 ~lng~~-~~g--r~l~v~~a~~~~  103 (112)
T 2dit_A           83 TLDGRW-FGG--RQITAQAWDGTT  103 (112)
T ss_dssp             HSTTCE-ETT--EECEEEECCSCC
T ss_pred             HcCCCE-ECC--cEEEEEEeCCCC
Confidence            999877 444  889999887643

>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=99.46  E-value=1.2e-13  Score=127.20  Aligned_cols=83  Identities=17%  Similarity=0.267  Sum_probs=68.8

Q ss_pred             cccCCCCCCeEEEcC--CCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554            7 EKKSSEERVKLFVGQ--VPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~--Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      -+..+.++++|||||  |+.++||++|+++|++||+|++|.+.+      +||||||+|++.++|++|+++|||+.++..
T Consensus        11 v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           11 IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             CCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             ceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            344578899999999  578999999999999999999987643      568999999999999999999999887533


Q ss_pred             --CCccceeeccc
Q 018554           85 --ASSPLQVKYAD   95 (354)
Q Consensus        85 --~~~~l~v~~~~   95 (354)
                        ....+.+.+..
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence              33356777664

>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=99.44  E-value=4.4e-14  Score=108.10  Aligned_cols=72  Identities=19%  Similarity=0.404  Sum_probs=62.4

Q ss_pred             EecCCCCCCHHHHHHhh------------ccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554          107 IGMLPKNVSEAEVSALF------------SIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus       107 V~~l~~~~t~~~l~~~F------------~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      +.+|++++++++|+++|            ++||.|++|.|.++.++.++|||||+|++.++|.+|++.|||+. ++|  +
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~-~~G--r   96 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW-FNG--Q   96 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCE-ETT--E
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCE-ECC--E
Confidence            56777777877777666            99999999999999888899999999999999999999999987 666  7


Q ss_pred             eEEEEec
Q 018554          175 PLVVKWA  181 (354)
Q Consensus       175 ~l~v~~a  181 (354)
                      .|+|.|+
T Consensus        97 ~i~v~~s  103 (104)
T 1jmt_A           97 PIHAELS  103 (104)
T ss_dssp             ECCEEEC
T ss_pred             EEEEEEc
Confidence            8888876

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.44  E-value=3.7e-13  Score=115.13  Aligned_cols=79  Identities=19%  Similarity=0.309  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFA-LVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G-~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .+.++|||+|||.++++++|+++|++|| .|.+|+++.+     .+|||||+|.+.++|.+|++.||+..+..+  +.|+
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~~l~  190 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLR  190 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSC--CSCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCC--CeEE
Confidence            3488999999999999999999999999 9999999775     368999999999999999999999775224  7899


Q ss_pred             eeccccc
Q 018554           91 VKYADGE   97 (354)
Q Consensus        91 v~~~~~~   97 (354)
                      |.|++++
T Consensus       191 v~~a~~~  197 (198)
T 1qm9_A          191 VSFSKST  197 (198)
T ss_dssp             EEEECCC
T ss_pred             EEeeccc
Confidence            9988754

>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=99.44  E-value=1.9e-13  Score=104.72  Aligned_cols=83  Identities=18%  Similarity=0.262  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHhhcCCeeEEEEeeCCCC--CCcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554           12 EERVKLFVGQV--PKHMT--------EAQLLAMFKEFALVDEVNIIKDKTT--RASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus        12 ~~~~~lfVg~L--p~~~t--------e~~L~~~F~~~G~v~~i~i~~d~~t--g~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      .+++.|.|.|+  +.++.        ++||++.|++||.|.+|+|++++.+  ++++|||||+|.+.++|.+|++.|||+
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            46789999998  44443        4799999999999999999999865  468999999999999999999999997


Q ss_pred             ccCCCCCccceeeccccc
Q 018554           80 KTLPGASSPLQVKYADGE   97 (354)
Q Consensus        80 ~~~~g~~~~l~v~~~~~~   97 (354)
                      . +.|  +.|++.+.+.+
T Consensus        83 ~-f~G--R~i~v~~~~~~   97 (105)
T 3v4m_A           83 K-FAN--RVVVTKYCDPD   97 (105)
T ss_dssp             E-ETT--EECEEEEECHH
T ss_pred             E-eCC--CEEEEEEeCHH
Confidence            7 555  88888887643

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.43  E-value=2.5e-13  Score=119.17  Aligned_cols=77  Identities=23%  Similarity=0.435  Sum_probs=69.7

Q ss_pred             ccceEEEecCCC-CCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPK-NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~-~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+. ++++++|+++|+.||.|++|+|+++.    +|||||+|.+.++|++|++.||+.. +.|  +.|.|.
T Consensus        33 ~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~-~~g--~~l~v~  105 (229)
T 2adc_A           33 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHK-LHG--KPIRIT  105 (229)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCB-CSS--SBCEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCe-ECC--eEEEEE
Confidence            468999999999 99999999999999999999999875    7899999999999999999999976 565  688999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      |++..
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            88643

>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=99.43  E-value=6.8e-13  Score=102.97  Aligned_cols=79  Identities=18%  Similarity=0.311  Sum_probs=66.0

Q ss_pred             cccceEEEecCCCCCC-----------HHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          100 RLEHKLFIGMLPKNVS-----------EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t-----------~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      ..+++|+|.||-...+           +++|+++|++||.|++|.| .++.  ++|||||+|.+.++|.+|++.|||.. 
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~--~~G~afV~f~~~~~A~~Ai~~lng~~-   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRH--PDGVASVSFRDPEEADYCIQTLDGRW-   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTC--TTCEEEEECSCHHHHHHHHHHSTTCE-
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCC--CCEEEEEEECCHHHHHHHHHHcCCCE-
Confidence            3468899999944332           5899999999999999966 4543  69999999999999999999999987 


Q ss_pred             cCCCceeEEEEecCCh
Q 018554          169 MEGSSVPLVVKWADTE  184 (354)
Q Consensus       169 ~~g~~~~l~v~~a~~~  184 (354)
                      ++|  +.|+|.|++.+
T Consensus        89 ~~g--r~l~v~~a~~~  102 (112)
T 2dit_A           89 FGG--RQITAQAWDGT  102 (112)
T ss_dssp             ETT--EECEEEECCSC
T ss_pred             ECC--cEEEEEEeCCC
Confidence            565  78999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=1.3e-12  Score=98.93  Aligned_cols=79  Identities=18%  Similarity=0.244  Sum_probs=63.9

Q ss_pred             CCCCCeEEEcCCC-------CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554           11 SEERVKLFVGQVP-------KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus        11 ~~~~~~lfVg~Lp-------~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      .....+|-|.-..       .++++++|+++|++||+|.+|.|+     ++++|||||+|.+.++|++|++.+++   +.
T Consensus         7 ~~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~---~~   78 (100)
T 2d9o_A            7 GQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG---LV   78 (100)
T ss_dssp             CCSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB---CS
T ss_pred             CCccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC---CC
Confidence            4446677776554       358999999999999999999988     36889999999999999999998543   33


Q ss_pred             CCCccceeeccccccc
Q 018554           84 GASSPLQVKYADGELE   99 (354)
Q Consensus        84 g~~~~l~v~~~~~~~~   99 (354)
                        .+.|+|.|++.+..
T Consensus        79 --g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           79 --DNPLKISWLEGQPQ   92 (100)
T ss_dssp             --SSBCEEECSSCCCC
T ss_pred             --CCeEEEEEccCCCC
Confidence              47899999876543

>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=99.41  E-value=4.3e-13  Score=102.71  Aligned_cols=81  Identities=20%  Similarity=0.369  Sum_probs=67.6

Q ss_pred             cceEEEecC--CCCCC--------HHHHHHhhccCCCeeEEEEeeCCC---CCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          102 EHKLFIGML--PKNVS--------EAEVSALFSIYGTIKDLQILRGSQ---QTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       102 ~~~l~V~~l--~~~~t--------~~~l~~~F~~~G~v~~i~i~~~~~---~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      ++.|.+.|+  +..+.        ++||++.|++||.|++|.|+++..   +.++|++||+|++.++|.+|++.|||+. 
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~-   83 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK-   83 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE-
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE-
Confidence            567888887  33333        468999999999999999998854   3678999999999999999999999987 


Q ss_pred             cCCCceeEEEEecCChH
Q 018554          169 MEGSSVPLVVKWADTEK  185 (354)
Q Consensus       169 ~~g~~~~l~v~~a~~~~  185 (354)
                      ++|  +.|+|.+++...
T Consensus        84 f~G--R~i~v~~~~~~~   98 (105)
T 3v4m_A           84 FAN--RVVVTKYCDPDS   98 (105)
T ss_dssp             ETT--EECEEEEECHHH
T ss_pred             eCC--CEEEEEEeCHHH
Confidence            666  789999987553

>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=99.41  E-value=3.7e-13  Score=123.92  Aligned_cols=78  Identities=22%  Similarity=0.407  Sum_probs=67.3

Q ss_pred             cccceEEEec--CCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccC--CCcee
Q 018554          100 RLEHKLFIGM--LPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKME--GSSVP  175 (354)
Q Consensus       100 ~~~~~l~V~~--l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~--g~~~~  175 (354)
                      ..+++|||+|  |++.+||++|+++|++||+|++|.+.+     +||||||+|++.++|++|++.|||+.+++  |+.+.
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            3467999999  578999999999999999999988764     38999999999999999999999998763  35457


Q ss_pred             EEEEecC
Q 018554          176 LVVKWAD  182 (354)
Q Consensus       176 l~v~~a~  182 (354)
                      |.|.+++
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            8888874

>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=99.41  E-value=8.3e-14  Score=106.56  Aligned_cols=72  Identities=17%  Similarity=0.364  Sum_probs=61.1

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554           19 VGQVPKHMTEAQLLAMF------------KEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus        19 Vg~Lp~~~te~~L~~~F------------~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      +.||++++++++|++.|            ++||+|.+|+|++|+. ++++|||||+|.+.++|++|++.||++. +.|  
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~-~~G--   95 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRW-FNG--   95 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCE-ETT--
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCE-ECC--
Confidence            56777778888777666            9999999999999875 7899999999999999999999999876 555  


Q ss_pred             ccceeecc
Q 018554           87 SPLQVKYA   94 (354)
Q Consensus        87 ~~l~v~~~   94 (354)
                      +.|+|.++
T Consensus        96 r~i~v~~s  103 (104)
T 1jmt_A           96 QPIHAELS  103 (104)
T ss_dssp             EECCEEEC
T ss_pred             EEEEEEEc
Confidence            77777764

>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=99.41  E-value=3.8e-13  Score=105.03  Aligned_cols=81  Identities=20%  Similarity=0.213  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCC--CC---CCHHHHHHHHhhcCCeeEEEEeeCCC----CCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554           13 ERVKLFVGQVP--KH---MTEAQLLAMFKEFALVDEVNIIKDKT----TRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus        13 ~~~~lfVg~Lp--~~---~te~~L~~~F~~~G~v~~i~i~~d~~----tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ++++|+|.|+-  .+   --++||++.|++||+|.+|+|++|+.    +++++||+||+|.+.++|.+|++.|||+. +.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~-f~   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW-FA   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCE-ET
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCE-EC
Confidence            68999999993  22   24789999999999999999999865    46788999999999999999999999977 55


Q ss_pred             CCCccceeecccc
Q 018554           84 GASSPLQVKYADG   96 (354)
Q Consensus        84 g~~~~l~v~~~~~   96 (354)
                      |  +.|++.+...
T Consensus        98 G--R~i~v~~~~~  108 (118)
T 3ue2_A           98 G--RKVVAEVYDQ  108 (118)
T ss_dssp             T--EECEEEEECH
T ss_pred             C--cEEEEEEcCh
Confidence            5  8888887654

>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=99.36  E-value=1.8e-12  Score=101.15  Aligned_cols=81  Identities=20%  Similarity=0.328  Sum_probs=68.0

Q ss_pred             ccceEEEecCC--CCC---CHHHHHHhhccCCCeeEEEEeeCCC-----CCcceEEEEEeCCHHHHHHHHHHhCCCcccC
Q 018554          101 LEHKLFIGMLP--KNV---SEAEVSALFSIYGTIKDLQILRGSQ-----QTSKGCAFLKYETKEQALAALEAINGKHKME  170 (354)
Q Consensus       101 ~~~~l~V~~l~--~~~---t~~~l~~~F~~~G~v~~i~i~~~~~-----~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~  170 (354)
                      .+++|++.|+-  .++   .++||++.|++||.|++|.|+++..     +.++|++||+|++.++|.+|++.|||+. ++
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~-f~   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW-FA   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCE-ET
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCE-EC
Confidence            46789999983  222   3689999999999999999998742     4678999999999999999999999987 66


Q ss_pred             CCceeEEEEecCCh
Q 018554          171 GSSVPLVVKWADTE  184 (354)
Q Consensus       171 g~~~~l~v~~a~~~  184 (354)
                      |  +.|.|.+++..
T Consensus        98 G--R~i~v~~~~~~  109 (118)
T 3ue2_A           98 G--RKVVAEVYDQE  109 (118)
T ss_dssp             T--EECEEEEECHH
T ss_pred             C--cEEEEEEcChH
Confidence            6  78999998654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.33  E-value=5.1e-12  Score=95.56  Aligned_cols=81  Identities=20%  Similarity=0.352  Sum_probs=63.5

Q ss_pred             CccceeeccccccccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554           86 SSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus        86 ~~~l~v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      ...++|.|.......         ...++++++|+++|++||+|++|.|+.    .++|||||+|++.++|++|++.+++
T Consensus        10 ~~~~~v~w~~~~~~~---------~~~~~te~~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~~Ai~~~~~   76 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDE---------SKGGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAVQNEVG   76 (100)
T ss_dssp             SCEEEEECCCCSSCS---------CCCSCCHHHHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHHHHHHTCCB
T ss_pred             cceEEEeeeccCccC---------cCCCCCHHHHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHHHHHHhcCC
Confidence            456677775432111         136789999999999999999999983    5689999999999999999998655


Q ss_pred             CcccCCCceeEEEEecCCh
Q 018554          166 KHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       166 ~~~~~g~~~~l~v~~a~~~  184 (354)
                         +.+  +.|+|+|++..
T Consensus        77 ---~~g--~~l~V~~a~~~   90 (100)
T 2d9o_A           77 ---LVD--NPLKISWLEGQ   90 (100)
T ss_dssp             ---CSS--SBCEEECSSCC
T ss_pred             ---CCC--CeEEEEEccCC
Confidence               334  68999998765

>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=99.20  E-value=2.1e-11  Score=94.41  Aligned_cols=77  Identities=14%  Similarity=0.251  Sum_probs=62.3

Q ss_pred             cceEEEecCCC--C--------CCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCC
Q 018554          102 EHKLFIGMLPK--N--------VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEG  171 (354)
Q Consensus       102 ~~~l~V~~l~~--~--------~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g  171 (354)
                      ++.|.+.|+=.  .        -.++||++.|++||.|++|.|.++.   ++|++||+|++.++|.+|++.|||+. ++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~-f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRW-FAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCE-ETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            45667776621  1        1245789999999999999998763   48999999999999999999999987 666


Q ss_pred             CceeEEEEecCCh
Q 018554          172 SSVPLVVKWADTE  184 (354)
Q Consensus       172 ~~~~l~v~~a~~~  184 (354)
                        +.|.|.|+...
T Consensus        83 --R~i~v~~~~~~   93 (114)
T 3s6e_A           83 --KMITAAYVPLP   93 (114)
T ss_dssp             --EECEEEEECHH
T ss_pred             --EEEEEEEEcHH
Confidence              78999998654

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.15  E-value=9.3e-11  Score=90.80  Aligned_cols=77  Identities=19%  Similarity=0.273  Sum_probs=62.5

Q ss_pred             CCCCeEEEcCCC--CC--------CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 018554           12 EERVKLFVGQVP--KH--------MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT   81 (354)
Q Consensus        12 ~~~~~lfVg~Lp--~~--------~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~   81 (354)
                      .+++.|.|.|+=  .+        --++||++.|++||.|.+|.|.++.    .+||+||+|.+.++|.+|++.|||+. 
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~-   79 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW-   79 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE-
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE-
Confidence            467788998882  22        1245889999999999999987653    58999999999999999999999877 


Q ss_pred             CCCCCccceeeccc
Q 018554           82 LPGASSPLQVKYAD   95 (354)
Q Consensus        82 ~~g~~~~l~v~~~~   95 (354)
                      +.|  +.|++.+..
T Consensus        80 f~G--R~i~v~~~~   91 (114)
T 3s6e_A           80 FAG--KMITAAYVP   91 (114)
T ss_dssp             ETT--EECEEEEEC
T ss_pred             ECC--EEEEEEEEc
Confidence            555  788888764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=2.2e-10  Score=88.88  Aligned_cols=80  Identities=19%  Similarity=0.275  Sum_probs=65.6

Q ss_pred             cceEEEecCCCC-CCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCC-HHHHHHHHHHhC-CCcccCCCceeEEE
Q 018554          102 EHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYET-KEQALAALEAIN-GKHKMEGSSVPLVV  178 (354)
Q Consensus       102 ~~~l~V~~l~~~-~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~-~~~A~~Ai~~l~-g~~~~~g~~~~l~v  178 (354)
                      .+.|||+||+++ +++++|+++|++||+|..|.+.++..     .|||+|.+ .++|.+|+++|| +...+.+  ..+++
T Consensus        18 G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g--~~~~~   90 (121)
T 1owx_A           18 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRN--KEVTW   90 (121)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTS--SSEEE
T ss_pred             CeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeC--cEEEE
Confidence            578999999999 99999999999999999999998843     69999999 899999999995 3344666  45666


Q ss_pred             EecCChHHHH
Q 018554          179 KWADTEKERQ  188 (354)
Q Consensus       179 ~~a~~~~~~~  188 (354)
                      +......++.
T Consensus        91 evL~GeeE~~  100 (121)
T 1owx_A           91 EVLEGEVEKE  100 (121)
T ss_dssp             EECCHHHHHH
T ss_pred             EECCCHHHHH
Confidence            6665554443

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.14  E-value=1.3e-10  Score=90.28  Aligned_cols=81  Identities=11%  Similarity=0.125  Sum_probs=66.0

Q ss_pred             cCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCC-HHHHHHHHHHhcCC-ccCCCC
Q 018554            9 KSSEERVKLFVGQVPKH-MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS-RQEADKAVNACHNK-KTLPGA   85 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~-~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~-~~~A~~Ai~~l~~~-~~~~g~   85 (354)
                      -.-...+.|||+||+.+ +++++|+++|++||+|..|.++++..      .|||+|.+ .++|.+|+++++.. ..+.+ 
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g-   85 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRN-   85 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTS-
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeC-
Confidence            34567889999999999 99999999999999999999999876      59999999 89999999998633 33444 


Q ss_pred             Cccceeeccccc
Q 018554           86 SSPLQVKYADGE   97 (354)
Q Consensus        86 ~~~l~v~~~~~~   97 (354)
                       ..+++.....+
T Consensus        86 -~~~~~evL~Ge   96 (121)
T 1owx_A           86 -KEVTWEVLEGE   96 (121)
T ss_dssp             -SSEEEEECCHH
T ss_pred             -cEEEEEECCCH
Confidence             55555544443

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.97  E-value=1.8e-09  Score=78.61  Aligned_cols=70  Identities=14%  Similarity=0.331  Sum_probs=57.3

Q ss_pred             ceEEEecCC----CCCCH----HHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554          103 HKLFIGMLP----KNVSE----AEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus       103 ~~l~V~~l~----~~~t~----~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      .+|+|.-++    .+..+    .+|.+.|++||+|..++|+.|       .+||+|.+.++|.+|++ |||.. ++|  +
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mnG~~-v~G--r   76 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LNGKE-LLN--R   76 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GTTCE-ETT--E
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cCCeE-eCC--e
Confidence            467777665    23444    568999999999999999976       38999999999999998 99987 666  7


Q ss_pred             eEEEEecCC
Q 018554          175 PLVVKWADT  183 (354)
Q Consensus       175 ~l~v~~a~~  183 (354)
                      .|+|+++.+
T Consensus        77 ~LkV~lkt~   85 (91)
T 2dnr_A           77 TITIALKSP   85 (91)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            888888764

>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=98.87  E-value=1.8e-08  Score=87.46  Aligned_cols=68  Identities=21%  Similarity=0.331  Sum_probs=59.2

Q ss_pred             CCHHHHHHhhccCCCeeEEEEeeCC-----CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          114 VSEAEVSALFSIYGTIKDLQILRGS-----QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       114 ~t~~~l~~~F~~~G~v~~i~i~~~~-----~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      -.+++|++.|++||.|.++.|.++.     ++.++|++||+|.+.++|.+|++.|||+. ++|  +.|.+.+.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~-~~g--r~i~~~~~~~~  213 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW-FAG--RKVVAEVYDQE  213 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCB-SSS--SBCEEEECCHH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCce-ECC--eEEEEEEcCHH
Confidence            4678899999999999999998663     33889999999999999999999999987 777  68899998744

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.85  E-value=4.4e-09  Score=76.57  Aligned_cols=74  Identities=16%  Similarity=0.238  Sum_probs=60.1

Q ss_pred             CCCCeEEEcCCC----CCCCH----HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554           12 EERVKLFVGQVP----KHMTE----AQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus        12 ~~~~~lfVg~Lp----~~~te----~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      ...-||+|.-.+    .++-.    .+|.+.|..||+|..++++.|+        +||+|.+.++|.+||+ |++.. +.
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~-v~   74 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKE-LL   74 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCE-ET
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeE-eC
Confidence            356688887766    23333    6899999999999999999985        8999999999999998 99987 55


Q ss_pred             CCCccceeeccccc
Q 018554           84 GASSPLQVKYADGE   97 (354)
Q Consensus        84 g~~~~l~v~~~~~~   97 (354)
                      |  +.|+|+.+.++
T Consensus        75 G--r~LkV~lkt~d   86 (91)
T 2dnr_A           75 N--RTITIALKSPS   86 (91)
T ss_dssp             T--EEEEEEECCCS
T ss_pred             C--eEEEEEeCCCC
Confidence            5  78888877653

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.80  E-value=9.3e-09  Score=89.36  Aligned_cols=69  Identities=20%  Similarity=0.206  Sum_probs=59.0

Q ss_pred             CCCHHHHHHHHhhcCCeeEEEEeeCCC----CCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecccc
Q 018554           25 HMTEAQLLAMFKEFALVDEVNIIKDKT----TRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADG   96 (354)
Q Consensus        25 ~~te~~L~~~F~~~G~v~~i~i~~d~~----tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~~   96 (354)
                      +-.+++|++.|++||.|.++.|.++..    +++++|++||+|.+.++|.+|++.|||+. +.|  +.|.+.+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~-~~g--r~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW-FAG--RKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCB-SSS--SBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCce-ECC--eEEEEEEcCH
Confidence            456789999999999999999996544    45899999999999999999999999976 555  8888887653

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=2.6e-08  Score=72.83  Aligned_cols=69  Identities=17%  Similarity=0.373  Sum_probs=56.5

Q ss_pred             cceEEEecCCCC-----CCH----HHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC
Q 018554          102 EHKLFIGMLPKN-----VSE----AEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS  172 (354)
Q Consensus       102 ~~~l~V~~l~~~-----~t~----~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  172 (354)
                      ..+|+|.-++..     +.+    .+|.+.|++||+|..++|..|+       +||+|.+.++|.+||+ |||.. ++| 
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~-v~G-   84 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMK-VKG-   84 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSE-ETT-
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCee-eCC-
Confidence            467888887632     333    4688999999999999999872       9999999999999998 99988 555 


Q ss_pred             ceeEEEEec
Q 018554          173 SVPLVVKWA  181 (354)
Q Consensus       173 ~~~l~v~~a  181 (354)
                       +.|+|++.
T Consensus        85 -r~L~V~~k   92 (95)
T 1ufw_A           85 -RAVKISGP   92 (95)
T ss_dssp             -EEEEEECC
T ss_pred             -eEEEEecc
Confidence             67888764

>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=98.64  E-value=3.7e-08  Score=72.01  Aligned_cols=72  Identities=11%  Similarity=0.162  Sum_probs=58.6

Q ss_pred             CCCCCeEEEcCCCCC-----CCH----HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 018554           11 SEERVKLFVGQVPKH-----MTE----AQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT   81 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~-----~te----~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~   81 (354)
                      -.+.-||+|.-++.+     +-.    .+|.+.|..||+|..++++.|+        +||+|.+.++|.+||+ |++.. 
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~-   81 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK-   81 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE-
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee-
Confidence            456789999888643     222    5799999999999999999985        9999999999999998 99887 


Q ss_pred             CCCCCccceeecc
Q 018554           82 LPGASSPLQVKYA   94 (354)
Q Consensus        82 ~~g~~~~l~v~~~   94 (354)
                      +.+  +.|+|++.
T Consensus        82 v~G--r~L~V~~k   92 (95)
T 1ufw_A           82 VKG--RAVKISGP   92 (95)
T ss_dssp             ETT--EEEEEECC
T ss_pred             eCC--eEEEEecc
Confidence            455  77777754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.22  E-value=4.7e-06  Score=62.11  Aligned_cols=70  Identities=16%  Similarity=0.218  Sum_probs=62.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccC-----CCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIY-----GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~-----G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      .++|-+=+||+.++++.|+.+++.+     |.+++|.+..|     -+=|+|+|.|...|.+|.-+|+|.. ++|  +.|
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~e-f~g--r~L   92 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQ-FQG--KVI   92 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEE-ETT--EEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCee-ecC--eEE
Confidence            5778899999999999999999999     99999999988     5569999999999999999999987 665  677


Q ss_pred             EEE
Q 018554          177 VVK  179 (354)
Q Consensus       177 ~v~  179 (354)
                      +|-
T Consensus        93 r~g   95 (117)
T 2l9w_A           93 RSG   95 (117)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            775

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.14  E-value=9.9e-06  Score=60.41  Aligned_cols=75  Identities=11%  Similarity=0.180  Sum_probs=64.3

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEF-----ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTL   82 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~-----G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~   82 (354)
                      +...+..++|-|-|||-.++++.|+.+++++     |.+..|.+..|..      =|+|+|.|..+|-+|.-+|+|.. +
T Consensus        15 ~~~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~e-f   87 (117)
T 2l9w_A           15 RNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQ-F   87 (117)
T ss_dssp             CCTTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEE-E
T ss_pred             cCCccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCee-e
Confidence            4445678999999999999999999999999     9999999999874      69999999999999999998877 3


Q ss_pred             CCCCcccee
Q 018554           83 PGASSPLQV   91 (354)
Q Consensus        83 ~g~~~~l~v   91 (354)
                      .+  +.|++
T Consensus        88 ~g--r~Lr~   94 (117)
T 2l9w_A           88 QG--KVIRS   94 (117)
T ss_dssp             TT--EEEEE
T ss_pred             cC--eEEEe
Confidence            33  44443

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.09  E-value=2.3e-05  Score=57.99  Aligned_cols=91  Identities=19%  Similarity=0.228  Sum_probs=70.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhh-c----CCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKE-F----ALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~-~----G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      .....++|.|.|||.+++++.|.-+|+. -    |+|+++....        +-|+|+|.+.+.|++.|+.  ..+.+.+
T Consensus         4 ~~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k--~~H~L~~   73 (104)
T 2dhx_A            4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ--ADHELHG   73 (104)
T ss_dssp             SCCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC--SCCBSSS
T ss_pred             CccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC--CcceecC
Confidence            3456789999999999999999999998 2    5898887644        3689999999999999875  2445555


Q ss_pred             CCccceeeccccccccccceEEEecCCCCCC
Q 018554           85 ASSPLQVKYADGELERLEHKLFIGMLPKNVS  115 (354)
Q Consensus        85 ~~~~l~v~~~~~~~~~~~~~l~V~~l~~~~t  115 (354)
                        ..|.|...-   .+...+|++.+|+..++
T Consensus        74 --~~LsV~P~~---~~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           74 --AQLSLRPAP---PRAPARLLLQGLPPGTS   99 (104)
T ss_dssp             --SBCEEEECC---CCCCCCCCCCSCCCCCC
T ss_pred             --eEEEEEcCC---CCCcceEeeecCCCCCC
Confidence              666665432   33356899999988764

>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=97.79  E-value=0.00029  Score=51.38  Aligned_cols=79  Identities=13%  Similarity=0.278  Sum_probs=63.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC--CC-CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCce--eEE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS--QQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSV--PLV  177 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~--~~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~--~l~  177 (354)
                      +||.|++||..+||+++.+.++...++....++..+  .+ ..-.-|+|.|.+.+++....+.++|..+.|.++.  +..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            579999999999999999999999888888877653  12 2236799999999999999999999987765433  334


Q ss_pred             EEec
Q 018554          178 VKWA  181 (354)
Q Consensus       178 v~~a  181 (354)
                      |++|
T Consensus        82 VE~A   85 (91)
T 1uw4_A           82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6665

>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=97.71  E-value=0.00015  Score=52.91  Aligned_cols=72  Identities=11%  Similarity=0.135  Sum_probs=59.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC--cccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRA--SRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~--~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ++|.|++||+.+||+++.+.+....++.....+.-+.+.+  .-.-|+|.|.+.+++....+.++|..+.+.++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg   75 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKG   75 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCC
Confidence            6899999999999999999999998887777666544332  12459999999999999999999987766543

>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=97.55  E-value=0.00032  Score=51.18  Aligned_cols=58  Identities=24%  Similarity=0.419  Sum_probs=47.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      ....+-++| ++|+++...||.++|+.||-| .|+.+.|-       -|||.|.+.+.|..|++.+.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            334455666 999999999999999999954 56677774       69999999999999999763

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.36  E-value=0.0016  Score=48.08  Aligned_cols=67  Identities=19%  Similarity=0.290  Sum_probs=53.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccC-----CCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIY-----GTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~-----G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      .++|.|.|||..++++.|.-+|+.-     |+|++++...       +-|+|+|.+.+.|++.++.  ..+.+.+  .+|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k--~~H~L~~--~~L   76 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ--ADHELHG--AQL   76 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC--SCCBSSS--SBC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC--CcceecC--eEE
Confidence            5789999999999999999999762     5899998874       4689999999999998864  2344666  456


Q ss_pred             EEE
Q 018554          177 VVK  179 (354)
Q Consensus       177 ~v~  179 (354)
                      .|.
T Consensus        77 sV~   79 (104)
T 2dhx_A           77 SLR   79 (104)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            665

>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=97.30  E-value=0.0013  Score=50.16  Aligned_cols=76  Identities=20%  Similarity=0.231  Sum_probs=58.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .+-|.|-+.+... ...|.++|++||+|.+......     ..+..|+|.++.+|++||.+ ||.. +++ ...|-|+..
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~-----~NWihI~Y~s~~~A~rAL~k-NG~i-i~g-~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALSK-DGRI-FGE-SIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHTT-TTCE-ETT-TEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC-----CCeEEEEeCCHHHHHHHHHh-CCeE-ecC-CEEEEEEEC
Confidence            5678888998874 5667789999999998886321     45899999999999999974 8865 554 367888887


Q ss_pred             CChHH
Q 018554          182 DTEKE  186 (354)
Q Consensus       182 ~~~~~  186 (354)
                      ..+..
T Consensus        95 ~d~~v   99 (119)
T 1wwh_A           95 IDKNV   99 (119)
T ss_dssp             CCHHH
T ss_pred             CCHHH
Confidence            55443

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.25  E-value=0.00066  Score=50.37  Aligned_cols=73  Identities=15%  Similarity=0.191  Sum_probs=59.7

Q ss_pred             cceEEEecCCCCCC-----HHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          102 EHKLFIGMLPKNVS-----EAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       102 ~~~l~V~~l~~~~t-----~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      .++|+|.+|+.++-     .+.++++|..|+.+.....++.     -.-..|.|.+.++|.+|-..|++.. +.|  ..+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~-f~g--~~~   76 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTE-FLG--KEM   76 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSE-ETT--EEC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccce-ecC--cee
Confidence            46899999987652     2567899999999888888864     2357899999999999999999987 555  578


Q ss_pred             EEEecC
Q 018554          177 VVKWAD  182 (354)
Q Consensus       177 ~v~~a~  182 (354)
                      +|-++.
T Consensus        77 r~YFgq   82 (104)
T 1wey_A           77 KLYFAQ   82 (104)
T ss_dssp             EEECCC
T ss_pred             EEEecC
Confidence            999886

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.15  E-value=0.0011  Score=48.56  Aligned_cols=80  Identities=14%  Similarity=0.280  Sum_probs=58.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC--CCCc-ceEEEEEeCCHHHHHHHHHHhCCCcccCCC--ceeE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS--QQTS-KGCAFLKYETKEQALAALEAINGKHKMEGS--SVPL  176 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~--~~~~-~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~--~~~l  176 (354)
                      +-+|.|+.||..+||+++.+.++..-++....++...  .+.+ -.-|+|.|.+.++.....+..+|..++|.+  .-+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            3579999999999999999888776565444433321  1111 256899999999999999999998877643  3345


Q ss_pred             EEEec
Q 018554          177 VVKWA  181 (354)
Q Consensus       177 ~v~~a  181 (354)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56665

>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=97.08  E-value=0.00069  Score=49.61  Aligned_cols=53  Identities=26%  Similarity=0.414  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      -++| ++|+++...||.++|+.||- ..|..+.|-       -|||.|.+.+.|..|++.+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3555 99999999999999999994 466777774       69999999999999999873

>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=97.01  E-value=0.0021  Score=46.93  Aligned_cols=55  Identities=24%  Similarity=0.448  Sum_probs=45.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN  164 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  164 (354)
                      ++.++| .+|.++...||.++|+.||. ..|+.+.|      ..|||.|.+++.|..|+..++
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            456677 99999999999999999983 44555554      369999999999999998774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.93  E-value=0.0019  Score=49.24  Aligned_cols=66  Identities=12%  Similarity=0.174  Sum_probs=50.9

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCC
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLP   83 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~   83 (354)
                      .+..+.+.|.|-++|.. ..+.|.+.|++||+|.+.....      ...+-.|.|.+..+|++||.+ |+ .++.
T Consensus        19 ~~~~~~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~k-NG-~ii~   84 (119)
T 1wwh_A           19 EDHLDDTWVTVFGFPQA-SASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSK-DG-RIFG   84 (119)
T ss_dssp             --CGGGGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTT-TT-CEET
T ss_pred             CCCCCCCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHh-CC-eEec
Confidence            34556889999999988 4777888999999999877621      224999999999999999976 34 4343

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.78  E-value=0.0013  Score=48.30  Aligned_cols=75  Identities=8%  Similarity=0.080  Sum_probs=54.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC-CCcc-cEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTT-RASR-GCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~t-g~~~-G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ..+-+|.|+.||+.+||+++.+.+..+-++.....+.-+.+ +.++ .-|+|.|.+.++.....+.+++..+.+.++
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg   83 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKG   83 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTC
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCC
Confidence            35678999999999999999988887655443332222222 2221 358999999999999999998877666543

>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=96.74  E-value=0.0025  Score=46.66  Aligned_cols=54  Identities=24%  Similarity=0.417  Sum_probs=45.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN  164 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  164 (354)
                      +.++| ++|.++...||.++|+.|| -..|+.+.|      ..|||.|.+++.|..|+..++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            55667 9999999999999999999 455666665      369999999999999998775

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.68  E-value=0.0032  Score=46.68  Aligned_cols=74  Identities=12%  Similarity=0.170  Sum_probs=58.3

Q ss_pred             CCCeEEEcCCCCCC-C----HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554           13 ERVKLFVGQVPKHM-T----EAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~-t----e~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      -.++|+|.||+.++ .    ++.++++|..|+++......+.-.      -..|.|.+.++|.+|...||+.. +.|  +
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~-f~g--~   74 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTE-FLG--K   74 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSE-ETT--E
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccce-ecC--c
Confidence            45789999998765 3    257789999999988877777542      57899999999999999998877 444  5


Q ss_pred             cceeeccc
Q 018554           88 PLQVKYAD   95 (354)
Q Consensus        88 ~l~v~~~~   95 (354)
                      .+++-+++
T Consensus        75 ~~r~YFgq   82 (104)
T 1wey_A           75 EMKLYFAQ   82 (104)
T ss_dssp             ECEEECCC
T ss_pred             eeEEEecC
Confidence            67776665

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.63  E-value=0.0003  Score=66.80  Aligned_cols=61  Identities=10%  Similarity=0.215  Sum_probs=45.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHH
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA   75 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~   75 (354)
                      +.....++|||. .+.++++.+|.++|++||.|.++..-+++.     -||.|||.+.+++..+++.
T Consensus        48 r~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           48 RREQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHSS
T ss_pred             HHHHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHhc
Confidence            345567899997 899999999999999999999987776542     4999999999999977654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.69  E-value=0.0047  Score=58.67  Aligned_cols=58  Identities=19%  Similarity=0.268  Sum_probs=43.8

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHH
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE  161 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~  161 (354)
                      +...+.|+|. .+..+++.+|.++|++||.|.++.+.++.    .-||.|+|.+.+++..++.
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHh
Confidence            3446889998 68899999999999999999999888753    3699999999999987764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.38  E-value=0.042  Score=42.42  Aligned_cols=77  Identities=27%  Similarity=0.413  Sum_probs=52.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCC---------C-----CcceEEEEEeCCHHHHHHHHHHhCCCc
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQ---------Q-----TSKGCAFLKYETKEQALAALEAINGKH  167 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~---------~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~  167 (354)
                      .-|.|-+.|.+.+. .+.++|++||.|.+ ..+.++..         .     ....+..|+|++..+|.+||.. ||+.
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGAV   85 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTCE
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCeE
Confidence            44667778766444 46689999999866 32221100         0     1246789999999999999974 8865


Q ss_pred             ccCCCceeEEEEecCCh
Q 018554          168 KMEGSSVPLVVKWADTE  184 (354)
Q Consensus       168 ~~~g~~~~l~v~~a~~~  184 (354)
                       ++|  ..|-|+..+..
T Consensus        86 -i~G--~mIGV~Py~~~   99 (132)
T 3p3d_A           86 -FNG--VLLGVIPYTKD   99 (132)
T ss_dssp             -ETT--EECEEEECCHH
T ss_pred             -eCc--EEEEEEECCHH
Confidence             777  47888888643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.10  E-value=0.038  Score=42.69  Aligned_cols=69  Identities=17%  Similarity=0.252  Sum_probs=45.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEee------------CCCCC-CcccEEEEEeCCHHHHHHHHHHhcC
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEV-NIIK------------DKTTR-ASRGCCFVICPSRQEADKAVNACHN   78 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i-~i~~------------d~~tg-~~~G~aFV~f~~~~~A~~Ai~~l~~   78 (354)
                      ....|.|-+.|.+ ....+.+.|++||.|.+- .+.+            .+... ....+..|+|++..+|++||..  +
T Consensus         6 ~e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~--N   82 (132)
T 3p3d_A            6 GELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE--N   82 (132)
T ss_dssp             --CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT--T
T ss_pred             CceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh--C
Confidence            4567888899766 455677889999997762 1111            00001 1345789999999999999976  4


Q ss_pred             CccCCC
Q 018554           79 KKTLPG   84 (354)
Q Consensus        79 ~~~~~g   84 (354)
                      ..++.|
T Consensus        83 G~ii~G   88 (132)
T 3p3d_A           83 GAVFNG   88 (132)
T ss_dssp             TCEETT
T ss_pred             CeEeCc
Confidence            454555

>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=92.13  E-value=0.44  Score=45.92  Aligned_cols=55  Identities=25%  Similarity=0.423  Sum_probs=45.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      ...++|+ ++..+...+|.++|+.||.| +|..+.|.       .|||.|.+.+.|..+++.+.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            4466665 99999999999999999964 55555553       79999999999999999884

>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=83.80  E-value=3.3  Score=39.85  Aligned_cols=56  Identities=23%  Similarity=0.416  Sum_probs=45.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAING  165 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  165 (354)
                      +..++|+ ++..+...+|.++|+.||. .+|..+.      ...|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~wid------dt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWID------DTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECS------SSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEc------CCeEEEEECCHHHHHHHHHHHHh
Confidence            4566666 8888899999999999994 4555554      34799999999999999998854

---

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	354
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	9e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-11
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-14
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-14
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-12
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-07
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	7e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	6e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	6e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-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-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	4e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.001
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	8e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.001
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.001
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.002
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.003
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.004

>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 = 87.0 bits (214), Expect = 6e-21
 Identities = 38/185 (20%), Positives = 82/185 (44%), Gaps = 8/185 (4%)

Query: 9   KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
           K  E+  KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 69  ADKAVNACHN---KKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSI 125
            D A+NA  +    + +    +  +             K+F+G + ++  E  +   F  
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120

Query: 126 YGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE 184
           YG I+ ++I+        +G AF+ ++  +     +      H + G      V+ A ++
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI--QKYHTVNGH--NCEVRKALSK 176

Query: 185 KERQA 189
           +E  +
Sbjct: 177 QEMAS 181

>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 = 73.0 bits (179), Expect = 6e-17
 Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 4/87 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALE 161
           K+ +  +P   ++ E+  LFS +G +K +++ +    T   +G  F+ + TK+ A  A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQ 188
           A+     + G    LV++WAD+E   Q
Sbjct: 70  ALCHSTHLYGR--RLVLEWADSEVTVQ 94

>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 = 69.2 bits (169), Expect = 2e-15
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 8/101 (7%)

Query: 3   ESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT-TRASRGCCFV 61
           +  K++ +S    K+ V  +P    + ++  +F  F  +  V + K  T T A RG  FV
Sbjct: 1   QVPKKQTTS----KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 56

Query: 62  ICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERLE 102
              ++Q+A KA NA  +   L G    L +++AD E   ++
Sbjct: 57  DFITKQDAKKAFNALCHSTHLYG--RRLVLEWADSE-VTVQ 94

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 71.1 bits (174), Expect = 2e-16
 Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 2/79 (2%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L++  LP+ +++ ++  +F  YG+I    ILR       +G AF++Y  +E+A  A+ A
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +N     EG S PL V+ A
Sbjct: 68  LNNV-IPEGGSQPLSVRLA 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 = 67.3 bits (164), Expect = 5e-15
 Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L+V  +P+ +T+ QL  +F ++  + + NI++DK T   RG  FV    R+EA +A++A
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 76 CHNKKTLPGASSPLQVKYA 94
           +N     G S PL V+ A
Sbjct: 68 LNNVI-PEGGSQPLSVRLA 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 = 68.9 bits (168), Expect = 1e-15
 Identities = 26/79 (32%), Positives = 48/79 (60%), Gaps = 2/79 (2%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEA 162
            L++  LPK +++ E+  LFS YG I   +IL       S+G  F++++ + +A  A++ 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +NG+ K  G++ P+ VK+A
Sbjct: 68  LNGQ-KPSGATEPITVKFA 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 = 64.3 bits (156), Expect = 8e-14
 Identities = 27/85 (31%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
          +S     L+V  +PK MT+ +L  +F ++  +    I+ D+ T  SRG  F+    R EA
Sbjct: 2  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 61

Query: 70 DKAVNACHNKKTLPGASSPLQVKYA 94
          ++A+   + +K   GA+ P+ VK+A
Sbjct: 62 EEAIKGLNGQK-PSGATEPITVKFA 85

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (165), Expect = 9e-15
 Identities = 24/99 (24%), Positives = 46/99 (46%), Gaps = 5/99 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L+I  LP  ++  E+  +F  YG I+ ++   G+   ++G A++ YE    A  A + +
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNL 202
           +G   +      LVV + +  +  Q    +K + Q   L
Sbjct: 67  SGF-NVCNR--YLVVLYYNANRAFQKMDTKKKEEQLKLL 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 = 47.3 bits (112), Expect = 2e-07
 Identities = 19/116 (16%), Positives = 41/116 (35%), Gaps = 13/116 (11%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            L++  +P  +T  ++  +F ++     +  I+   T  +RG  +V+     +A  A + 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKY---GPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 76  CHNKKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKD 131
                 +      L V Y +      +       +     E ++  L   YG   D
Sbjct: 66  LSGFN-VCN--RYLVVLYYNANRAFQK-------MDTKKKEEQLKLLKEKYGINTD 111

>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 = 67.0 bits (163), Expect = 1e-14
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQI---LRGSQQTSKGCAFLKYETKEQALAAL 160
           +LFIG +PK     E+    +         I       +  ++G AF++YE+   A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
             +    +++     + V WA+ E +      + 
Sbjct: 63  RKLMP-GRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-11
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDE--VNIIKDKTTRASRGCCFVICPSRQEADKAV 73
           +LF+G +PK     ++L    +        +          +RG  FV   S + A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 74  NACHNKKTLPGASSPLQVKYADGELER 100
                 +        + V +A+ E++ 
Sbjct: 63  RKLMPGRIQLW-GHQIAVDWAEPEIDV 88

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.7 bits (160), Expect = 2e-14
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           KL +  L   VS+A++  LF+ +GT+K   +       S G A + +E K  AL A++  
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 164 NGKHKMEGSSVPLVVKWADT 183
           NG   ++G   P+ ++   +
Sbjct: 62  NGV-PLDGR--PMNIQLVTS 78

>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 = 56.9 bits (137), Expect = 3e-11
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KL V  +   +++A +  +F EF  + +  +  D++ R S G   V    + +A KA+  
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAMKQ 60

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           +    L G   P+ ++   
Sbjct: 61 YNGVP-LDG--RPMNIQLVT 77

>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 = 65.5 bits (159), Expect = 2e-14
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 7/85 (8%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           +KL+IG L   V+  ++  LF         Q+L        G AF+ Y  +  A+ A+E 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIET 56

Query: 163 INGKHKMEGSSVPLVVKWADTEKER 187
           ++GK ++ G    + V ++ ++K R
Sbjct: 57  LSGKVELHGK--IMEVDYSVSKKLR 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 = 48.9 bits (116), Expect = 2e-08
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           KL++G +   +T   L  +F +  L     ++         G  FV  P +  A +A+  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIET 56

Query: 76  CHNKKTLPGASSPLQVKYADGELER 100
              K  L G    ++V Y+  +  R
Sbjct: 57  LSGKVELHG--KIMEVDYSVSKKLR 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 = 64.6 bits (157), Expect = 5e-14
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L+VG +   +TEA L   F     +  + + +D  TR S G  +V      +A++A++ 
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 76 CHNKKTLPGASSPLQVKYA 94
           +    + G   P+++ ++
Sbjct: 62 MNFDV-IKG--KPVRIMWS 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 = 63.8 bits (155), Expect = 8e-14
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L++G L  +V+EA +   FS  G I  +++ R    + S G A++ ++    A  AL+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +N    ++G   P+ + W+
Sbjct: 62  MNFD-VIKGK--PVRIMWS 77

>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 = 63.6 bits (154), Expect = 1e-13
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 5/85 (5%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAALEA 162
           +FIG L   + E  +   FS +G I     +     T  SKG AF+ + + + + AA+EA
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 163 INGKHKMEGSSVPLVVKWADTEKER 187
           +NG   +     P+ V +A  +  +
Sbjct: 61  MNG-QYLCNR--PITVSYAFKKDSK 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 = 54.4 bits (130), Expect = 2e-10
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 4/85 (4%)

Query: 17  LFVGQVPKHMTEAQLLAMFKEFALVDEVNII-KDKTTRASRGCCFVICPSRQEADKAVNA 75
           +F+G +   + E  L   F  F ++ +   I +D  T  S+G  F+   S   +D A+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 76  CHNKKTLPGASSPLQVKYADGELER 100
            + +  L     P+ V YA  +  +
Sbjct: 61  MNGQY-LCN--RPITVSYAFKKDSK 82

>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 = 63.1 bits (153), Expect = 2e-13
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 5/93 (5%)

Query: 8   KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
           K++ ++   L V  +P   TE  L   F  F  V  V + KD  T  S+G  FV     +
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 68  EADKAVNACHNKKTLPGASSPLQVKYADGELER 100
              K ++  H    + G       K  + +  +
Sbjct: 62  TQVKVMSQRH---MIDG--RWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 16/85 (18%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L +  LP   +E ++   FS +G +  +Q+ +  +   SKG  F+++   E     ++ 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE---TQVKV 66

Query: 163 INGKHKMEGSSVPLVVKWADTEKER 187
           ++ +H ++G       K  ++++ +
Sbjct: 67  MSQRHMIDGR--WCDCKLPNSKQSQ 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 = 61.6 bits (149), Expect = 7e-13
 Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            +FI  L K++    +   FS +G I   +++   +  SKG  F+ +ET+E A  A+E +
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-DENGSKGYGFVHFETQEAAERAIEKM 68

Query: 164 NGKHKMEGSSVPLVVKWADTEKER 187
           NG   +      + V    + KER
Sbjct: 69  NG-MLLNDR--KVFVGRFKSRKER 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 = 49.6 bits (118), Expect = 1e-08
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            +F+  + K +    L   F  F  +    ++ D+    S+G  FV   +++ A++A+  
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 67

Query: 76  CHNKKTLPGASSPLQVKYADGELER 100
            +    L      + V       ER
Sbjct: 68  MNGML-LND--RKVFVGRFKSRKER 89

>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 = 9e-13
 Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 2   AESKKEKKSSEERV--KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCC 59
                +  S EER    +F  Q+   +    L   F     V +V II D+ +R S+G  
Sbjct: 4   VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 63

Query: 60  FVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADGELERL 101
           +V     Q    A+      + L G   P+ V+ +  E  RL
Sbjct: 64  YVEFCEIQSVPLAIGL--TGQRLLG--VPIIVQASQAEKNRL 101

>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 = 56.6 bits (136), Expect = 5e-11
 Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 5/90 (5%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQAL 157
           ER    +F   L   +   ++   FS  G ++D++I+     + SKG A++++   +   
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 158 AALEAINGKHKMEGSSVPLVVKWADTEKER 187
            A+    G  ++ G   P++V+ +  EK R
Sbjct: 75  LAIGL-TG-QRLLGV--PIIVQASQAEKNR 100

>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 = 60.4 bits (146), Expect = 1e-12
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 5/88 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALE 161
           HKLFIG LP  +++ +V  L + +G +K   +++ S    SKG AF +Y        A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQA 189
            +NG  ++      L+V+ A +   + A
Sbjct: 62  GLNG-MQLGDK--KLLVQRA-SVGAKNA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 8e-12
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          KLF+G +P ++ + Q+  +   F  +   N++KD  T  S+G  F         D+A+  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           +  + L      L V+ A 
Sbjct: 63 LNGMQ-LGD--KKLLVQRAS 79

>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 = 60.5 bits (146), Expect = 3e-12
 Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 4/91 (4%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
           +++K+  E+  KLF+G +    TE  L   ++++  + +  +++D  ++ SRG  FV  
Sbjct: 10 LERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 69

Query: 64 PSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           S  E D A+ A     ++ G    ++ K A
Sbjct: 70 SSMAEVDAAMAA--RPHSIDG--RVVEPKRA 96

>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 = 54.3 bits (130), Expect = 3e-10
 Identities = 29/110 (26%), Positives = 51/110 (46%), Gaps = 10/110 (9%)

Query: 79  KKTLPGASSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS 138
           +KTL   + PL+ K  + E  R   KLFIG L    +E  +   +  +G + D  ++R  
Sbjct: 2   EKTL--ETVPLERKKREKEQFR---KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP 56

Query: 139 Q-QTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKER 187
             + S+G  F+ + +  +  AA+ A    H ++G    +  K A   +E 
Sbjct: 57  ASKRSRGFGFVTFSSMAEVDAAMAARP--HSIDGR--VVEPKRAVAREES 102

>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 = 59.2 bits (143), Expect = 4e-12
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+F+G +    T+  L   F +F  V E  +++D  T+ SRG  FV    +   DK +  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 76 CHNKKTLPGASSPLQVKYA 94
            ++  L      +  K A
Sbjct: 62 --SRHELDS--KTIDPKVA 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 = 57.7 bits (139), Expect = 1e-11
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+FIG L    ++  +   F  +G +K+  ++R    + S+G  F+ +  +      L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 163 INGKHKMEGSSVPLVVKWA 181
              +H+++     +  K A
Sbjct: 62  --SRHELDSK--TIDPKVA 76

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (143), Expect = 6e-12
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 4/93 (4%)

Query: 97  ELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC-AFLKYETKEQ 155
           +L +    L++G L    +E ++  LFS  G IK + +     + +     F++Y ++  
Sbjct: 2   KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 61

Query: 156 ALAALEAINGKHKMEGSSVPLVVKWADTEKERQ 188
           A  A+  ING  +++     +   W    KE +
Sbjct: 62  AENAMRYING-TRLDDR--IIRTDWDAGFKEGR 91

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 3e-11
 Identities = 24/96 (25%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 5   KKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICP 64
           K  KKS      L+VG +  + TE Q+  +F +   + ++ +  DK  + + G CFV   
Sbjct: 2   KLLKKSC----TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 57

Query: 65  SRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           SR +A+ A+   +  + L      ++  +  G  E 
Sbjct: 58  SRADAENAMRYINGTR-LDD--RIIRTDWDAGFKEG 90

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 8e-12
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+F+G +    T+  L   F +F  V +  +  D  T  SRG  FV+    +  DK ++ 
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 76 CHNKKTLPGASSPLQVKYA 94
             +  L G    +  K A
Sbjct: 61 --KEHKLNG--KVIDPKRA 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 = 50.8 bits (121), Expect = 3e-09
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+FIG L  + ++ ++   FS +G + D  +        S+G  F+ ++  E     ++ 
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 163 INGKHKMEGSSVPLVVKWA 181
               HK+ G    +  K A
Sbjct: 61  KE--HKLNGK--VIDPKRA 75

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 22/92 (23%), Positives = 45/92 (48%), Gaps = 9/92 (9%)

Query: 103 HKLFIGMLPKNVSEAEV----SALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           H ++I  L + + + E+     A+FS +G I D+ + R      +G AF+ ++    A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATN 61

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQAR 190
           AL ++ G         P+ +++A T+ +  A+
Sbjct: 62  ALRSMQG-FPFYDK--PMRIQYAKTDSDIIAK 90

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 4/86 (4%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKE-FALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVN 74
            +++  + + + + +L       F+   ++  I    +   RG  FVI      A  A+ 
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 75  ACHNKKTLPGASSPLQVKYADGELER 100
           +            P++++YA  + + 
Sbjct: 65  SMQGFP-FYD--KPMRIQYAKTDSDI 87

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 23/86 (26%), Positives = 45/86 (52%), Gaps = 4/86 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L++G L + V +  + A F  +G I D+QI    + +  +G AF+++E  E A AA++ 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQ 188
           +N   ++ G    + V  A   + ++
Sbjct: 67  MNE-SELFGR--TIRVNLAKPMRIKE 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 = 56.2 bits (135), Expect = 6e-11
 Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 12/94 (12%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
          MA +K+          L+VG + + + +  L A F  F  + ++ I  D  T   RG  F
Sbjct: 1  MATTKR---------VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 51

Query: 61 VICPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
          V     ++A  A++  +  + L G    ++V  A
Sbjct: 52 VEFELAEDAAAAIDNMNESE-LFG--RTIRVNLA 82

>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 = 56.8 bits (137), Expect = 4e-11
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 11/86 (12%)

Query: 104 KLFIGML-PKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           ++FIG L    V +++V A+FS YG I    +        KG AF++Y  +  A AA+  
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAG 69

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQ 188
            +G   + G    L +  A   K  +
Sbjct: 70  EDG-RMIAGQ--VLDINLAAEPKVNR 92

>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 = 41.4 bits (97), Expect = 1e-05
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 12/92 (13%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLL-AMFKEFALVDEVNIIKDKTTRASRGCCFVI 62
          S  +        ++F+G +   + +   + A+F ++  +   ++         +G  FV 
Sbjct: 5  SSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQ 56

Query: 63 CPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
            + + A  AV     +  + G    L +  A
Sbjct: 57 YVNERNARAAVAGEDGRM-IAG--QVLDINLA 85

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 5e-11
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 4/86 (4%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
          K  E+  KLF+G +    T+  L + F+++  + +  +++D  T+ SRG  FV   + +E
Sbjct: 1  KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 69 ADKAVNACHNKKTLPGASSPLQVKYA 94
           D A+NA      + G    ++ K A
Sbjct: 61 VDAAMNA--RPHKVDG--RVVEPKRA 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 = 53.9 bits (129), Expect = 3e-10
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           KLFIG L    ++  + + F  +GT+ D  ++R    + S+G  F+ Y T E+  AA+ A
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 163 INGKHKMEGSSVPLVVKWA 181
               HK++G    +  K A
Sbjct: 68  RP--HKVDGR--VVEPKRA 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 = 56.2 bits (135), Expect = 5e-11
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 4/79 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRGSQQTSKGCAFLKYETKEQALAALEA 162
            L +  LP+++++ E+ ALF   G I     +       S G AF+ + ++  +  A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +NG   +      L V +A
Sbjct: 64  LNG-ITVRNK--RLKVSYA 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 = 53.5 bits (128), Expect = 5e-10
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L V  +P+ MT+ +L A+F+    ++   I++D  T  S G  FV   S  ++ +A+  
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 76 CHNKKTLPGASSPLQVKYA 94
           +    +      L+V YA
Sbjct: 64 LNGIT-VRN--KRLKVSYA 79

>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 = 56.2 bits (135), Expect = 5e-11
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             L++G L ++V+E  +  LFS  G  K  ++      ++    F+++     A AAL A
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKM-ITEHTSNDPYCFVEFYEHRDAAAALAA 67

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQ 188
           +NG  K+ G    + V WA T   ++
Sbjct: 68  MNG-RKILGK--EVKVNWATTPSSQK 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 = 48.1 bits (114), Expect = 5e-08
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L+VG + + +TE  +L +F +        +I + T+      CFV     ++A  A+ A
Sbjct: 10 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 67

Query: 76 CHNKKTLPGASSPLQVKYA 94
           + +K + G    ++V +A
Sbjct: 68 MNGRK-ILG--KEVKVNWA 83

>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 = 56.3 bits (135), Expect = 6e-11
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 5/81 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           +  G L   VS  ++  +    G +  L         +K  +F +Y T E++  A   +N
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALL-----MPPNKPYSFARYRTTEESKRAYVTLN 77

Query: 165 GKHKMEGSSVPLVVKWADTEK 185
           GK  ++     + +     EK
Sbjct: 78  GKEVVDDLGQKITLYLNFVEK 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 = 48.2 bits (114), Expect = 5e-08
 Identities = 15/89 (16%), Positives = 34/89 (38%), Gaps = 8/89 (8%)

Query: 8  KKSSEERVKLFV--GQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS 65
          +  S     L V  G +   ++  QLL + ++  LVD + +  +K         F    +
Sbjct: 12 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRT 65

Query: 66 RQEADKAVNACHNKKTLPGASSPLQVKYA 94
           +E+ +A    + K+ +      + +   
Sbjct: 66 TEESKRAYVTLNGKEVVDDLGQKITLYLN 94

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 7e-11
 Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 4/86 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 160
           +  +++G L + VSE  +  LF   G + +  + +       +G  F+++ ++E A  A+
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKE 186
           + ++   K+ G   P+ V  A    +
Sbjct: 69  KIMDM-IKLYGK--PIRVNKASAHNK 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 = 52.3 bits (125), Expect = 2e-09
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           ++VG + + ++E  L  +F +   V   ++ KD+ T   +G  FV   S ++AD A+  
Sbjct: 11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 76 CHNKKTLPGASSPLQVKYAD 95
              K L G   P++V  A 
Sbjct: 71 MDMIK-LYG--KPIRVNKAS 87

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.8 bits (134), Expect = 8e-11
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKG----CAFLKYETKEQALAAL 160
           LFI  L  + +E  +  +FS  G IK   I +   +          F++Y+  EQA  AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQA 189
           + + G H ++G    L V+ ++    + A
Sbjct: 61  KQLQG-HTVDGH--KLEVRISE-RATKPA 85

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT---TRASRGCCFVICPSRQEADKAV 73
          LF+  +    TE  L  +F +   +    I K K       S G  FV     ++A KA+
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 74 NACHNKKTLPGASSPLQVKYAD 95
                  + G    L+V+ ++
Sbjct: 61 KQLQGHT-VDG--HKLEVRISE 79

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+FVG +     E ++   F  F  V+ + +  D  T   RG CF+     +   K +  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 76 CHNKKTLPGASSPLQVKYA 94
                +    S  ++K A
Sbjct: 61 --KYHNVGL--SKCEIKVA 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 = 53.0 bits (127), Expect = 6e-10
 Identities = 15/79 (18%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G L  +  E ++   F  +G ++ +++   ++    +G  F+ ++ +E     +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 163 INGKHKMEGSSVPLVVKWA 181
               H +  S     +K A
Sbjct: 60  -KKYHNVGLSKC--EIKVA 75

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 2e-10
 Identities = 25/100 (25%), Positives = 51/100 (51%), Gaps = 4/100 (4%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETK 153
           D  ++R    +F+G +P   +E ++  +FS  G +   +++   +    KG  F +Y+ +
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 154 EQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQ 193
           E AL+A+  +NG  +  G    L V  A +EK ++  ++ 
Sbjct: 61  ETALSAMRNLNG-REFSGR--ALRVDNAASEKNKEELKSL 97

>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 = 45.9 bits (108), Expect = 3e-07
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            +FVG +P   TE QL  +F E   V    ++ D+ T   +G  F     ++ A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 76  CHNKKTLPGASSPLQVKYADGELERLEHK 104
            + ++   G    L+V  A  E  + E K
Sbjct: 70  LNGRE-FSG--RALRVDNAASEKNKEELK 95

>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 = 54.8 bits (131), Expect = 3e-10
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 7/102 (6%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQA--LAALEA 162
            F G L       ++  LFS +G IK +  +R           + ++ K +     A +A
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-----GAKEGIILFKEKAKEALGKAKDA 68

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPN 204
            NG  ++    V   V   + EKE   +  +  Q   N   +
Sbjct: 69  NNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKS 110

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 7e-07
 Identities = 15/98 (15%), Positives = 33/98 (33%), Gaps = 11/98 (11%)

Query: 10  SSEER---VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
           S EE+   +  F G +        L  +F     +  ++ ++            ++   +
Sbjct: 4   SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEK 57

Query: 67  QEA--DKAVNACHNKKTLPGASSPLQVKYADGELERLE 102
            +    KA +A +    L       +V   + E E L+
Sbjct: 58  AKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALK 95

>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 = 53.6 bits (128), Expect = 3e-10
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+FVG +  + T   +   F++F  VD+  ++ DKTT   RG  FV   S    +K    
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 76 CHNKKTLPGASSPLQVKYA 94
            +   +      ++ K A
Sbjct: 61 --HFHEINN--KMVECKKA 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 = 52.4 bits (125), Expect = 7e-10
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G L  N +  +V   F  +G + D  ++        +G  F+ +E+++      E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 163 INGKHKMEGSSVPLVVKWA 181
            +  H++      +  K A
Sbjct: 61  -HF-HEINNK--MVECKKA 75

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 3e-10
 Identities = 25/89 (28%), Positives = 48/89 (53%), Gaps = 4/89 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 160
           E KLF+G L  + +E  +  +FS YG I ++ +++  + Q S+G  F+ +E  + A  A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 161 EAINGKHKMEGSSVPLVVKWADTEKERQA 189
            A+NG   ++G    + V  A    + ++
Sbjct: 65  MAMNG-KSVDGR--QIRVDQAGKSSDNRS 90

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 3e-09
 Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 4/85 (4%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
          +S+E  KLFVG +     E  L  +F ++  + EV ++KD+ T+ SRG  FV   +  +A
Sbjct: 2  ASDEG-KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 70 DKAVNACHNKKTLPGASSPLQVKYA 94
            A+ A + K  + G    ++V  A
Sbjct: 61 KDAMMAMNGKS-VDG--RQIRVDQA 82

>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 = 53.5 bits (128), Expect = 5e-10
 Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 5/94 (5%)

Query: 94  ADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETK 153
            + E +    +L +  +P    + ++  +F  +G I D   +  +++ SKG  F+ +E  
Sbjct: 3   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILD-VEIIFNERGSKGFGFVTFENS 61

Query: 154 EQALAALEAINGKHKMEGSSVPLVVKWADTEKER 187
             A  A E ++G   +EG    + V  A T +  
Sbjct: 62  ADADRAREKLHG-TVVEGR--KIEVNNA-TARVM 91

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 5/91 (5%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S    +S     +L V  +P    +  L  MF +F  + +V II ++    S+G  FV  
Sbjct: 1  SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 58

Query: 64 PSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           +  +AD+A    H    + G    ++V  A
Sbjct: 59 ENSADADRAREKLHGTV-VEG--RKIEVNNA 86

>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 = 53.7 bits (128), Expect = 6e-10
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
            E   +F+  +     E  L  + ++F  +  V ++    T  S+GC F    +++ A 
Sbjct: 5  VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 71 KAVNACHNKKTLPGAS---SPLQVKYA 94
          K + A   +    G       L+V  A
Sbjct: 65 KCLAAASLEAEGGGLKLDGRQLKVDLA 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 = 47.9 bits (113), Expect = 6e-08
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRGSQQTSKGCAFLKYETKEQALAALEA 162
            +FI  L  +  E  +  +   +G +K +  +L    + SKGCAF ++ T+E A   L A
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 163 INGKHKMEGSSV---PLVVKWADTEKER 187
            + + +  G  +    L V  A T  E 
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 53.1 bits (127), Expect = 6e-10
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 9  KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQE 68
          + +++   + V  + +   E  L  +F+ F  +  + + KDKTT  S+G  F+    R++
Sbjct: 3  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 69 ADKAVNACHNKKTLPGASSPLQVKYA 94
          A +A+               L V++A
Sbjct: 63 AARAIAGVSGFG-YDH--LILNVEWA 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 = 49.3 bits (117), Expect = 2e-08
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAAL 160
              + +  L ++  E ++  LF  +G+I  + + +      SKG AF+ +  +E A  A+
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 161 EAINGKHKMEGSSVPLVVKWA 181
             ++G    +     L V+WA
Sbjct: 68  AGVSG-FGYDHL--ILNVEWA 85

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 17/86 (19%), Positives = 43/86 (50%), Gaps = 5/86 (5%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
           + ++++G LP ++   ++  +F  YG I+D+ +    ++     AF+++E    A  A+ 
Sbjct: 14  DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVY 71

Query: 162 AINGKHKMEGSSVPLVVKWADTEKER 187
             +G +  +G    L V++  + +  
Sbjct: 72  GRDG-YDYDGY--RLRVEFPRSGRGT 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 = 42.7 bits (100), Expect = 4e-06
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEA 69
          +     +++VG +P  +    +  +F ++     +  I  K  R      FV     ++A
Sbjct: 10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKY---GAIRDIDLKNRRGGPPFAFVEFEDPRDA 66

Query: 70 DKAVNACHNKKTLPGASSPLQVKYADGE 97
          + AV          G    L+V++    
Sbjct: 67 EDAVYGRDGYD-YDG--YRLRVEFPRSG 91

>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 = 18/86 (20%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            L++  L  + SE  +   F+        ++ +      +  AF+ +  +E A+ A++A+
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKAL 64

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQA 189
           NG   ++GS  P+ V  A    ++ +
Sbjct: 65  NG-KVLDGS--PIEVTLA-KPVDKDS 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 10/88 (11%)

Query: 7  EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
          E   S  ++ L+V  +    +E  +   F              +  +  R   FV   +R
Sbjct: 2  EDTMSSVKI-LYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNR 54

Query: 67 QEADKAVNACHNKKTLPGASSPLQVKYA 94
          ++A +A+ A + K  L G  SP++V  A
Sbjct: 55 EDAVEAMKALNGKV-LDG--SPIEVTLA 79

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            ++ G +   +++  +   FS +G I ++++           +F+++ T E A  A+ ++
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFVRFSTHESAAHAIVSV 74

Query: 164 NGKHKMEGSSVPLVVKWA 181
           NG   +EG    +   W 
Sbjct: 75  NG-TTIEGH--VVKCYWG 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 = 49.6 bits (118), Expect = 1e-08
 Identities = 13/87 (14%), Positives = 34/87 (39%), Gaps = 9/87 (10%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
           +SS +   ++ G +   +T+  +   F  F  + E+ +  +K         FV   + +
Sbjct: 12 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHE 65

Query: 68 EADKAVNACHNKKTLPGASSPLQVKYA 94
           A  A+ + +    + G    ++  + 
Sbjct: 66 SAAHAIVSVNGTT-IEG--HVVKCYWG 89

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 17/104 (16%), Positives = 43/104 (41%), Gaps = 5/104 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           ++ +  L   V+   +  +FS +GT+  +       + ++  A L+Y     A  A  ++
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF---TKNNQFQALLQYADPVSAQHAKLSL 65

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQAN-NLPNAD 206
           +G+  +  +   L + ++            K++     +LP+ D
Sbjct: 66  DGQ-NIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGD 108

>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 = 42.7 bits (100), Expect = 5e-06
 Identities = 10/79 (12%), Positives = 28/79 (35%), Gaps = 5/79 (6%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          ++ V  +   +T   L  +F +F  V ++          ++    +       A  A  +
Sbjct: 9  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS 64

Query: 76 CHNKKTLPGASSPLQVKYA 94
             +  +  A   L++ ++
Sbjct: 65 LDGQN-IYNACCTLRIDFS 82

>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 = 50.9 bits (121), Expect = 3e-09
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+FVG + +   E  L   F+++  ++ + I+ D+ +   RG  FV        DK V  
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 76 CHNKKTLPGASSPLQVKYA 94
               T+ G     +V+ A
Sbjct: 63 -QKYHTVNG--HNCEVRKA 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 = 40.9 bits (95), Expect = 1e-05
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
           K+F+G + ++  E  +   F  YG I+ ++I+        +G AF+ ++  +     +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 163 INGKHKMEGSSVPLVVKWA 181
               H + G      V+ A
Sbjct: 64  -KY-HTVNGH--NCEVRKA 78

>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 = 22/78 (28%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           +LF+G LP +++E E+  LF  YG   ++          KG  F++ ET+  A  A   +
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVF-----IHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 164 NGKHKMEGSSVPLVVKWA 181
           +    + G    L V++A
Sbjct: 65  DN-MPLRGK--QLRVRFA 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 = 47.7 bits (113), Expect = 5e-08
 Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 10/88 (11%)

Query: 7  EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
          EK  ++   +LFVG +P  +TE ++  +F+++    EV I KDK         F+   +R
Sbjct: 2  EKTFTQRS-RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETR 54

Query: 67 QEADKAVNACHNKKTLPGASSPLQVKYA 94
            A+ A     N   L G    L+V++A
Sbjct: 55 TLAEIAKVELDNMP-LRG--KQLRVRFA 79

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 4e-09
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 3/97 (3%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
           +   +K   E   LF+  +P+   +  LL MF  F  V    +  DK T  S+   FV  
Sbjct: 8   AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
            +   A  A+ + +  + +      L+V+    + + 
Sbjct: 68  DNPVSAQAAIQSMNGFQ-IGM--KRLKVQLKRSKNDS 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 = 50.9 bits (121), Expect = 6e-09
 Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEA 162
            LFI  LP+   + ++  +F  +G +   ++    Q   SK   F+ Y+    A AA+++
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 163 INGKHKMEGSSVPLVVKWADTEKER 187
           +NG  ++      L V+   ++ + 
Sbjct: 80  MNG-FQIGMK--RLKVQLKRSKNDS 101

>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 = 50.5 bits (120), Expect = 4e-09
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEA 162
            L +  LP+N+++ E  +LF   G I+  +++R      S G  F+ Y   + A  A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 163 INGKHKMEGSSVPLVVKWA 181
           +NG  +++     + V +A
Sbjct: 64  LNG-LRLQTK--TIKVSYA 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 = 47.4 bits (112), Expect = 5e-08
 Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 3/81 (3%)

Query: 14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAV 73
          +  L V  +P++MT+ +  ++F     ++   +++DK T  S G  FV     ++A+KA+
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 74 NACHNKKTLPGASSPLQVKYA 94
          N  +  + L      ++V YA
Sbjct: 62 NTLNGLR-LQT--KTIKVSYA 79

>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 = 50.9 bits (121), Expect = 5e-09
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 4/88 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT-SKGCAFLKYETKEQALAALEA 162
           +LF+  L    SE ++  LFS YG + +L     S     KG AF+ +   E A+ A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQAR 190
           ++G    +G    L V  +  +KE    
Sbjct: 70  VDG-QVFQGR--MLHVLPSTIKKEASQS 94

>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 = 47.4 bits (112), Expect = 8e-08
 Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 3/90 (3%)

Query: 11  SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEAD 70
           S    +LFV  +    +E  L  +F  +  + E++   D  T+  +G  FV     + A 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 71  KAVNACHNKKTLPGASSPLQVKYADGELER 100
           KA      +    G    L V  +  + E 
Sbjct: 65  KAYAEVDGQV-FQG--RMLHVLPSTIKKEA 91

>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 = 50.2 bits (119), Expect = 7e-09
 Identities = 13/80 (16%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L++   P   T+  +  + ++  +V     +       SR   ++   S+++A   V  
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 76 CHNKKTLPGASSPLQVKYAD 95
           +  K + G    L  K ++
Sbjct: 63 LNGLK-IEG--YTLVTKVSN 79

>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 = 49.4 bits (117), Expect = 1e-08
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 102 EHKLFIGMLPKNVSEAEVSALFSIYGTIK-DLQILRGSQQTSKGCAFLKYETKEQALAAL 160
           E  L++   P + ++  +  L      +   +++      TS+  A++   +KE A   +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 161 EAINGKHKMEGSSVPLVVKWAD 182
           E +NG  K+EG    LV K ++
Sbjct: 61  EKLNG-LKIEGY--TLVTKVSN 79

>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 = 8e-09
 Identities = 17/73 (23%), Positives = 36/73 (49%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
          + + +    L V  +  + TE  L  +F ++  + +V+I+ D+ +R SRG  FV   +  
Sbjct: 3  RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62

Query: 68 EADKAVNACHNKK 80
          +A +A    +  +
Sbjct: 63 DAKEAKERANGME 75

>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 = 48.2 bits (114), Expect = 3e-08
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALE 161
             L +  L    +E ++  +FS YG I D+ I+   Q + S+G AF+ +E  + A  A E
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 162 AINGK 166
             NG 
Sbjct: 70  RANGM 74

>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 = 50.2 bits (119), Expect = 1e-08
 Identities = 20/95 (21%), Positives = 40/95 (42%), Gaps = 3/95 (3%)

Query: 6   KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPS 65
                 E    L++  +   +TE  L+++F  F       I     T   RG  F+  P+
Sbjct: 10  SSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN 69

Query: 66  RQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
           ++ A +A++  +  K L G    L +++   + +R
Sbjct: 70  KEIAWQALHLVNGYK-LYG--KILVIEFGKNKKQR 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 = 46.7 bits (110), Expect = 2e-07
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRGSQQTSKGCAFLKYETKEQALAALE 161
             L++  L   V+E ++ +LF+ +   K      R      +G AF+ +  KE A  AL 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 162 AINGKHKMEGSSVPLVVKWADTEKER 187
            +NG +K+ G    LV+++   +K+R
Sbjct: 79  LVNG-YKLYGK--ILVIEFGKNKKQR 101

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
            +L++G L  N S A ++  F  +G+I+ +             A+++YE+ + A AA   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTID-----HVKGDSFAYIQYESLDAAQAACAK 72

Query: 163 INGKHKMEGSSVPLVVKWADTEK 185
           + G   + G    L V +A +  
Sbjct: 73  MRGF-PLGGPDRRLRVDFAKSGP 94

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          +L+VG +  + + A L   F  F  +  ++ +K  +        ++   S   A  A   
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACAK 72

Query: 76 CHNKKTLPGASSPLQVKYADGE 97
                L G    L+V +A   
Sbjct: 73 MRGFP-LGGPDRRLRVDFAKSG 93

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 6/97 (6%)

Query: 2   AESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFV 61
            +++  K+  ++   L++  +P  M E +L  M K F  V    I++D +   SRG  F 
Sbjct: 6   VQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT-SRGVGFA 64

Query: 62  ICPSRQEADKAVNACHN-----KKTLPGASSPLQVKY 93
              S ++ +  +   +         +   + PL  K+
Sbjct: 65  RMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKF 101

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 27/99 (27%), Positives = 48/99 (48%), Gaps = 6/99 (6%)

Query: 86  SSPLQVKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGC 145
           +S +Q + A  + E+    L+I  LP ++ E E+  +   +G +   +ILR S  TS+G 
Sbjct: 3   ASGVQAQMAKQQ-EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 61

Query: 146 AFLKYETKEQALAALEAING-----KHKMEGSSVPLVVK 179
            F + E+ E+  A +   NG        +   + PL+ K
Sbjct: 62  GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 100

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 14/84 (16%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
           +     ++I   P + +  ++       G + ++Q+ R   +  KG  F+ +++ E A  
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 159 ALEAINGKHKMEGSSVPLVVKWAD 182
            +E      K + +   L++ + D
Sbjct: 63  FVET--PGQKYKET--DLLILFKD 82

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
          K   + R  +++   P   T   +    ++   V     ++    +A +G  FV+  S +
Sbjct: 1  KNDVKNR-SVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIE 58

Query: 68 EADKAVNACHNKKTLPGASSPLQVKYAD 95
           A K V      +      + L + + D
Sbjct: 59 SAKKFVET--PGQKYKE--TDLLILFKD 82

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 3e-08
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 12/104 (11%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ---------QTSKGC 145
           D + +     +++  L  +V+  +++  F   G +K  +                  KG 
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 146 AFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTEKERQA 189
           A + YE    A AA+E  +G    +GS   L V  A  +    +
Sbjct: 61  ATVSYEDPPTAKAAVEWFDG-KDFQGS--KLKVSLARKKPPMNS 101

>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 = 44.8 bits (105), Expect = 8e-07
 Identities = 21/92 (22%), Positives = 32/92 (34%), Gaps = 11/92 (11%)

Query: 11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALV--------DEVNIIKDKTTRASRGCCFVI 62
            +   ++V  +   +T   L   FK+  +V          ++I  DK T   +G   V 
Sbjct: 5  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 63 CPSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
                A  AV     K    G  S L+V  A
Sbjct: 65 YEDPPTAKAAVEWFDGKD-FQG--SKLKVSLA 93

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 9/90 (10%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             +F+G    +++E E+   FS YG + D+ I     +  +  AF+ +   + A +    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFI----PKPFRAFAFVTFADDQIAQSLCGE 61

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRA 192
                 ++G    + +  A+ +    +  +
Sbjct: 62  ---DLIIKGI--SVHISNAEPKHNSNSGPS 86

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 10/79 (12%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           +FVG+    MTE +L   F ++      +++     +  R   FV     Q A      
Sbjct: 7  GVFVGRCTGDMTEDELREFFSQYG-----DVMDVFIPKPFRAFAFVTFADDQIAQSLCG- 60

Query: 76 CHNKKTLPGASSPLQVKYA 94
                + G    + +  A
Sbjct: 61 --EDLIIKG--ISVHISNA 75

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 4/87 (4%)

Query: 8  KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQ 67
          ++S E  + LFV  + +   E ++   F ++  +  +++  D+ T  S+G   V   + +
Sbjct: 2  QRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 68 EADKAVNACHNKKTLPGASSPLQVKYA 94
          +A  A  A +  + + G    +QV + 
Sbjct: 61 QALAAKEALNGAE-IMG--QTIQVDWC 84

>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 = 47.4 bits (112), Expect = 7e-08
 Identities = 28/82 (34%), Positives = 43/82 (52%), Gaps = 4/82 (4%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALE 161
             LF+  + +   E E+   F  YG IK++ +    +   SKG A ++YET +QALAA E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 162 AINGKHKMEGSSVPLVVKWADT 183
           A+NG  ++ G    + V W   
Sbjct: 68  ALNGA-EIMGQ--TIQVDWCFV 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 4e-08
 Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNI-----IKDKTTRASRGCCFVICPSRQEAD 70
          +L+VG +P  +TE  ++  F     +  +       +        +   F+   S  E  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 71 KAVNACHNKKTLPGASSPLQVK 92
          +A+    +     G    L+++
Sbjct: 63 QAM--AFDGIIFQG--QSLKIR 80

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 10/84 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQT------SKGCAFLKYETKEQAL 157
           +L++G +P  ++E  +   F+    +  L    G+          K  AFL++ + ++  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 158 AALEAINGKHKMEGSSVPLVVKWA 181
            A+   +G    +G    L ++  
Sbjct: 63  QAMA-FDG-IIFQGQ--SLKIRRP 82

>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 = 48.1 bits (114), Expect = 5e-08
 Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
            R    L    L  N++E E+  +F     I+ +         SKG A+++++++  A  
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEK 68

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQARR 191
            LE   G  +++G    + + +     E+   R
Sbjct: 69  NLEEKQG-AEIDGR--SVSLYYT---GEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 48.1 bits (114), Expect = 5e-08
 Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 1  MAESKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCF 60
          M E     K       L    +  ++TE +L  +F++   +  V+         S+G  +
Sbjct: 3  MLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAY 57

Query: 61 VICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD 95
          +   S  +A+K +      + + G    + + Y  
Sbjct: 58 IEFKSEADAEKNLEEKQGAE-IDG--RSVSLYYTG 89

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 6e-08
 Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 5/90 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALE 161
            K+F+G LP + ++A +   F  +G I++  ++   Q   S+G  F+    +  A  A +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARR 191
             N    ++G      V  A    + ++ +
Sbjct: 71  DPN--PIIDGR--KANVNLAYLGAKPRSLQ 96

>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 = 44.7 bits (105), Expect = 8e-07
 Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
          K+FVG +P H T+A L   F+ F  ++E  +I D+ T  SRG  FV    R  A++A   
Sbjct: 12 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 76 CHNKKTLPGASSPLQVKYADGE 97
           +    + G      V  A   
Sbjct: 72 PN--PIIDG--RKANVNLAYLG 89

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           + V  +P  ++  ++L  F  + ++     +K        G   V   SR EA  AV  
Sbjct: 11 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 76 CHNKKTLPGASSPLQVKYA 94
           +++      S  +++   
Sbjct: 71 LNDRPI---GSRKVKLVLG 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 = 45.4 bits (107), Expect = 3e-07
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAALE 161
             + +  +P  VS  E+   F  Y  I   + +    +    G A + +E++++A AA+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 162 AINGKHKMEGSSVPLVVKWA 181
            +N    +      + +   
Sbjct: 70  DLND-RPIGSR--KVKLVLG 86

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 5/79 (6%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             L +  +P +VSE ++  LFS  G +          +     A ++  + E+A+ AL  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK---MALIQMGSVEEAVQALID 67

Query: 163 INGKHKMEGSSVPLVVKWA 181
           ++     E     L V ++
Sbjct: 68  LHNHDLGENH--HLRVSFS 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 = 37.4 bits (86), Expect = 3e-04
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L +  +P  ++E  L  +F     V    +   K  +  R    +   S +EA +A+   
Sbjct: 13 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 77 HNKKTLPGASSPLQVKYA 94
          HN          L+V ++
Sbjct: 69 HNHDLGEN--HHLRVSFS 84

>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 = 45.8 bits (108), Expect = 4e-07
 Identities = 9/63 (14%), Positives = 25/63 (39%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            + +        E   + +   YG ++++ +         G  ++K+  +E A  A+  +
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 164 NGK 166
           N +
Sbjct: 89  NNR 91

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 4/97 (4%)

Query: 4   SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
           S   +         F+G +P  +TE  +   F+   +       +       +G  +   
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64

Query: 64  PSRQEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
                   A++   N+++L      ++V  AD   ++
Sbjct: 65  EDLDSLLSALSL--NEESLGN--KRIRVDVADQAQDK 97

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALE 161
           +  F+G LP +V+E  +   F              S  +  KG  + ++E  +  L+AL 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQ 188
             N    +      + V  AD  +++ 
Sbjct: 76  L-NE-ESLGNK--RIRVDVADQAQDKD 98

>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 = 44.4 bits (104), Expect = 5e-07
 Identities = 17/64 (26%), Positives = 27/64 (42%)

Query: 17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC 76
          L++  +    T+  L+ + + +  +     I DKTT   +G  FV   S   A KAV A 
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 77 HNKK 80
              
Sbjct: 61 KASG 64

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 3e-05
 Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQ-QTSKGCAFLKYETKEQALAALEAI 163
           L+I  L    ++ ++  L   YG I   + +        KG  F+ +++   A  A+ A+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 164 NGKH 167
               
Sbjct: 61  KASG 64

>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 = 45.2 bits (106), Expect = 7e-07
 Identities = 15/94 (15%), Positives = 31/94 (32%), Gaps = 4/94 (4%)

Query: 7   EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR 66
           E   +  +V   +  +P  +T+  +L   +   + +    +         G   V   + 
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 67  QEADKAVNACHNKKTLPGASSPLQVKYADGELER 100
            +A K+     ++K L G      V     E  R
Sbjct: 61  DDARKSERL--HRKKLNG--REAFVHVVTLEDMR 90

>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 = 41.0 bits (95), Expect = 2e-05
 Identities = 15/105 (14%), Positives = 41/105 (39%), Gaps = 5/105 (4%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTI-KDLQILRGSQQTSKGCAFLKYETK 153
           +G++   +    I  +P ++++ +V             + +L  +     G A ++++ +
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 154 EQALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQ 198
           + A  +   ++   K+ G      V     E  R+  +   AQ +
Sbjct: 61  DDARKSER-LHR-KKLNG--REAFVHVVTLEDMREIEKNPPAQGK 101

>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 = 43.8 bits (102), Expect = 2e-06
 Identities = 19/110 (17%), Positives = 37/110 (33%), Gaps = 8/110 (7%)

Query: 95  DGELERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKE 154
            G   R +  +    LP     AE+   FS +G++  +             A +++    
Sbjct: 3   SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL-----LPEGGITAIVEFLEPL 57

Query: 155 QALAALEAINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPN 204
           +A  A   +          VPL ++WA       A + + +Q +      
Sbjct: 58  EARKAFRHLAYSKFHH---VPLYLEWAPIGVFGAAPQKKDSQHEQPAEKA 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 = 41.7 bits (97), Expect = 1e-05
 Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + +  L ++V EA++      +GTI  + +        K  A +++E  + A   +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMM-----MPFKRQALVEFENIDSAKECVTFAA 72

Query: 165 GKHKMEGSSVPLVVKWADTEKER 187
               +  +       ++ +++  
Sbjct: 73  D-VPVYIAGQQAFFNYSTSKRIT 94

>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 = 37.9 bits (87), Expect = 2e-04
 Identities = 12/91 (13%), Positives = 26/91 (28%), Gaps = 7/91 (7%)

Query: 4  SKKEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVIC 63
          S            + V  + + + EA L+   ++F  +  V ++  K          V  
Sbjct: 5  SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEF 58

Query: 64 PSRQEADKAVNACHNKKTLPGASSPLQVKYA 94
           +   A + V    +              Y+
Sbjct: 59 ENIDSAKECVTFAADVPVYIA-GQQAFFNYS 88

>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 = 42.2 bits (98), Expect = 1e-05
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQ-TSKGCAFLKYETKEQALAALEA 162
            L +  +P  V E ++  LF  YG I+ ++I+   +   S+G  F+K+++   A  A+  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 163 INGKHKMEGSSVPLVVKWADTEKER 187
           +NG   +      L V  A +  +R
Sbjct: 104 LNG-FNILNK--RLKVALAASGHQR 125

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.9 bits (92), Expect = 8e-05
 Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 16  KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
            L V  +P  + E QL  +F+ +  ++ V I+ D+ TR SRG  FV   S   A +A+  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 76  CHNKKTLPGASSPLQVKYADGELER 100
            +    +      L+V  A    +R
Sbjct: 104 LNGFN-ILN--KRLKVALAASGHQR 125

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 9/81 (11%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            + +  LP++ +  EV  L   Y               +K  AF+     EQA  A++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYC------YVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 164 NGKHKMEGSSVPLVVKWADTE 184
           +  +   G    L+V+   T+
Sbjct: 61  HQ-YSFRGK--DLIVQLQPTD 78

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 104 KLFIGMLPKNV-SEAEVSALFSIYGTIKDLQILRGSQQT--SKGCAFLKYETKEQALAAL 160
           ++ I  L   +  E  +   F  +G+I+ + I  G ++   +  CAF+ +E K+ A  AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 161 EAINGKHKMEGSSVPLVVKWAD 182
           +  N    +      + V  AD
Sbjct: 66  QM-NR-SLLGNR--EISVSLAD 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 = 39.5 bits (91), Expect = 4e-05
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             LF+  LP+  +E  +S LF+ +   K++++           AF+++ T+ Q+ AA EA
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVRL----VPNRHDIAFVEFTTELQSNAAKEA 64

Query: 163 INGKHKMEGSSVPLVVKWA 181
           + G          + + +A
Sbjct: 65  LQGFKITPTH--AMKITFA 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 = 39.4 bits (91), Expect = 8e-05
 Identities = 13/95 (13%), Positives = 28/95 (29%), Gaps = 13/95 (13%)

Query: 103 HKLFIGMLPKNV-----SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQAL 157
             L   +   +V     + A+  +LF  Y      Q  +     S     + +     A 
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAA 60

Query: 158 AALEAINGKHKMEGSSVPLVVKWADTEKERQARRA 192
            A   ++    +      + + +A T     +  A
Sbjct: 61  DARLRLHKTEFL---GKEMKLYFAQTLHIGSSHLA 92

>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 = 38.9 bits (90), Expect = 8e-05
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 7/85 (8%)

Query: 105 LFIGMLPK-NVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
           + I    +      ++  L   +G I +  IL    +     AF++  T E A AA++  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINE-----AFIEMATTEDAQAAVDYY 65

Query: 164 NGKHKMEGSSVPLVVKWADTEKERQ 188
                      P+ V  +   K  +
Sbjct: 66  TT-TPALVFGKPVRVHLSQKYKRIK 89

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.7 bits (84), Expect = 4e-04
 Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 7/71 (9%)

Query: 103 HKLFIGMLPKNVSEAEVSALF---SIYGTIKDLQILR----GSQQTSKGCAFLKYETKEQ 155
           + +F+  L + +++ EV         +G I  + I         Q     A++ Y   E 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 156 ALAALEAINGK 166
           AL A++ +N  
Sbjct: 69  ALRAIQCVNNV 79

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.4 bits (83), Expect = 4e-04
 Identities = 21/80 (26%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN 164
           + I  LP +V+  EV  L S Y                KG AF+     EQA AA+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYC------FVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 165 GKHKMEGSSVPLVVKWADTE 184
                      L V+   T+
Sbjct: 55  QSRLR---ERELSVQLQPTD 71

>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 = 36.8 bits (85), Expect = 4e-04
 Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 3/61 (4%)

Query: 122 LFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA 181
           L         ++ L    +   G A + +   E+A   ++ ++G+    G    +  +  
Sbjct: 36  LRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR-WFGGR--QITAQAW 92

Query: 182 D 182
           D
Sbjct: 93  D 93

>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 = 9/63 (14%), Positives = 19/63 (30%), Gaps = 4/63 (6%)

Query: 34 MFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY 93
          +  E +   ++  +         G   V     +EAD  +     +    G    +  + 
Sbjct: 36 LRVECSKFGQIRKLLLFDRH-PDGVASVSFRDPEEADYCIQTLDGRW-FGG--RQITAQA 91

Query: 94 ADG 96
           DG
Sbjct: 92 WDG 94

>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 = 35.6 bits (81), Expect = 8e-04
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 6/79 (7%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           + V  +PK   + ++   FK    +  V++              +       A  A+  
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAITK 59

Query: 76 CHNKKTLPGASSPLQVKYA 94
           H  K +    + + V + 
Sbjct: 60 TH--KVVGQ--NEIIVSHL 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 = 34.4 bits (78), Expect = 0.002
 Identities = 12/71 (16%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAI 163
            + +  LPK+ ++ +V   F   G I  + +    ++  +  A +++   + ALAA+   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAITKT 60

Query: 164 NGKHKMEGSSV 174
           +    +  + +
Sbjct: 61  H--KVVGQNEI 69

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAA 159
           R  + L++      ++   +   FS +G I DL          + CAF+ YE  E A  A
Sbjct: 3   RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLS-----MDPPRNCAFVTYEKMESADQA 55

Query: 160 LEAINGKHKMEGSSVPLVVKWA 181
           +  +NG  ++E     L V  A
Sbjct: 56  VAELNG-TQVESV--QLKVNIA 74

>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 = 35.9 bits (82), Expect = 0.001
 Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 9/91 (9%)

Query: 99  ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALA 158
            R + ++ +  LP + S  ++       G +        +     G   ++Y  KE    
Sbjct: 12  RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCY------ADVQKDGMGMVEYLRKEDMEY 65

Query: 159 ALEAINGKHKMEGSSVPLVVKWADTEKERQA 189
           AL  ++   K           +     ER +
Sbjct: 66  ALRKLDDT-KFRSH--EGETSYIRVYPERSS 93

>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 = 35.9 bits (82), Expect = 0.001
 Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 8/103 (7%)

Query: 103 HKLFIGML-PKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALE 161
             L +  L P+ V+   +  LF +YG ++ ++I        K  A ++     QA  A+ 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI----LFNKKENALVQMADGNQAQLAMS 58

Query: 162 AINGKHKMEGSSVPLVVKWADTEKERQARRAQKAQSQANNLPN 204
            +NG  K+ G   P+ +  +  +  +  R  Q+ Q    +  N
Sbjct: 59  HLNGH-KLHGK--PIRITLSKHQNVQLPREGQEDQGLTKDYGN 98

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.9 bits (79), Expect = 0.002
 Identities = 9/92 (9%), Positives = 28/92 (30%), Gaps = 9/92 (9%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
           +++ +  LP + S  ++       G +        +     G   +++  KE    A+  
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGDVCY------ADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQARRAQK 194
           ++   K           +   + +     +  
Sbjct: 55  LDNT-KFRSH--EGETAYIRVKVDGPRSPSYG 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 = 34.4 bits (78), Expect = 0.003
 Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNA 75
           L + ++P  +TE +++A+   F        + +      +   F+   + + A   VN 
Sbjct: 10 VLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 76 CHNKKTLPGASSPLQVKYA 94
                    + P+ ++Y+
Sbjct: 64 YSAVTPHLR-NQPIYIQYS 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 = 34.1 bits (77), Expect = 0.004
 Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA 162
             L I  LP  V+E EV AL   +G + ++          K  AFL+  T+E A+  +  
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKVTNIL-----MLKGKNQAFLELATEEAAITMVNY 63

Query: 163 INGKHKMEGSSVPLVVKWADTEKERQ 188
            +       +  P+ ++++   KE +
Sbjct: 64  YSAVTPHLRNQ-PIYIQYS-NHKELK 87

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	354
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.84
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.79
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.78
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.78
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.74
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.73
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.72
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.72
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	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
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.72
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.72
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.7
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.7
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.7
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.69
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.69
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.68
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.67
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.67
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.67
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.66
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.65
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.63
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.62
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.61
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.57
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.57
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.54
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	99.52
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	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.5
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.47
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.47
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.4
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.36
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.34
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.27
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.24
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.8
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.71
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.27
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.81
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.28
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.92
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.41
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.7

>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=100.00  E-value=1.1e-33  Score=239.07  Aligned_cols=170  Identities=24%  Similarity=0.391  Sum_probs=143.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .+..++|||+|||+++|+++|+++|++||.|.++.+++|..+++++|||||+|.+.++|++|++.++. . +..  ..+.
T Consensus         3 p~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~-~-~~~--~~~~   78 (183)
T d1u1qa_           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH-K-VDG--RVVE   78 (183)
T ss_dssp             CHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC-E-ETT--EECE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCC-c-ccc--cchh
Confidence            44568999999999999999999999999999999999999999999999999999999999987543 3 222  3333


Q ss_pred             eeccccc-------cccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHH
Q 018554           91 VKYADGE-------LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEA  162 (354)
Q Consensus        91 v~~~~~~-------~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~  162 (354)
                      +.+....       .....++|||+||+..+|+++|+++|+.||.|..+.|+.|. ++.++|||||+|.++++|.+|++ 
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-  157 (183)
T d1u1qa_          79 PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-  157 (183)
T ss_dssp             EEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-
T ss_pred             hhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-
Confidence            3332211       12236799999999999999999999999999999999984 68999999999999999999997 


Q ss_pred             hCCCcccCCCceeEEEEecCChHHHH
Q 018554          163 INGKHKMEGSSVPLVVKWADTEKERQ  188 (354)
Q Consensus       163 l~g~~~~~g~~~~l~v~~a~~~~~~~  188 (354)
                      +++.. ++|  +.|+|++|.++.++.
T Consensus       158 ~~~~~-~~G--~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         158 QKYHT-VNG--HNCEVRKALSKQEMA  180 (183)
T ss_dssp             SSCEE-ETT--EEEEEEECCCHHHHH
T ss_pred             hCCCe-ECC--EEEEEEecCCccccc
Confidence            67755 666  789999999876654

>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=99.87  E-value=4.3e-22  Score=145.55  Aligned_cols=82  Identities=32%  Similarity=0.550  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .+.++|||+|||.++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++|++.||+.. +.|..++|+|
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~-~~G~~~~i~V   82 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK-PSGATEPITV   82 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCE-eCCCCEEEEE
Confidence            456789999999999999999999999999999999999999999999999999999999999998876 6777788999


Q ss_pred             ecc
Q 018554           92 KYA   94 (354)
Q Consensus        92 ~~~   94 (354)
                      +||
T Consensus        83 ~~A   85 (85)
T d1fxla2          83 KFA   85 (85)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            886

>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=99.86  E-value=8.9e-22  Score=143.90  Aligned_cols=83  Identities=35%  Similarity=0.558  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      +.+.++|||+|||++++|++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|.+|++.||+.. +.+..++|+
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g~~~~l~   81 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI-PEGGSQPLS   81 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCE-eCCCCeEEE
Confidence            4567789999999999999999999999999999999999999999999999999999999999999876 555568899


Q ss_pred             eecc
Q 018554           91 VKYA   94 (354)
Q Consensus        91 v~~~   94 (354)
                      |+||
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9886

>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=99.85  E-value=1.3e-21  Score=144.25  Aligned_cols=86  Identities=23%  Similarity=0.266  Sum_probs=76.7

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      +..+..++|||+|||+++||++|+++|++||.|.+|+|++|+.||++||||||+|.+.++|++||+..   ..+.|  +.
T Consensus         3 ~~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~---~~l~G--r~   77 (90)
T d2cqga1           3 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR---HMIDG--RW   77 (90)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC---EEETT--EE
T ss_pred             CCCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC---CccCC--EE
Confidence            34557789999999999999999999999999999999999999999999999999999999999854   34666  78


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |.|+++..+.+
T Consensus        78 i~v~~a~~k~~   88 (90)
T d2cqga1          78 CDCKLPNSKQS   88 (90)
T ss_dssp             EEEECCCTTCC
T ss_pred             eEEEeCCCCCC
Confidence            99998887654

>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=99.85  E-value=1.7e-21  Score=144.73  Aligned_cols=87  Identities=25%  Similarity=0.381  Sum_probs=78.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +....++|||+|||.++|+++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l   81 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK-LYG--KPI   81 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB-CSS--CBC
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCE-ECC--EEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999998876 555  789


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|+|++.+..
T Consensus        82 ~V~~A~~~~~   91 (93)
T d1x5ua1          82 RVNKASAHNK   91 (93)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEEcCCCCC
Confidence            9999877643

>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=99.85  E-value=2.4e-21  Score=142.42  Aligned_cols=85  Identities=21%  Similarity=0.308  Sum_probs=77.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ++.+.++|||+|||.++|+++|+++|++||+|.+|++++|+.||+++|||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~-l~g--~~l   79 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE-IMG--QTI   79 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCE-ECC--EEE
Confidence            35567899999999999999999999999999999999999999999999999999999999999999876 555  889


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      +|+|+..+
T Consensus        80 ~V~~a~~k   87 (88)
T d1rk8a_          80 QVDWCFVK   87 (88)
T ss_dssp             EEEESEEC
T ss_pred             EEEEecCC
Confidence            99998653

>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=99.84  E-value=1.7e-21  Score=141.38  Aligned_cols=80  Identities=26%  Similarity=0.456  Sum_probs=74.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .++|||+|||.++|+++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|++|++.||+.. +.+  +.|+|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~-~~g--~~l~v~~   78 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGIT-VRN--KRLKVSY   78 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            5789999999999999999999999999999999999999999999999999999999999999876 555  8899998


Q ss_pred             ccc
Q 018554           94 ADG   96 (354)
Q Consensus        94 ~~~   96 (354)
                      +++
T Consensus        79 a~p   81 (82)
T d1b7fa1          79 ARP   81 (82)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.84  E-value=1.1e-21  Score=144.75  Aligned_cols=85  Identities=24%  Similarity=0.349  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||+++|+++|+++|++||+|.+|+|++|+.|++++|||||+|.+.++|++|++.||+.. +.|  +.|+|
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~-i~g--~~l~v   79 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--RTIRV   79 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE-ETT--EEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            356899999999999999999999999999999999999999999999999999999999999998865 555  78999


Q ss_pred             eccccccc
Q 018554           92 KYADGELE   99 (354)
Q Consensus        92 ~~~~~~~~   99 (354)
                      .++++++.
T Consensus        80 ~~a~p~~~   87 (89)
T d2cqba1          80 NLAKPMRI   87 (89)
T ss_dssp             EECCCCCC
T ss_pred             EEeCCCCC
Confidence            99986543

>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=99.84  E-value=2.6e-21  Score=139.64  Aligned_cols=78  Identities=23%  Similarity=0.437  Sum_probs=73.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD   95 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~   95 (354)
                      +|||+|||.++||++|+++|++||+|.+|+|++|+.||+++|||||+|.+.++|++|++.|++.. +.+  +.|+|.|++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~-~~g--r~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDV-IKG--KPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCE-ETT--EECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999998876 555  789999886


Q ss_pred             c
Q 018554           96 G   96 (354)
Q Consensus        96 ~   96 (354)
                      .
T Consensus        79 ~   79 (80)
T d1cvja1          79 R   79 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.84  E-value=4.5e-21  Score=144.95  Aligned_cols=90  Identities=23%  Similarity=0.344  Sum_probs=80.9

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      +.+..+.++|||+|||+++++++|+++|++||.|.++.++.|+.+|++||||||+|.+.++|++||+.||+.. +.+  +
T Consensus        12 ~~~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~-~~g--~   88 (102)
T d2cpza1          12 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ-IGM--K   88 (102)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE-ETT--E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCE-ECC--E
Confidence            3344567899999999999999999999999999999999999999999999999999999999999999876 555  8


Q ss_pred             cceeecccccccc
Q 018554           88 PLQVKYADGELER  100 (354)
Q Consensus        88 ~l~v~~~~~~~~~  100 (354)
                      .|+|.|++.+.+.
T Consensus        89 ~i~V~~a~~k~~~  101 (102)
T d2cpza1          89 RLKVQLKRSKNDS  101 (102)
T ss_dssp             ECEEECCCCSCCC
T ss_pred             EEEEEEeCCCCCC
Confidence            9999999877653

>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=99.84  E-value=5.8e-21  Score=141.83  Aligned_cols=85  Identities=22%  Similarity=0.373  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ...+++|||+|||+++|+++|+++|++||+|.+|.+++|+.+++++|||||+|.+.++|++|++.||+.. +.+  +.|+
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--r~i~   80 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR-LDD--RIIR   80 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSE-ETT--EECE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEE
Confidence            4578899999999999999999999999999999999999999999999999999999999999998876 555  8899


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      |.|+....
T Consensus        81 V~~a~~~~   88 (93)
T d1h2vz_          81 TDWDAGFK   88 (93)
T ss_dssp             EEEESCCC
T ss_pred             EEEcCCCC
Confidence            99986543

>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=99.84  E-value=3e-21  Score=142.62  Aligned_cols=86  Identities=22%  Similarity=0.387  Sum_probs=78.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||.++++++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++||+.||+.. +.+  +.|
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~i   80 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG-YDH--LIL   80 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999998866 555  889


Q ss_pred             eeecccccc
Q 018554           90 QVKYADGEL   98 (354)
Q Consensus        90 ~v~~~~~~~   98 (354)
                      +|.|++++.
T Consensus        81 ~v~~akp~~   89 (90)
T d2cq0a1          81 NVEWAKPST   89 (90)
T ss_dssp             EEEESSCCC
T ss_pred             EEEeeeCCC
Confidence            999998653

>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=99.84  E-value=3.1e-21  Score=140.83  Aligned_cols=81  Identities=25%  Similarity=0.398  Sum_probs=75.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .+|||+|||+++||++|+++|++||+|.+|+|++|+.||+++|||||+|.+.++|.+|++.||+.. +.+  +.|.|.++
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   78 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ-LGD--KKLLVQRA   78 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCC-CSS--SCCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999999998866 555  78999998


Q ss_pred             cccc
Q 018554           95 DGEL   98 (354)
Q Consensus        95 ~~~~   98 (354)
                      +...
T Consensus        79 ~~~~   82 (85)
T d2u2fa_          79 SVGA   82 (85)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.84  E-value=8.2e-21  Score=137.78  Aligned_cols=80  Identities=26%  Similarity=0.483  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .++|||+|||.+++|++|+++|++||+|.+|++++|..+++++|||||+|.+.++|++|++.||+.. +.+  +.|+|.|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~-~~g--~~l~v~~   78 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLR-LQT--KTIKVSY   78 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            4679999999999999999999999999999999999999999999999999999999999999876 555  8899998


Q ss_pred             ccc
Q 018554           94 ADG   96 (354)
Q Consensus        94 ~~~   96 (354)
                      +++
T Consensus        79 AkP   81 (82)
T d1fxla1          79 ARP   81 (82)
T ss_dssp             CCC
T ss_pred             eeC
Confidence            875

>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=99.83  E-value=1.1e-20  Score=137.93  Aligned_cols=79  Identities=32%  Similarity=0.646  Sum_probs=74.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||.++|+++|+++|++||+|++++|++|+ ++.++|||||+|.+.++|.+|++.|||.. ++|+.++|+|+|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~-~~G~~~~i~V~~   84 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK-PSGATEPITVKF   84 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CTTCSSCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCE-eCCCCEEEEEEe
Confidence            5789999999999999999999999999999999984 78999999999999999999999999976 888888999999


Q ss_pred             c
Q 018554          181 A  181 (354)
Q Consensus       181 a  181 (354)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.83  E-value=5.4e-21  Score=143.83  Aligned_cols=87  Identities=23%  Similarity=0.280  Sum_probs=78.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||++++++||+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++||+.||+.. +.+  +.|
T Consensus         4 ~~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--r~i   80 (99)
T d1whwa_           4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV-FQG--RML   80 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEE-SSS--CEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCE-ECC--EEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999998865 555  789


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.++..+.+
T Consensus        81 ~V~~a~~~~~   90 (99)
T d1whwa_          81 HVLPSTIKKE   90 (99)
T ss_dssp             EEEECCCCST
T ss_pred             EEEECCCCCc
Confidence            9998876554

>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=99.83  E-value=5.5e-21  Score=139.00  Aligned_cols=81  Identities=25%  Similarity=0.381  Sum_probs=72.3

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      +.+..+.++|||+|||.++||++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|++|+++||+.. +.+  +
T Consensus         3 r~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--r   79 (83)
T d2cqca1           3 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME-LDG--R   79 (83)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEE-ETT--E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCE-ECC--E
Confidence            3455678899999999999999999999999999999999999999999999999999999999999998866 444  5


Q ss_pred             ccee
Q 018554           88 PLQV   91 (354)
Q Consensus        88 ~l~v   91 (354)
                      .|+|
T Consensus        80 ~i~V   83 (83)
T d2cqca1          80 RIRV   83 (83)
T ss_dssp             EEEE
T ss_pred             EeEC
Confidence            5543

>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=99.83  E-value=1.1e-20  Score=140.54  Aligned_cols=87  Identities=31%  Similarity=0.475  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC-CCCcccEEEEEeCCHHHHHHHHHHh-cCCccCCCCCc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKT-TRASRGCCFVICPSRQEADKAVNAC-HNKKTLPGASS   87 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~-tg~~~G~aFV~f~~~~~A~~Ai~~l-~~~~~~~g~~~   87 (354)
                      .....++|||+|||.++++++|+++|++||.|.+|+|++|.. +|+++|||||+|.+.++|.+||+.| |+.. +.|  +
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~-~~G--r   80 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH-LYG--R   80 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCB-SSS--C
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcE-ECC--E
Confidence            345678899999999999999999999999999999998854 7999999999999999999999998 5544 666  8


Q ss_pred             cceeeccccccc
Q 018554           88 PLQVKYADGELE   99 (354)
Q Consensus        88 ~l~v~~~~~~~~   99 (354)
                      .|.|.|++.+..
T Consensus        81 ~l~V~~A~~~~~   92 (94)
T d2cpha1          81 RLVLEWADSEVT   92 (94)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987643

>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=99.83  E-value=1.2e-20  Score=139.34  Aligned_cols=85  Identities=29%  Similarity=0.465  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .+.++|||+|||+++++++|+++|++||.|..|.+++++.+++++|||||+|.+.++|++|++.|++.. +.|  +.|+|
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~-~~g--~~l~V   79 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS-VDG--RQIRV   79 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCC-TTS--CCCEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            467889999999999999999999999999999999999999999999999999999999999999876 555  88999


Q ss_pred             eccccccc
Q 018554           92 KYADGELE   99 (354)
Q Consensus        92 ~~~~~~~~   99 (354)
                      +++..+.+
T Consensus        80 ~~a~~~~~   87 (90)
T d1x5sa1          80 DQAGKSSD   87 (90)
T ss_dssp             EEEECCCC
T ss_pred             EEcCCCCC
Confidence            98876544

>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=99.83  E-value=1.1e-20  Score=151.28  Aligned_cols=88  Identities=27%  Similarity=0.426  Sum_probs=78.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +....++|||+|||+++||++|+++|++||+|.+|.|++|+.|++++|||||+|.+.++|.+||+.||+.. +.+  +.|
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~-~~g--r~l  114 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN-ILN--KRL  114 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEE-CSS--CEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999998866 555  889


Q ss_pred             eeecccccccc
Q 018554           90 QVKYADGELER  100 (354)
Q Consensus        90 ~v~~~~~~~~~  100 (354)
                      +|++++.+..+
T Consensus       115 ~V~~a~~~~~~  125 (139)
T d1u6fa1         115 KVALAASGHQR  125 (139)
T ss_dssp             EEEESSCCCCC
T ss_pred             EEEEcCCCCCC
Confidence            99998765543

>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=99.82  E-value=9.7e-21  Score=143.37  Aligned_cols=85  Identities=31%  Similarity=0.445  Sum_probs=75.7

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ..+...++|||+|||++++|+||+++|++||+|.+|+|++|+.||+++|||||+|.+.++|++||+.+++ . +.|  +.
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~-l~G--r~   80 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-I-IDG--RK   80 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-E-ETT--EE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-c-CCC--EE
Confidence            4455678899999999999999999999999999999999999999999999999999999999998864 3 655  78


Q ss_pred             ceeeccccc
Q 018554           89 LQVKYADGE   97 (354)
Q Consensus        89 l~v~~~~~~   97 (354)
                      |+|+++..+
T Consensus        81 l~V~~a~~~   89 (103)
T d2cqda1          81 ANVNLAYLG   89 (103)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcCCC
Confidence            888887644

>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=99.82  E-value=1.6e-20  Score=136.63  Aligned_cols=82  Identities=29%  Similarity=0.466  Sum_probs=72.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      +.+..++|||+|||+++|+++|+++|++||.|.+|.|++|+.||+++|||||+|.+.++|++|++. ++.. +.|  +.|
T Consensus         2 epe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~~-i~G--r~i   77 (84)
T d1l3ka1           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHK-VDG--RVV   77 (84)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCE-ETT--EEC
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCCE-ECC--EEE
Confidence            445668999999999999999999999999999999999999999999999999999999999975 5654 555  778


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      +|+.|.
T Consensus        78 ~V~~A~   83 (84)
T d1l3ka1          78 EPKRAV   83 (84)
T ss_dssp             EEEECC
T ss_pred             EEEeee
Confidence            877653

>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=99.82  E-value=5.8e-21  Score=145.03  Aligned_cols=83  Identities=27%  Similarity=0.417  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .+.++|||+|||+++++++|+++|++||+|.+|+|++|+.||+++|||||+|.+.++|++|++.||+.. +.+  +.|+|
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~-~~g--~~i~V   82 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE-FSG--RALRV   82 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBS-CSS--SCBEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            346789999999999999999999999999999999999999999999999999999999999998766 555  78899


Q ss_pred             eccccc
Q 018554           92 KYADGE   97 (354)
Q Consensus        92 ~~~~~~   97 (354)
                      .++..+
T Consensus        83 ~~a~~~   88 (104)
T d1p1ta_          83 DNAASE   88 (104)
T ss_dssp             EETTCT
T ss_pred             EECCCC
Confidence            887654

>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=99.82  E-value=6.5e-21  Score=136.21  Aligned_cols=76  Identities=28%  Similarity=0.416  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      |+|||+|||+++||++|+++|++||.|.+++|++|+.|+++||||||+|.+.++|++|++ +++. .+.|  +.|+|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~-~i~G--r~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRH-ELDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTC-CCSS--CCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCC-EECC--eEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999997 5554 4666  66776654

>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=99.81  E-value=6.2e-20  Score=133.93  Aligned_cols=79  Identities=33%  Similarity=0.647  Sum_probs=73.4

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||.++++++|+++|++||.|.++++++| .++.++|||||+|.+.++|.+|++.|||.. ++|..++|.|+|
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g~~~~l~V~~   84 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI-PEGGSQPLSVRL   84 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC-CTTCSSCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCE-eCCCCeEEEEEE
Confidence            467999999999999999999999999999999998 579999999999999999999999999976 666668899999


Q ss_pred             c
Q 018554          181 A  181 (354)
Q Consensus       181 a  181 (354)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.81  E-value=4.1e-21  Score=144.70  Aligned_cols=84  Identities=24%  Similarity=0.379  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .+.++|||+|||.++++++|+++|+.||+|.+|+|++|+.||+++|||||+|.+.++|.+|++ ||+.. +.|  +.|+|
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~-~~G--~~l~V   91 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQR-LLG--VPIIV   91 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEE-ETT--EEEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCE-ECC--EEEEE
Confidence            346799999999999999999999999999999999999999999999999999999999995 88865 555  88899


Q ss_pred             eccccccc
Q 018554           92 KYADGELE   99 (354)
Q Consensus        92 ~~~~~~~~   99 (354)
                      ++++.++.
T Consensus        92 ~~a~~~~n   99 (101)
T d2cq4a1          92 QASQAEKN   99 (101)
T ss_dssp             EEHHHHHH
T ss_pred             EECCCCCC
Confidence            88765543

>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=99.81  E-value=2e-20  Score=135.37  Aligned_cols=80  Identities=16%  Similarity=0.267  Sum_probs=67.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .+||||+|||+++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.||+.. +.|  +.|+|++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~-~~g--~~i~V~~   77 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK-IEG--YTLVTKV   77 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            4799999999999999999999999999999999998899999999999999999999999998876 555  8899998


Q ss_pred             ccc
Q 018554           94 ADG   96 (354)
Q Consensus        94 ~~~   96 (354)
                      +++
T Consensus        78 a~P   80 (81)
T d2ghpa1          78 SNP   80 (81)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            865

>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=99.81  E-value=3.7e-20  Score=131.70  Aligned_cols=75  Identities=29%  Similarity=0.438  Sum_probs=67.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      +|||+|||+++||++|+++|++||+|.+|.|++|+.|++++|||||+|.+.++|++||+ +++.. +.|  +.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~-l~G--r~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHK-LNG--KVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCC-BTT--BCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCE-ECC--CEEEeeEC
Confidence            69999999999999999999999999999999999999999999999999999999997 55554 655  77777643

>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=99.81  E-value=5.4e-20  Score=135.74  Aligned_cols=85  Identities=22%  Similarity=0.445  Sum_probs=75.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ++.+.++|||+|||.++|+++|+++|++||.|.+|+|++|+.++  +|||||+|.+.++|.+|++.+++.. +.+  +.|
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~-~~g--~~i   78 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRK-ILG--KEV   78 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEE-ETT--EEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCE-ECC--EEE
Confidence            45567899999999999999999999999999999999998654  7899999999999999999998866 555  899


Q ss_pred             eeeccccccc
Q 018554           90 QVKYADGELE   99 (354)
Q Consensus        90 ~v~~~~~~~~   99 (354)
                      +|.|++....
T Consensus        79 ~v~~a~~~~~   88 (90)
T d2cqia1          79 KVNWATTPSS   88 (90)
T ss_dssp             EEEECCCTTC
T ss_pred             EEEEcCCCCC
Confidence            9999876544

>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=8.1e-20  Score=134.13  Aligned_cols=81  Identities=35%  Similarity=0.538  Sum_probs=73.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++|+++|+++|++||+|++|+|++| .++.++|||||+|++.++|++|++.|||.. ++|  +.|+|+
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~-l~g--~~l~V~   82 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE-IMG--QTIQVD   82 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCE-ECC--EEEEEE
Confidence            3578999999999999999999999999999999998 579999999999999999999999999987 566  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ||.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            98653

>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=99.80  E-value=7e-20  Score=131.28  Aligned_cols=77  Identities=30%  Similarity=0.506  Sum_probs=72.4

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCC
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADT  183 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~  183 (354)
                      +|||+|||+++|+++|+++|++||.|++++|.++++++++|||||+|.+.++|.+|++.|||.. ++|  +.|+|++|++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-l~g--~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVP-LDG--RPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEeeC
Confidence            6999999999999999999999999999999999999999999999999999999999999987 666  7899998864

>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=99.80  E-value=6.4e-20  Score=132.97  Aligned_cols=79  Identities=27%  Similarity=0.500  Sum_probs=73.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||.++|+++|+++|++||.|++++|+++ .++.++|||||+|++.++|++|++.|||.. ++|  +.|+|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~-~~g--~~l~v~~   78 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGIT-VRN--KRLKVSY   78 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            468999999999999999999999999999999997 578999999999999999999999999987 555  7899999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      |++
T Consensus        79 a~p   81 (82)
T d1b7fa1          79 ARP   81 (82)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            975

>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=99.80  E-value=2e-20  Score=132.77  Aligned_cols=74  Identities=23%  Similarity=0.417  Sum_probs=65.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      +|||||||+++|+++|+++|++||.|.+|+|++|+.|+++||||||+|.+.++|++||+.. + ..+.+  +.++|+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~-~-~~i~g--~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK-Y-HNVGL--SKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCS-S-CCBTT--BCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhC-C-CEECC--EEeEEEE
Confidence            6999999999999999999999999999999999999999999999999999999999763 3 34655  5566654

>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=99.80  E-value=9.1e-20  Score=136.83  Aligned_cols=89  Identities=20%  Similarity=0.286  Sum_probs=77.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC---CC
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG---AS   86 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g---~~   86 (354)
                      +..+.++|||+|||+++||++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++||+.+++.....+   .+
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            456778999999999999999999999999999999999999999999999999999999999999975432222   23


Q ss_pred             ccceeecccccc
Q 018554           87 SPLQVKYADGEL   98 (354)
Q Consensus        87 ~~l~v~~~~~~~   98 (354)
                      +.|+|.++..+.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            788999887654

>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=99.80  E-value=1.4e-20  Score=142.21  Aligned_cols=87  Identities=25%  Similarity=0.404  Sum_probs=76.3

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ++.+..++|||+|||+++++++|+++|++||+|.++.|.+|+.|++++|||||+|.+.++|++|++ +++.. +.|  +.
T Consensus        15 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~-l~G--~~   90 (103)
T d1x4ba1          15 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHS-IDG--RV   90 (103)
T ss_dssp             CHHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEE-ETT--EE
T ss_pred             CCcCCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCe-ECC--EE
Confidence            334456899999999999999999999999999999999999999999999999999999999996 45654 655  88


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |.|+++.++.+
T Consensus        91 i~V~~a~~ke~  101 (103)
T d1x4ba1          91 VEPKRAVAREE  101 (103)
T ss_dssp             EEEECCSSCCC
T ss_pred             EEEEECcccCC
Confidence            99999887654

>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=99.80  E-value=6.4e-20  Score=131.49  Aligned_cols=76  Identities=22%  Similarity=0.381  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD   95 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~   95 (354)
                      +|||+|||+++++++|+++|++||.|.+|+|.+|+ +++++|||||+|.+.++|.+|++.+|+.. +.+  +.|+|++++
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-SGRSLGTADVHFERKADALKAMKQYNGVP-LDG--RPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEee
Confidence            69999999999999999999999999999999997 69999999999999999999999999876 555  788888764

>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=1.8e-19  Score=130.51  Aligned_cols=78  Identities=26%  Similarity=0.497  Sum_probs=72.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++|||+|||.++++++|+++|++||.|.+|+++++ .++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|+||
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~-~~g--~~l~v~~A   79 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLR-LQT--KTIKVSYA   79 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEe
Confidence            57999999999999999999999999999999998 578999999999999999999999999976 565  78999999


Q ss_pred             CC
Q 018554          182 DT  183 (354)
Q Consensus       182 ~~  183 (354)
                      ++
T Consensus        80 kP   81 (82)
T d1fxla1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             eC
Confidence            75

>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=99.80  E-value=3.3e-20  Score=134.81  Aligned_cols=80  Identities=26%  Similarity=0.453  Sum_probs=72.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccc
Q 018554           17 LFVGQVPKHMTEAQLLAMFKEFALVDE-VNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD   95 (354)
Q Consensus        17 lfVg~Lp~~~te~~L~~~F~~~G~v~~-i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~   95 (354)
                      |||+|||+++||++|+++|++||.|.+ ++|++|+.||+++|||||+|.+.++|++|++.+++.. +.+  +.|+|+++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~-~~g--r~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY-LCN--RPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCE-ETT--EECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcE-ECC--EEEEEEEec
Confidence            899999999999999999999999866 4789999999999999999999999999999998876 555  889999987


Q ss_pred             cccc
Q 018554           96 GELE   99 (354)
Q Consensus        96 ~~~~   99 (354)
                      .+..
T Consensus        78 ~k~~   81 (83)
T d1x5ta1          78 KKDS   81 (83)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            6543

>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=99.80  E-value=1.7e-19  Score=133.76  Aligned_cols=87  Identities=25%  Similarity=0.437  Sum_probs=77.4

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ..+.....++|||+|||+++++++|+++|++||+|.+|+++.|+.  .++|||||+|.+.++|++||+.||+.. +.+  
T Consensus         4 ~~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~-~~g--   78 (93)
T d2cq3a1           4 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTV-VEG--   78 (93)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCE-ETT--
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCE-ECC--
Confidence            445666788999999999999999999999999999999999875  478999999999999999999998866 555  


Q ss_pred             ccceeecccccc
Q 018554           87 SPLQVKYADGEL   98 (354)
Q Consensus        87 ~~l~v~~~~~~~   98 (354)
                      +.|+|.+++.+.
T Consensus        79 ~~l~V~~A~~r~   90 (93)
T d2cq3a1          79 RKIEVNNATARV   90 (93)
T ss_dssp             EECEEEECCSSC
T ss_pred             EEEEEEecCcCC
Confidence            899999998754

>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=99.80  E-value=8.1e-20  Score=138.61  Aligned_cols=87  Identities=28%  Similarity=0.556  Sum_probs=77.1

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~  177 (354)
                      ++..++|||+||++++|+++|+++|++||+|.+|+|+++ .++.++|||||+|.+.++|.+|++.||+.. ++|  +.|+
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~-~~g--~~i~   81 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE-FSG--RALR   81 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBS-CSS--SCBE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCE-ECC--EEEE
Confidence            334578999999999999999999999999999999998 478999999999999999999999999976 666  6789


Q ss_pred             EEecCChHHHH
Q 018554          178 VKWADTEKERQ  188 (354)
Q Consensus       178 v~~a~~~~~~~  188 (354)
                      |+||...+.+.
T Consensus        82 V~~a~~~~~~~   92 (104)
T d1p1ta_          82 VDNAASEKNKE   92 (104)
T ss_dssp             EEETTCTTHHH
T ss_pred             EEECCCCCCcc
Confidence            99998765544

>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=99.80  E-value=1.4e-19  Score=134.19  Aligned_cols=82  Identities=24%  Similarity=0.415  Sum_probs=74.9

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      +.+++|||+|||+++|+++|+++|++||.|++|.|+++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--r~i~V   81 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR-LDD--RIIRT   81 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSE-ETT--EECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            34789999999999999999999999999999999998 478899999999999999999999999987 566  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|+...
T Consensus        82 ~~a~~~   87 (93)
T d1h2vz_          82 DWDAGF   87 (93)
T ss_dssp             EEESCC
T ss_pred             EEcCCC
Confidence            998654

>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=1.6e-19  Score=133.07  Aligned_cols=81  Identities=23%  Similarity=0.477  Sum_probs=74.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++|+++|+++|++||.|.++.|++| .++.++|||||+|.+.++|++|++.|||.. ++|  +.|.|+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~i~v~   83 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG-YDH--LILNVE   83 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCE-ETT--EECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCE-ECC--EEEEEE
Confidence            3578999999999999999999999999999999998 478999999999999999999999999976 565  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ||+++
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99864

>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=99.79  E-value=3.4e-20  Score=136.51  Aligned_cols=81  Identities=28%  Similarity=0.486  Sum_probs=74.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|++||.|++++|++|. ++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|+|
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~-i~g--~~l~v~~   81 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE-LFG--RTIRVNL   81 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE-ETT--EEEEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEE
Confidence            5789999999999999999999999999999999984 68999999999999999999999999976 666  6899999


Q ss_pred             cCChH
Q 018554          181 ADTEK  185 (354)
Q Consensus       181 a~~~~  185 (354)
                      |++++
T Consensus        82 a~p~~   86 (89)
T d2cqba1          82 AKPMR   86 (89)
T ss_dssp             CCCCC
T ss_pred             eCCCC
Confidence            98653

>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=99.79  E-value=9.2e-20  Score=133.04  Aligned_cols=78  Identities=24%  Similarity=0.373  Sum_probs=70.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCC---CcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTR---ASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        17 lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg---~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      |||+|||+++|+++|+++|++||.|.+|+|++|+.++   ++||||||+|.+.++|++|++.+|+.. +.+  +.|.|++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~-~~g--~~i~V~~   77 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT-VDG--HKLEVRI   77 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE-ETT--EECEEEC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            8999999999999999999999999999999988765   579999999999999999999998866 555  8899999


Q ss_pred             cccc
Q 018554           94 ADGE   97 (354)
Q Consensus        94 ~~~~   97 (354)
                      ++..
T Consensus        78 a~~~   81 (85)
T d2cpfa1          78 SERA   81 (85)
T ss_dssp             SSCS
T ss_pred             CCCC
Confidence            8643

>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=2e-19  Score=129.52  Aligned_cols=77  Identities=27%  Similarity=0.506  Sum_probs=71.7

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      +|||+||+.++|+++|+++|++||+|.+|+|++|+ ++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~-~~g--r~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDV-IKG--KPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCE-ETT--EECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEEeC
Confidence            69999999999999999999999999999999984 68999999999999999999999999987 666  789999986


Q ss_pred             C
Q 018554          183 T  183 (354)
Q Consensus       183 ~  183 (354)
                      .
T Consensus        79 ~   79 (80)
T d1cvja1          79 R   79 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=2.3e-19  Score=135.21  Aligned_cols=86  Identities=22%  Similarity=0.377  Sum_probs=75.2

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      .+....+.++|||+|||.++++++|+++|++||.|.++.++.+. +++++|||||+|.+.++|++||+.|||.. +.+  
T Consensus        11 ~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~-i~g--   86 (101)
T d1x5oa1          11 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKF-IKT--   86 (101)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCC-CCC--
T ss_pred             hccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCE-ECC--
Confidence            34456677899999999999999999999999999999999985 68999999999999999999999999977 544  


Q ss_pred             ccceeecccc
Q 018554           87 SPLQVKYADG   96 (354)
Q Consensus        87 ~~l~v~~~~~   96 (354)
                      +++.+.++++
T Consensus        87 r~~~v~~~~P   96 (101)
T d1x5oa1          87 PPGVSAPTEP   96 (101)
T ss_dssp             CTTSCCCSSC
T ss_pred             cCCccCCCCC
Confidence            6777776654

>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=1.4e-19  Score=131.97  Aligned_cols=79  Identities=30%  Similarity=0.552  Sum_probs=72.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .+|||+|||+++|+++|+++|++||+|++++|++| .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|+||
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   78 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ-LGD--KKLLVQRA   78 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCC-CSS--SCCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEC
Confidence            47999999999999999999999999999999998 479999999999999999999999999977 666  68999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +..
T Consensus        79 ~~~   81 (85)
T d2u2fa_          79 SVG   81 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.79  E-value=1e-19  Score=135.90  Aligned_cols=86  Identities=21%  Similarity=0.305  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCC-CCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFAL-VDEVNIIKDK-TTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~-v~~i~i~~d~-~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      +|+|||+|||.++|+++|+++|++||+ |.++.+++|. .+++++|||||+|.+.++|.+|++.|++..+.. ..+.|+|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~-~g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQL-WGHQIAV   79 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCB-TTBCCEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEE-CCEEEEE
Confidence            479999999999999999999999996 9999999985 468999999999999999999999997655332 2489999


Q ss_pred             ecccccccc
Q 018554           92 KYADGELER  100 (354)
Q Consensus        92 ~~~~~~~~~  100 (354)
                      .|++++.+.
T Consensus        80 ~~A~p~~~~   88 (96)
T d2disa1          80 DWAEPEIDV   88 (96)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCC
Confidence            999876554

>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=99.79  E-value=2.3e-19  Score=133.08  Aligned_cols=81  Identities=21%  Similarity=0.369  Sum_probs=74.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||.++|+++|+++|++||.|++++|++| .++.++|||||+|.+.++|++|++.|||.. ++|  +.|+|+|
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~~   85 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK-LYG--KPIRVNK   85 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB-CSS--CBCEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEE
Confidence            578999999999999999999999999999999998 578999999999999999999999999987 666  6899999


Q ss_pred             cCChH
Q 018554          181 ADTEK  185 (354)
Q Consensus       181 a~~~~  185 (354)
                      |+.+.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97653

>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=99.78  E-value=2.3e-19  Score=134.72  Aligned_cols=80  Identities=28%  Similarity=0.439  Sum_probs=74.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++++|+++|+++|++||.|.+++|++| .++.++|||||+|.+.++|++|++.||+.. ++|  +.|+|++
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~-~~g--r~i~V~~   84 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV-FQG--RMLHVLP   84 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEE-SSS--CEEEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEE
Confidence            578999999999999999999999999999999998 579999999999999999999999999976 666  6899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |+.+
T Consensus        85 a~~~   88 (99)
T d1whwa_          85 STIK   88 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9865

>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=2.3e-19  Score=129.59  Aligned_cols=79  Identities=24%  Similarity=0.350  Sum_probs=67.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      +++|||+|||+++|+++|+++|++||.|..+.++.+ ..+.++|||||+|.+.++|.+|++.|||.. ++|  ++|+|++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~-~~g--~~i~V~~   77 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK-IEG--YTLVTKV   77 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE-ETT--EECEEEE
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            479999999999999999999999999998888776 578899999999999999999999999987 565  7999999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      +++
T Consensus        78 a~P   80 (81)
T d2ghpa1          78 SNP   80 (81)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            875

>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=99.78  E-value=3.6e-19  Score=127.96  Aligned_cols=77  Identities=25%  Similarity=0.439  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           14 RVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        14 ~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      .++|||+|||+++|+++|+++|++||.|..+.+..|+.+++++|||||+|.+.++|++|++ +++.. +.|  +.|+|+.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~-l~G--r~i~V~~   77 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHT-VNG--HNCEVRK   77 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCE-ETT--EECEEEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCE-ECC--EEEEEEE
Confidence            4799999999999999999999999999999999999999999999999999999999985 66665 666  7788775


Q ss_pred             c
Q 018554           94 A   94 (354)
Q Consensus        94 ~   94 (354)
                      |
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=2.4e-19  Score=138.39  Aligned_cols=105  Identities=16%  Similarity=0.295  Sum_probs=84.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .+.+++|||+|||.++|+++|+++|++||.|.+|++..+   ++++|||||+|.+.++|.+|++.||+.. +.|  +.|.
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~-~~g--r~l~   77 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFN-VCN--RYLV   77 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCE-ETT--EECE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEE
Confidence            456789999999999999999999999999999999865   5678999999999999999999999877 555  8899


Q ss_pred             eeccccccccccceEEEecCCCCCCHHHHHHhhccCCC
Q 018554           91 VKYADGELERLEHKLFIGMLPKNVSEAEVSALFSIYGT  128 (354)
Q Consensus        91 v~~~~~~~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~  128 (354)
                      |.++..+....       .......++++..+.+.+|.
T Consensus        78 V~~a~~~~~~~-------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          78 VLYYNANRAFQ-------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             EEECCHHHHTT-------TSCHHHHHHHHHHHHHHHCC
T ss_pred             EEEcCCCchhh-------hhHHHHHHHHHHHHHHHhCC
Confidence            99886543321       11222356677888777764

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=4e-19  Score=132.02  Aligned_cols=81  Identities=28%  Similarity=0.601  Sum_probs=73.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC--CCCCcceEEEEEeCCHHHHHHHHHHh-CCCcccCCCceeEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG--SQQTSKGCAFLKYETKEQALAALEAI-NGKHKMEGSSVPLV  177 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~--~~~~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~~g~~~~l~  177 (354)
                      ..++|||+|||.++++++|+++|++||.|.+++|+++  .++.++|||||+|.+.++|.+|++.| |+.. ++|  ++|.
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~-~~G--r~l~   83 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH-LYG--RRLV   83 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCB-SSS--CBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcE-ECC--EEEE
Confidence            4578999999999999999999999999999999887  36889999999999999999999998 7865 676  6899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+||+.+
T Consensus        84 V~~A~~~   90 (94)
T d2cpha1          84 LEWADSE   90 (94)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999865

>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=99.78  E-value=6.6e-19  Score=127.73  Aligned_cols=80  Identities=20%  Similarity=0.373  Sum_probs=71.2

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .+..++++|||+|||.++|+++|+++|++||.|.+|+++++     .+|||||+|.+.++|.+|++.||+..+..+  +.
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~--~~   75 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPT--HA   75 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTT--CB
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCC--cE
Confidence            45667899999999999999999999999999999999865     358999999999999999999999876544  67


Q ss_pred             ceeeccc
Q 018554           89 LQVKYAD   95 (354)
Q Consensus        89 l~v~~~~   95 (354)
                      |+|.|++
T Consensus        76 i~v~~ak   82 (83)
T d2b0ga1          76 MKITFAK   82 (83)
T ss_dssp             CEEEECC
T ss_pred             EEEEEec
Confidence            8999886

>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=99.77  E-value=5.7e-19  Score=129.85  Aligned_cols=80  Identities=20%  Similarity=0.357  Sum_probs=71.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|++|. ++.+||||||+|.+.++|.+|++..   +.++|  +.|.|+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~---~~l~G--r~i~v~   81 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR---HMIDG--RWCDCK   81 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC---EEETT--EEEEEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC---CccCC--EEeEEE
Confidence            35789999999999999999999999999999999994 7999999999999999999999843   24777  689999


Q ss_pred             ecCChH
Q 018554          180 WADTEK  185 (354)
Q Consensus       180 ~a~~~~  185 (354)
                      +|+++.
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            998753

>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=99.77  E-value=1.4e-19  Score=133.19  Aligned_cols=82  Identities=18%  Similarity=0.300  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      ...+|||+|||.++|+++|+++|++||.|.+|+|+.|+.  .++|||||+|.+.++|++|++.||+.. +.+  +.|.|.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~i~V~   81 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGML-LND--RKVFVG   81 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEE-ETT--EEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEE
Confidence            456899999999999999999999999999999999974  478999999999999999999998866 555  899999


Q ss_pred             ccccccc
Q 018554           93 YADGELE   99 (354)
Q Consensus        93 ~~~~~~~   99 (354)
                      +++.+.+
T Consensus        82 ~a~~~~~   88 (89)
T d1cvja2          82 RFKSRKE   88 (89)
T ss_dssp             ECCCTTT
T ss_pred             ECCCCCC
Confidence            9887654

>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=2e-19  Score=128.36  Aligned_cols=75  Identities=20%  Similarity=0.391  Sum_probs=67.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      |+|||+|||+++|+++|+++|++||.|++++|++|+ ++.+||||||+|++.++|.+|++ +|++. ++|  +.|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~-i~G--r~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHE-LDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCC-CSS--CCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCE-ECC--eEEEEEEC
Confidence            689999999999999999999999999999999985 69999999999999999999997 68865 777  46777765

>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=99.77  E-value=4.8e-19  Score=133.56  Aligned_cols=88  Identities=24%  Similarity=0.311  Sum_probs=77.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVD--------EVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK   80 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~--------~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~   80 (354)
                      .++.+.++|||+|||.++|+++|+++|+.||.|.        .+.+.+|+.+++++|||||+|.+.++|++||+.||+..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            4566789999999999999999999999999874        57778888999999999999999999999999999876


Q ss_pred             cCCCCCccceeeccccccc
Q 018554           81 TLPGASSPLQVKYADGELE   99 (354)
Q Consensus        81 ~~~g~~~~l~v~~~~~~~~   99 (354)
                       +.|  +.|+|++++.+..
T Consensus        83 -~~g--r~i~V~~a~~~~p   98 (101)
T d2cpea1          83 -FQG--SKLKVSLARKKPP   98 (101)
T ss_dssp             -ETT--EECEEECSSCCCC
T ss_pred             -ECC--EEEEEEEcCCCCC
Confidence             555  8999999876543

>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=99.77  E-value=6.2e-19  Score=133.01  Aligned_cols=81  Identities=22%  Similarity=0.406  Sum_probs=74.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|+.||.|.+++++.+ .++.+||||||+|.+.++|++|++.|||.. +.|  +.|+|+|
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~-~~g--~~i~V~~   94 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ-IGM--KRLKVQL   94 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE-ETT--EECEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            578999999999999999999999999999999998 578999999999999999999999999987 555  7899999


Q ss_pred             cCChH
Q 018554          181 ADTEK  185 (354)
Q Consensus       181 a~~~~  185 (354)
                      |+++.
T Consensus        95 a~~k~   99 (102)
T d2cpza1          95 KRSKN   99 (102)
T ss_dssp             CCCSC
T ss_pred             eCCCC
Confidence            98764

>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=1.4e-18  Score=128.84  Aligned_cols=81  Identities=25%  Similarity=0.456  Sum_probs=73.3

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...++|||+|||+++|+++|+++|++||.|++|+++++..+ ++|||||+|.+.++|.+|++.||+.. ++|  +.|+|+
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~-~~g--~~l~V~   84 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTV-VEG--RKIEVN   84 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEE
Confidence            34678999999999999999999999999999999998654 58999999999999999999999986 666  789999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ||+++
T Consensus        85 ~A~~r   89 (93)
T d2cq3a1          85 NATAR   89 (93)
T ss_dssp             ECCSS
T ss_pred             ecCcC
Confidence            99865

>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=99.77  E-value=4e-19  Score=126.42  Aligned_cols=75  Identities=29%  Similarity=0.433  Sum_probs=68.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           16 KLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        16 ~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      +|||+|||.++||++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ +|+.. +.|  +.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~-l~g--r~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHE-INN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCC-BTT--BCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCE-ECC--eEEEEEEC
Confidence            69999999999999999999999999999999999999999999999999999999996 87765 655  78888764

>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=99.77  E-value=1.3e-19  Score=137.10  Aligned_cols=88  Identities=23%  Similarity=0.347  Sum_probs=79.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...++++|||+|||.++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.||+.. +.|  +.|
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~-~~g--~~l   90 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYK-LYG--KIL   90 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCB-CSS--CBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCE-ECC--EEE
Confidence            34568899999999999999999999999999999999998899999999999999999999999998876 444  899


Q ss_pred             eeecccccccc
Q 018554           90 QVKYADGELER  100 (354)
Q Consensus        90 ~v~~~~~~~~~  100 (354)
                      +|.|++.+.++
T Consensus        91 ~V~~ak~k~~r  101 (102)
T d2cpxa1          91 VIEFGKNKKQR  101 (102)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEeCCCcccC
Confidence            99999876654

>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=99.76  E-value=2.6e-19  Score=131.72  Aligned_cols=81  Identities=28%  Similarity=0.448  Sum_probs=73.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..+|||+|||+++|+++|+++|++||.|.+++|+.+..+ ++|||||+|++.++|++|++.|||.. ++|  +.|.|++|
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~-~kg~afV~f~~~~~A~~Ai~~l~g~~-~~g--~~i~V~~a   83 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGML-LND--RKVFVGRF   83 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB-CCSCEEEEESCHHHHHHHTTSSSEEE-ETT--EEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC-CcceeEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEEC
Confidence            457999999999999999999999999999999988644 68999999999999999999999976 665  79999999


Q ss_pred             CChHH
Q 018554          182 DTEKE  186 (354)
Q Consensus       182 ~~~~~  186 (354)
                      +++++
T Consensus        84 ~~~~~   88 (89)
T d1cvja2          84 KSRKE   88 (89)
T ss_dssp             CCTTT
T ss_pred             CCCCC
Confidence            87653

>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=4.1e-19  Score=133.57  Aligned_cols=81  Identities=23%  Similarity=0.493  Sum_probs=72.7

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+||+.++|+++|+++|+.||.|.+|+|++| .++.+||||||+|.+.++|.+|++ |||.. ++|  +.|+|+
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~   92 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQR-LLG--VPIIVQ   92 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEE-ETT--EEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCE-ECC--EEEEEE
Confidence            3578999999999999999999999999999999998 579999999999999999999995 99976 666  789999


Q ss_pred             ecCChH
Q 018554          180 WADTEK  185 (354)
Q Consensus       180 ~a~~~~  185 (354)
                      +++.++
T Consensus        93 ~a~~~~   98 (101)
T d2cq4a1          93 ASQAEK   98 (101)
T ss_dssp             EHHHHH
T ss_pred             ECCCCC
Confidence            885443

>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=99.76  E-value=1.7e-18  Score=125.51  Aligned_cols=75  Identities=29%  Similarity=0.416  Sum_probs=68.3

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++|||+||+.++|+++|+++|++||.|++++|+++ .++.++|||||+|.+.++|.+|++.|||.. ++|  +.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g--r~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME-LDG--RRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCE-ECC--EEeEC
Confidence            3578999999999999999999999999999999998 468999999999999999999999999976 666  56665

>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=99.76  E-value=1e-18  Score=132.08  Aligned_cols=80  Identities=23%  Similarity=0.353  Sum_probs=72.2

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ..++|||+|||+++|+++|+++|++||.|++|+|++|. ++.++|||||+|.+.++|++|++.+|+ . ++|  +.|+|+
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~-l~G--r~l~V~   84 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-I-IDG--RKANVN   84 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-E-ETT--EECEEE
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-c-CCC--EEEEEE
Confidence            35689999999999999999999999999999999984 799999999999999999999998876 4 666  689999


Q ss_pred             ecCCh
Q 018554          180 WADTE  184 (354)
Q Consensus       180 ~a~~~  184 (354)
                      ||..+
T Consensus        85 ~a~~~   89 (103)
T d2cqda1          85 LAYLG   89 (103)
T ss_dssp             ESTTT
T ss_pred             EcCCC
Confidence            98654

>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=99.76  E-value=3.2e-19  Score=130.33  Aligned_cols=82  Identities=20%  Similarity=0.383  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCCCCC-HHHHHHHHhhcCCeeEEEEeeC-CCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           12 EERVKLFVGQVPKHMT-EAQLLAMFKEFALVDEVNIIKD-KTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~t-e~~L~~~F~~~G~v~~i~i~~d-~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .+.++|||+|||++++ |++|+++|++||.|++|+|.++ +.+++++|||||+|.+.++|++|++ +|+.. +.|  +.|
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~-~~g--r~l   77 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSL-LGN--REI   77 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEE-ETT--EEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCE-ECC--EEE
Confidence            3678999999999976 5669999999999999998764 5689999999999999999999996 87765 555  889


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      +|++++.+
T Consensus        78 ~V~~a~~k   85 (86)
T d2ghpa3          78 SVSLADKK   85 (86)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99988754

>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=3e-18  Score=124.33  Aligned_cols=77  Identities=29%  Similarity=0.459  Sum_probs=69.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|++||.|.+++|++|. ++.++|||||+|.+.++|.+|++ +++.. ++|  +.|+|+.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~-i~G--r~i~V~~   81 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHK-VDG--RVVEPKR   81 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCE-ETT--EECEEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCE-ECC--EEEEEEe
Confidence            4689999999999999999999999999999999995 69999999999999999999997 57765 666  6888888


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      |.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            75

>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=99.75  E-value=1e-18  Score=128.78  Aligned_cols=80  Identities=29%  Similarity=0.527  Sum_probs=72.1

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+|||.++|+++|+++|+.||.|++|+|+++.... ++||||+|.+.++|.+|++.|||.. +.|  +.|+|.||
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~-~~~afV~f~~~~~A~~A~~~l~~~~-~~g--~~i~v~~a   83 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRK-ILG--KEVKVNWA   83 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS-CCEEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc-ceeeEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEEc
Confidence            5789999999999999999999999999999999985443 8999999999999999999999976 565  78999999


Q ss_pred             CChH
Q 018554          182 DTEK  185 (354)
Q Consensus       182 ~~~~  185 (354)
                      +++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7653

>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=99.75  E-value=8.7e-19  Score=129.19  Aligned_cols=80  Identities=33%  Similarity=0.579  Sum_probs=73.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|++||.|.++.++++ .++.++|||||+|+++++|++|++.|||.. ++|  +.|+|+|
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~-~~g--~~l~V~~   81 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS-VDG--RQIRVDQ   81 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCC-TTS--CCCEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEEEE
Confidence            578999999999999999999999999999998887 578899999999999999999999999986 666  5888999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |..+
T Consensus        82 a~~~   85 (90)
T d1x5sa1          82 AGKS   85 (90)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            8655

>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=99.75  E-value=1.7e-18  Score=126.17  Aligned_cols=76  Identities=32%  Similarity=0.496  Sum_probs=68.4

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CC---CcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQ---TSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      |||+|||+++|+++|+++|++||.|++++|+++. ++   .+||||||+|++.++|.+|++.|||.. ++|  +.|+|+|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~-~~g--~~i~V~~   77 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT-VDG--HKLEVRI   77 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE-ETT--EECEEEC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            8999999999999999999999999999999874 22   468999999999999999999999976 666  6899999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      |+.
T Consensus        78 a~~   80 (85)
T d2cpfa1          78 SER   80 (85)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

>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=99.75  E-value=6.3e-19  Score=140.86  Aligned_cols=80  Identities=26%  Similarity=0.502  Sum_probs=73.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+||++++|+++|+++|++||.|++|+|++| .++.++|||||+|.+.++|.+||+.|||.. ++|  +.|+|+|
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~-~~g--r~l~V~~  118 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN-ILN--KRLKVAL  118 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEE-CSS--CEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            468999999999999999999999999999999998 478999999999999999999999999976 666  6899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |...
T Consensus       119 a~~~  122 (139)
T d1u6fa1         119 AASG  122 (139)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            8754

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.7e-18  Score=128.98  Aligned_cols=79  Identities=16%  Similarity=0.397  Sum_probs=70.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||.++++++|+++|++||+|.+|+|++|      ||||||+|.+.++|++|++.||+.. +.+  +.|
T Consensus        14 ~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~-i~g--~~l   84 (96)
T d1x4ga1          14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTT-IEG--HVV   84 (96)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            3456789999999999999999999999999999999976      5799999999999999999999877 555  889


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      +|.|++.+
T Consensus        85 ~v~~ak~~   92 (96)
T d1x4ga1          85 KCYWGKES   92 (96)
T ss_dssp             EEECCCCC
T ss_pred             EEEEcCCC
Confidence            99998764

>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=99.75  E-value=6.7e-19  Score=127.78  Aligned_cols=77  Identities=32%  Similarity=0.552  Sum_probs=69.6

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEE-EEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i-~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      |||+|||.++|+++|+++|++||.|.++ +++++ .+++++|||||+|++.++|.+|++.|+|.. ++|  +.|+|+||.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~-~~g--r~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY-LCN--RPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCE-ETT--EECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcE-ECC--EEEEEEEec
Confidence            7999999999999999999999998764 77887 478999999999999999999999999986 666  789999997


Q ss_pred             Ch
Q 018554          183 TE  184 (354)
Q Consensus       183 ~~  184 (354)
                      ++
T Consensus        78 ~k   79 (83)
T d1x5ta1          78 KK   79 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.75  E-value=3.7e-18  Score=125.16  Aligned_cols=80  Identities=19%  Similarity=0.211  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      .++++|||+|||.++++++|+++|++||.|.++.++.+    +++|||||+|.+.++|.+|++.||+..+..+  +.|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g--~~l~v   81 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLRV   81 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSS--CBCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCC--CEEEE
Confidence            56789999999999999999999999999988877654    4678999999999999999999999876555  88999


Q ss_pred             eccccc
Q 018554           92 KYADGE   97 (354)
Q Consensus        92 ~~~~~~   97 (354)
                      .|++..
T Consensus        82 ~~sk~~   87 (88)
T d2adca2          82 SFSKST   87 (88)
T ss_dssp             EECSSC
T ss_pred             EeCCCC
Confidence            998753

>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=99.74  E-value=3.8e-18  Score=126.95  Aligned_cols=82  Identities=16%  Similarity=0.401  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...+.++|||+|||.++|++||+++|++||.|..+.+.++   +.++|||||+|.+.++|++||+.||+.. +.+  +.|
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~-~~g--~~l   83 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYD-YDG--YRL   83 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            3567789999999999999999999999999999987665   4578999999999999999999999876 555  889


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      +|.|++..
T Consensus        84 ~V~~a~~~   91 (95)
T d1x4aa1          84 RVEFPRSG   91 (95)
T ss_dssp             EEECCCCC
T ss_pred             EEEeccCC
Confidence            99998764

>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=2.3e-18  Score=130.48  Aligned_cols=87  Identities=15%  Similarity=0.302  Sum_probs=72.5

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCC-CCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDK-TTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~-~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ....+.++|||+|||+++||++|+++|++|| |.++.++.++ .+++++|||||+|.+.++|++|+ .+|+.. +.+  +
T Consensus        10 ~p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~-~~g--r   84 (104)
T d1wi8a_          10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEES-LGN--K   84 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCE-ETT--E
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCE-ECC--E
Confidence            3455679999999999999999999999999 6777777765 57899999999999999998777 588866 555  8


Q ss_pred             cceeecccccccc
Q 018554           88 PLQVKYADGELER  100 (354)
Q Consensus        88 ~l~v~~~~~~~~~  100 (354)
                      .|+|.++..+..+
T Consensus        85 ~l~V~~a~~~~~~   97 (104)
T d1wi8a_          85 RIRVDVADQAQDK   97 (104)
T ss_dssp             ECEEEECCCCCCC
T ss_pred             EEEEEECCCCCCC
Confidence            8999988765543

>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=99.74  E-value=1.9e-18  Score=122.68  Aligned_cols=74  Identities=22%  Similarity=0.390  Sum_probs=66.2

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +|||+|||+++|+++|+++|++||.|.+++|+++ .+++++|||||+|.+.++|++|++ +++.. ++|  +.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~-l~G--r~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHK-LNG--KVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCC-BTT--BCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCE-ECC--CEEEeeEC
Confidence            5999999999999999999999999999999998 478999999999999999999997 67765 677  56777644

>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=2.2e-18  Score=129.70  Aligned_cols=79  Identities=29%  Similarity=0.472  Sum_probs=70.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+|||.++|+++|+++|++||.|..+.+..+.++.++|||||+|.+.++|.+|++.|||+. +.|  +++.|.+
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~-i~g--r~~~v~~   93 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF-IKT--PPGVSAP   93 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC-CCC--CTTSCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCE-ECC--cCCccCC
Confidence            3578999999999999999999999999999999999889999999999999999999999999987 555  4555555


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      ++
T Consensus        94 ~~   95 (101)
T d1x5oa1          94 TE   95 (101)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.74  E-value=1.7e-19  Score=133.17  Aligned_cols=83  Identities=19%  Similarity=0.325  Sum_probs=72.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .+....++|||+|||+++|+++|+++|++||.|.+++|+.+ .+|+++|||||+|.+.++|++||+ +|+.. +.|  +.
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~-~~g--~~   82 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLK-VFG--NE   82 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEE-ETT--EE
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcE-ECC--EE
Confidence            44556779999999999999999999999999999988765 479999999999999999999996 87766 555  89


Q ss_pred             ceeecccc
Q 018554           89 LQVKYADG   96 (354)
Q Consensus        89 l~v~~~~~   96 (354)
                      |+|.+++.
T Consensus        83 i~V~~ak~   90 (91)
T d1fjeb1          83 IKLEKPKG   90 (91)
T ss_dssp             EEEECCCC
T ss_pred             EEEEecCC
Confidence            99998875

>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=99.74  E-value=1.1e-18  Score=123.00  Aligned_cols=67  Identities=25%  Similarity=0.353  Sum_probs=63.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 018554           17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPG   84 (354)
Q Consensus        17 lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g   84 (354)
                      |||+|||.++|+++|+++|++||.|..+++.+++.+++++|||||+|.+.++|++|++.||+.. +.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~-~~G   67 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG-VQA   67 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT-CCE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCE-ECC
Confidence            8999999999999999999999999999999999999999999999999999999999999866 444

>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=99.74  E-value=2.2e-18  Score=128.40  Aligned_cols=75  Identities=23%  Similarity=0.538  Sum_probs=69.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||+.++++++|+++|++||.|++|+|+++     ||||||+|++.++|.+|++.|||.. ++|  +.|+|.|+
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~-i~g--~~l~v~~a   89 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTT-IEG--HVVKCYWG   89 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEECC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEc
Confidence            578999999999999999999999999999999987     8999999999999999999999987 565  78999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus        90 k~~   92 (96)
T d1x4ga1          90 KES   92 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.74  E-value=1.1e-18  Score=125.46  Aligned_cols=78  Identities=24%  Similarity=0.363  Sum_probs=68.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .+|||+|||.++|+++|+++|++||.|.++.+++      ++|||||+|.+.++|++|++.||+...+.|  +.|+|.|+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G--~~i~V~~a   73 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHG--KIMEVDYS   73 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETT--EECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECC--EEEEEEEc
Confidence            5799999999999999999999999988777665      468999999999999999999988654666  89999999


Q ss_pred             cccccc
Q 018554           95 DGELER  100 (354)
Q Consensus        95 ~~~~~~  100 (354)
                      .++..+
T Consensus        74 ~~k~~r   79 (80)
T d2cqha1          74 VSKKLR   79 (80)
T ss_dssp             CCCCCC
T ss_pred             CCcCcC
Confidence            876553

>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=99.73  E-value=3.6e-18  Score=127.55  Aligned_cols=78  Identities=27%  Similarity=0.479  Sum_probs=72.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+||+.++++++|+++|++||.|+.+++.++     ++||||+|.+.++|.+|++.||+.. ++|..++|+|+|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~-i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFP-LGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCB-CSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCE-eCCCceEEEEEe
Confidence            3578999999999999999999999999999999876     7899999999999999999999987 787778999999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |+..
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9864

>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=99.73  E-value=3.8e-18  Score=124.12  Aligned_cols=79  Identities=18%  Similarity=0.285  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|.+++ +|+++|||||+|.+.++|.+||+ +++.. +.+  +.|.|
T Consensus         4 ~~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~-~~g--~~l~v   78 (85)
T d1zh5a2           4 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQK-YKE--TDLLI   78 (85)
T ss_dssp             HHTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCE-ETT--EECEE
T ss_pred             CCcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCE-ECC--EEEEE
Confidence            356899999999999999999999999999999998886 69999999999999999999996 55655 555  78888


Q ss_pred             eccc
Q 018554           92 KYAD   95 (354)
Q Consensus        92 ~~~~   95 (354)
                      .|.+
T Consensus        79 ~~~~   82 (85)
T d1zh5a2          79 LFKD   82 (85)
T ss_dssp             EEGG
T ss_pred             EEcC
Confidence            7753

>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=99.73  E-value=6.1e-19  Score=126.89  Aligned_cols=77  Identities=29%  Similarity=0.442  Sum_probs=68.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      ++|||+|||.++|+++|+++|++||.|.++++...     +|||||+|.+.++|.+|++.|||...++|  +.|+|+||.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G--~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHG--KIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETT--EECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECC--EEEEEEEcC
Confidence            47999999999999999999999999988777764     89999999999999999999999755776  789999998


Q ss_pred             ChHH
Q 018554          183 TEKE  186 (354)
Q Consensus       183 ~~~~  186 (354)
                      ++++
T Consensus        75 ~k~~   78 (80)
T d2cqha1          75 SKKL   78 (80)
T ss_dssp             CCCC
T ss_pred             CcCc
Confidence            7643

>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=99.73  E-value=7e-18  Score=122.67  Aligned_cols=78  Identities=18%  Similarity=0.373  Sum_probs=70.9

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+|||.++|+++|+++|+.||.|++|++.++.++.++|||||+|.+.++|.+|++ +++.. +.|  +.|.|+|
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~-~~g--~~l~v~~   80 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQK-YKE--TDLLILF   80 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCE-ETT--EECEEEE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCE-ECC--EEEEEEE
Confidence            3578999999999999999999999999999999999999999999999999999999996 68866 565  6889988


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      ++
T Consensus        81 ~~   82 (85)
T d1zh5a2          81 KD   82 (85)
T ss_dssp             GG
T ss_pred             cC
Confidence            64

>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=99.73  E-value=4.6e-18  Score=128.13  Aligned_cols=80  Identities=23%  Similarity=0.404  Sum_probs=71.9

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|++||+|.++.|.+|. ++.++|||||+|.+.++|.+|++ +++.. ++|  +.|.|++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~-l~G--~~i~V~~   95 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHS-IDG--RVVEPKR   95 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEE-ETT--EEEEEEC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCe-ECC--EEEEEEE
Confidence            4789999999999999999999999999999999984 67899999999999999999996 68865 666  7899999


Q ss_pred             cCChH
Q 018554          181 ADTEK  185 (354)
Q Consensus       181 a~~~~  185 (354)
                      |.++.
T Consensus        96 a~~ke  100 (103)
T d1x4ba1          96 AVARE  100 (103)
T ss_dssp             CSSCC
T ss_pred             CcccC
Confidence            88653

>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=99.73  E-value=1.2e-17  Score=119.78  Aligned_cols=76  Identities=20%  Similarity=0.393  Sum_probs=68.5

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|+++|+++|++||.|..+.+..+ .++.++|||||+|.+.++|.+|++ +||.. ++|  +.|+|+.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~-l~G--r~i~V~~   77 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHT-VNG--HNCEVRK   77 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCE-ETT--EECEEEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCE-ECC--EEEEEEE
Confidence            368999999999999999999999999999999998 478899999999999999999985 79976 676  6788887


Q ss_pred             c
Q 018554          181 A  181 (354)
Q Consensus       181 a  181 (354)
                      |
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=1.4e-18  Score=123.09  Aligned_cols=74  Identities=19%  Similarity=0.400  Sum_probs=65.4

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +|||+|||+++|+++|+++|++||.|.+|+|++| .++.+||||||+|++.++|++|++. ++.. ++|+  .|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHN-VGLS--KCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCC-BTTB--CCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCE-ECCE--EeEEEEC
Confidence            6999999999999999999999999999999998 4799999999999999999999975 5544 7774  6777654

>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=99.73  E-value=9e-18  Score=125.36  Aligned_cols=82  Identities=20%  Similarity=0.317  Sum_probs=73.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ...++++|||+|||.++++++|+++|++||+|.+|++.++      ++||||+|.+.++|++|++.||+.. +.+..+.|
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~-i~g~~~~l   85 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFP-LGGPDRRL   85 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCB-CSSSSCBC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCE-eCCCceEE
Confidence            4567899999999999999999999999999999998765      4699999999999999999999876 66667899


Q ss_pred             eeecccccc
Q 018554           90 QVKYADGEL   98 (354)
Q Consensus        90 ~v~~~~~~~   98 (354)
                      +|.|++.+.
T Consensus        86 ~v~~ak~~~   94 (97)
T d1whya_          86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999998654

>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=99.73  E-value=9.9e-18  Score=121.40  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=68.5

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .+++|||+||+.++|+++|+++|++||.|+++++++++    +|||||+|.+.++|.+|++.|+|..+.+|  +.|+|+|
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~--~~i~v~~   80 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEALQGFKITPT--HAMKITF   80 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT----CSCEEEEESSHHHHHHHHHHHTTCBSSTT--CBCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc----ceeEEEecCCHHHHHHHHHHhCCcEeCCC--cEEEEEE
Confidence            46799999999999999999999999999999998753    68999999999999999999999875454  5799999


Q ss_pred             cC
Q 018554          181 AD  182 (354)
Q Consensus       181 a~  182 (354)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

>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=99.72  E-value=6.8e-18  Score=130.02  Aligned_cols=78  Identities=24%  Similarity=0.440  Sum_probs=70.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +++|||+||+.++|+++|+++|++||.|++|++..+  +.++|||||+|.+.++|.+|++.|||.. ++|  +.|.|.|+
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~-~~g--r~l~V~~a   81 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFN-VCN--RYLVVLYY   81 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCE-ETT--EECEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEc
Confidence            578999999999999999999999999999999864  4568999999999999999999999987 565  78999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            644

>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=99.72  E-value=7.2e-18  Score=128.50  Aligned_cols=83  Identities=12%  Similarity=0.137  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      ..+..+|||+|||+++||++|+++|++||.|.+|.|++++    ++|||||+|.+.++|++|++.||+..+ .+..+.++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l-~~~~~~l~   78 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNI-YNACCTLR   78 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCS-STTCCCCE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEe-ccCCcEEE
Confidence            3466789999999999999999999999999999999874    579999999999999999999999874 44468889


Q ss_pred             eecccccc
Q 018554           91 VKYADGEL   98 (354)
Q Consensus        91 v~~~~~~~   98 (354)
                      +.+++.+.
T Consensus        79 v~~s~~~~   86 (108)
T d2adba1          79 IDFSKLTS   86 (108)
T ss_dssp             EEECSSCS
T ss_pred             EEecCCcc
Confidence            98886543

>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=99.72  E-value=4.3e-18  Score=124.17  Aligned_cols=79  Identities=25%  Similarity=0.440  Sum_probs=67.3

Q ss_pred             cceEEEecCCCCCC-HHHHHHhhccCCCeeEEEEeeC--CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          102 EHKLFIGMLPKNVS-EAEVSALFSIYGTIKDLQILRG--SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       102 ~~~l~V~~l~~~~t-~~~l~~~F~~~G~v~~i~i~~~--~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      .++|||+|||.++| +++|+++|++||.|++|+|..+  .++.++|||||+|.+.++|++|++ ||+.. ++|  +.|+|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~-~~g--r~l~V   79 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSL-LGN--REISV   79 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEE-ETT--EEEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCE-ECC--EEEEE
Confidence            47899999999876 5569999999999999999765  478899999999999999999995 99976 666  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +||+.+
T Consensus        80 ~~a~~k   85 (86)
T d2ghpa3          80 SLADKK   85 (86)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999764

>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=2e-18  Score=126.74  Aligned_cols=78  Identities=17%  Similarity=0.313  Sum_probs=68.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHH---HHHHhhcCCeeEEEEeeCCCCCCc---ccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554           12 EERVKLFVGQVPKHMTEAQL---LAMFKEFALVDEVNIIKDKTTRAS---RGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L---~~~F~~~G~v~~i~i~~d~~tg~~---~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ...++|||+|||++++++||   +++|++||+|.+|.|++|+.++.+   +|||||+|.+.++|++|++.||+.. +.| 
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~-~~g-   83 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV-VDG-   83 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE-ETT-
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCE-ECC-
Confidence            35678999999999999999   778999999999999999887765   4999999999999999999998866 555 


Q ss_pred             Cccceee
Q 018554           86 SSPLQVK   92 (354)
Q Consensus        86 ~~~l~v~   92 (354)
                       +.|+++
T Consensus        84 -r~lkvS   89 (89)
T d2cpia1          84 -RTLKAS   89 (89)
T ss_dssp             -EEEEEE
T ss_pred             -EEEEEC
Confidence             666653

>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=5.5e-18  Score=120.37  Aligned_cols=74  Identities=22%  Similarity=0.401  Sum_probs=67.4

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS-QQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~-~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +|||+|||.++|+++|+++|++||.|+.+.++.+. ++.+++||||+|.+.++|++|++ +|+.. ++|  +.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~-l~g--r~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHE-INN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCC-BTT--BCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCE-ECC--eEEEEEEC
Confidence            59999999999999999999999999999998884 68899999999999999999996 89976 666  68888876

>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=6.8e-18  Score=123.02  Aligned_cols=75  Identities=31%  Similarity=0.551  Sum_probs=68.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+|||.++++++|+++|++||.|.+|++.++     ++||||+|++.++|.+|++.|||.. ++|  +.|+|+||
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~-i~g--~~l~V~~A   79 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMP-LRG--KQLRVRFA   79 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCC-BTT--BCCEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEC
Confidence            467999999999999999999999999999999976     7899999999999999999999987 566  68999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ...
T Consensus        80 ~~~   82 (86)
T d2cpja1          80 CHS   82 (86)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            754

>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=5.4e-18  Score=126.40  Aligned_cols=83  Identities=24%  Similarity=0.428  Sum_probs=72.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCC-eeEEEEeeCC--CCCcceEEEEEeCCHHHHHHHHHHhCCCcc-cCCCceeEE
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGT-IKDLQILRGS--QQTSKGCAFLKYETKEQALAALEAINGKHK-MEGSSVPLV  177 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~-v~~i~i~~~~--~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~-~~g~~~~l~  177 (354)
                      .|+|||+|||.++|+++|+++|+.||. |+++.++++.  +++++|||||+|.+.++|.+|++.|++..+ ++|  +.|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g--~~i~   78 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG--HQIA   78 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT--BCCE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECC--EEEE
Confidence            378999999999999999999999996 9999999874  578899999999999999999999976543 344  6899


Q ss_pred             EEecCChHH
Q 018554          178 VKWADTEKE  186 (354)
Q Consensus       178 v~~a~~~~~  186 (354)
                      |+||+++.+
T Consensus        79 V~~A~p~~~   87 (96)
T d2disa1          79 VDWAEPEID   87 (96)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987543

>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=99.72  E-value=1.6e-17  Score=124.32  Aligned_cols=81  Identities=28%  Similarity=0.451  Sum_probs=71.7

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCc-----ccCCCcee
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKH-----KMEGSSVP  175 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-----~~~g~~~~  175 (354)
                      .++|||+|||+++|+++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|++.||+..     .++|  +.
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g--r~   85 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG--RQ   85 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS--CE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC--EE
Confidence            578999999999999999999999999999999988 478889999999999999999999998533     2445  58


Q ss_pred             EEEEecCCh
Q 018554          176 LVVKWADTE  184 (354)
Q Consensus       176 l~v~~a~~~  184 (354)
                      |+|.||.++
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999999764

>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=99.72  E-value=3.6e-18  Score=127.36  Aligned_cols=86  Identities=16%  Similarity=0.269  Sum_probs=73.3

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ...+...+.++|||+|||+++|++||+++|++||.|..+.     .+++++|||||+|.+.++|++|++.||+.. +.+ 
T Consensus         8 ~~~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~-~~g-   80 (96)
T d1fjca_           8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAE-IDG-   80 (96)
T ss_dssp             TTTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEE-ETT-
T ss_pred             CccCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCE-ECC-
Confidence            3445566789999999999999999999999999876653     257899999999999999999999998765 555 


Q ss_pred             Cccceeeccccccc
Q 018554           86 SSPLQVKYADGELE   99 (354)
Q Consensus        86 ~~~l~v~~~~~~~~   99 (354)
                       +.|+|.|+.++..
T Consensus        81 -r~i~V~~a~~k~~   93 (96)
T d1fjca_          81 -RSVSLYYTGEKGG   93 (96)
T ss_dssp             -EEEEEEECSSSCC
T ss_pred             -EEEEEEEeCCCCC
Confidence             8999999887654

>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=1.2e-17  Score=121.73  Aligned_cols=78  Identities=32%  Similarity=0.513  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||.++++++|+++|++||+|.+|++.++      +|||||+|.+.++|++|++.||+.. +.+  +.|+|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~-i~g--~~l~V   76 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMP-LRG--KQLRV   76 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCC-BTT--BCCEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            34678999999999999999999999999999999876      4699999999999999999999877 555  89999


Q ss_pred             ecccccc
Q 018554           92 KYADGEL   98 (354)
Q Consensus        92 ~~~~~~~   98 (354)
                      +|+....
T Consensus        77 ~~A~~~~   83 (86)
T d2cpja1          77 RFACHSA   83 (86)
T ss_dssp             EESSCCS
T ss_pred             EECCCcC
Confidence            9987643

>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=99.72  E-value=1.7e-17  Score=125.53  Aligned_cols=87  Identities=14%  Similarity=0.183  Sum_probs=73.7

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+..+..+|||+|||+++||+||+++|+.+|.|..+.++.+..+++++|||||+|.+.++|++|++ +|+.. +.+  +
T Consensus         9 ~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~-i~g--R   84 (104)
T d1wg5a_           9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKER-IGH--R   84 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCC-SSS--S
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCE-Ecc--e
Confidence            3445566789999999999999999999999999887788887889999999999999999999996 76655 655  7


Q ss_pred             cceeecccccc
Q 018554           88 PLQVKYADGEL   98 (354)
Q Consensus        88 ~l~v~~~~~~~   98 (354)
                      .|+|.++..+.
T Consensus        85 ~i~V~~~~~~~   95 (104)
T d1wg5a_          85 YIEIFKSSRAE   95 (104)
T ss_dssp             CCEEEEECTTT
T ss_pred             EEEEEECCHHH
Confidence            78888776543

>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=6.9e-19  Score=129.79  Aligned_cols=80  Identities=25%  Similarity=0.318  Sum_probs=72.6

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...+|||+||++++|+++|+++|+.||.|++++|+.+.+++++|||||+|++.++|++|++ |||.. ++|  +.|+|++
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~-~~g--~~i~V~~   87 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLK-VFG--NEIKLEK   87 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEE-ETT--EEEEEEC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcE-ECC--EEEEEEe
Confidence            3568999999999999999999999999999999887889999999999999999999996 89976 666  7999999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |+.+
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8753

>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=99.71  E-value=1.3e-17  Score=125.59  Aligned_cols=84  Identities=25%  Similarity=0.368  Sum_probs=72.5

Q ss_pred             cccccceEEEecCCCCCCHHHHHHhhccCCCee--------EEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554           98 LERLEHKLFIGMLPKNVSEAEVSALFSIYGTIK--------DLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus        98 ~~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~--------~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      .....++|||+||+.++|+++|+++|+.||.|.        .+.+.++ .++.+++||||+|.++++|.+|++.|||.. 
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~-   82 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD-   82 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE-
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE-
Confidence            344468999999999999999999999999874        4566666 468899999999999999999999999987 


Q ss_pred             cCCCceeEEEEecCCh
Q 018554          169 MEGSSVPLVVKWADTE  184 (354)
Q Consensus       169 ~~g~~~~l~v~~a~~~  184 (354)
                      ++|  +.|+|+||+.+
T Consensus        83 ~~g--r~i~V~~a~~~   96 (101)
T d2cpea1          83 FQG--SKLKVSLARKK   96 (101)
T ss_dssp             ETT--EECEEECSSCC
T ss_pred             ECC--EEEEEEEcCCC
Confidence            565  79999999764

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=9.4e-18  Score=128.61  Aligned_cols=79  Identities=19%  Similarity=0.206  Sum_probs=68.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||+++++++|+++|++||+|.+|.|.      +++|||||+|.+.++|.+|++.||+.. +.+  +.|
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~-~~g--r~l   76 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSK-FHH--VPL   76 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCB-SSS--SBC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCc-cCC--CeE
Confidence            34456899999999999999999999999999999874      356899999999999999999999977 444  788


Q ss_pred             eeeccccc
Q 018554           90 QVKYADGE   97 (354)
Q Consensus        90 ~v~~~~~~   97 (354)
                      .|.|+...
T Consensus        77 ~v~~a~~~   84 (111)
T d1whxa_          77 YLEWAPIG   84 (111)
T ss_dssp             EEEEEETT
T ss_pred             EEEECCCC
Confidence            88887543

>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=5.1e-18  Score=123.86  Aligned_cols=79  Identities=16%  Similarity=0.237  Sum_probs=67.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||++++++||+++|+.||.|.+..++.+..+++++|||||+|.+.++|++|++.||+.. +.+  +.|+|
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~-l~g--r~i~v   83 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP-IGS--RKVKL   83 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCE-ETT--EECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            345679999999999999999999999998775445555679999999999999999999999998877 444  77777


Q ss_pred             ec
Q 018554           92 KY   93 (354)
Q Consensus        92 ~~   93 (354)
                      ++
T Consensus        84 ~l   85 (86)
T d2cqpa1          84 VL   85 (86)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>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=99.71  E-value=1.8e-17  Score=126.53  Aligned_cols=76  Identities=21%  Similarity=0.375  Sum_probs=67.4

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           14 RVKLFVGQVPK-HMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        14 ~~~lfVg~Lp~-~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +++|||+||++ .+|+++|+++|++||+|++|+|++|+     +|||||+|.+.++|++|++.||+.. +.+  +.|+|.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~-l~g--~~l~v~   73 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHK-LHG--KPIRIT   73 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCB-CSS--SBCEEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEE
Confidence            57999999964 69999999999999999999999874     5899999999999999999998877 555  789999


Q ss_pred             ccccc
Q 018554           93 YADGE   97 (354)
Q Consensus        93 ~~~~~   97 (354)
                      |++.+
T Consensus        74 ~s~~~   78 (109)
T d2adca1          74 LSKHQ   78 (109)
T ss_dssp             CCSCC
T ss_pred             ECCCC
Confidence            88643

>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=99.71  E-value=2.3e-17  Score=122.59  Aligned_cols=79  Identities=22%  Similarity=0.492  Sum_probs=70.2

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..++|||+|||.++|+++|+++|+.||.|+.+.+.++  ..+++||||+|++.++|++|++.||+.. ++|  +.|+|+|
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~-~~g--~~l~V~~   87 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYD-YDG--YRLRVEF   87 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCE-ETT--EECEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEe
Confidence            3578999999999999999999999999999998755  3458999999999999999999999987 565  7899999


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      |+..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            9753

>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=99.70  E-value=1e-17  Score=122.39  Aligned_cols=72  Identities=18%  Similarity=0.184  Sum_probs=63.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      .+|||+|||+++++++|+++|++||+|.+|++++|       |||||+|.+.++|++||+.||+.. +.+  +.++|.++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~-~~g--~~i~v~~~   70 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTK-FRS--HEGETAYI   70 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCB-CCC--TTSCCCBC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCE-ECC--cEeEEeEE
Confidence            47999999999999999999999999999998765       799999999999999999999877 555  66666665


Q ss_pred             cc
Q 018554           95 DG   96 (354)
Q Consensus        95 ~~   96 (354)
                      +.
T Consensus        71 ~~   72 (87)
T d3begb1          71 RV   72 (87)
T ss_dssp             EE
T ss_pred             ec
Confidence            43

>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=2.7e-17  Score=120.50  Aligned_cols=77  Identities=22%  Similarity=0.302  Sum_probs=68.4

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      +++|||+|||.++|+++|+++|+.||.|.++.+..+.   +++||||+|++.++|.+|+..|+|..+.+|  +.|+|+|+
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~~~afV~f~~~~~A~~A~~~l~~~~i~~g--~~l~v~~s   84 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLRVSFS   84 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS---STTCEEEEESSHHHHHHHHHHHTTCBSSSS--CBCEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec---ccceeEEEECCHHHHHHHHHhccCCEecCC--CEEEEEeC
Confidence            5789999999999999999999999999888777543   378999999999999999999999875566  67899998


Q ss_pred             CC
Q 018554          182 DT  183 (354)
Q Consensus       182 ~~  183 (354)
                      ++
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>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=99.70  E-value=1.7e-17  Score=121.04  Aligned_cols=79  Identities=23%  Similarity=0.255  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+|||.++++++|+++|++||.|..+.+.      +++|||||+|.+.++|.+|++.||+.. +.+  +.|+|
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~-i~g--~~i~V   76 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKV-LDG--SPIEV   76 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEE-ETT--EEEEE
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            345799999999999999999999999998887764      356899999999999999999998866 555  89999


Q ss_pred             eccccccc
Q 018554           92 KYADGELE   99 (354)
Q Consensus        92 ~~~~~~~~   99 (354)
                      .|+++...
T Consensus        77 ~~akP~~~   84 (86)
T d2cpda1          77 TLAKPVDK   84 (86)
T ss_dssp             ECCCCCCC
T ss_pred             EeccCCCC
Confidence            99886543

>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=99.70  E-value=1.4e-17  Score=127.56  Aligned_cols=78  Identities=22%  Similarity=0.361  Sum_probs=68.7

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      .+..++|||+|||.++++++|+++|+.||+|.+|.|.+.     ++||||+|.+.++|.+|++.|||.. +.|  +.|.|
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~-----kg~afV~f~~~~~A~~A~~~lng~~-~~g--r~l~v   78 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSK-FHH--VPLYL   78 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-----SSCEEEEESCHHHHHHHHHHHTTCB-SSS--SBCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeecc-----CceEEEEEcCHHHHHHHHHHHcCCc-cCC--CeEEE
Confidence            344679999999999999999999999999999988643     8999999999999999999999987 555  68889


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|+...
T Consensus        79 ~~a~~~   84 (111)
T d1whxa_          79 EWAPIG   84 (111)
T ss_dssp             EEEETT
T ss_pred             EECCCC
Confidence            998654

>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=2.4e-17  Score=118.16  Aligned_cols=73  Identities=30%  Similarity=0.470  Sum_probs=66.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+||+  +|+++|+++|++||+|.++++.++     ++||||+|++.++|.+|++.|||.. ++|  +.|+|+||
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~-~~g--~~l~V~~a   74 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQ-VES--VQLKVNIA   74 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCB-CSS--CBCEEEEC
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCE-ECC--EEEEEEEe
Confidence            5789999985  899999999999999999999875     7899999999999999999999987 666  68999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            754

>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=99.70  E-value=1.7e-17  Score=123.96  Aligned_cols=78  Identities=17%  Similarity=0.350  Sum_probs=67.3

Q ss_pred             CCCCCCeEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           10 SSEERVKLFVGQVP-KHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp-~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      .....++|||+||+ ..++++||+++|++||+|.+|+|        +||||||+|.+.++|++||+.||+.. +.+  +.
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~-~~g--~~   79 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRM-IAG--QV   79 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCE-ETT--EE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCE-ECC--EE
Confidence            34556789999997 67889999999999999999988        46899999999999999999998876 555  88


Q ss_pred             ceeecccccc
Q 018554           89 LQVKYADGEL   98 (354)
Q Consensus        89 l~v~~~~~~~   98 (354)
                      |+|.+++.+.
T Consensus        80 l~V~~a~~~~   89 (98)
T d1wf2a_          80 LDINLAAEPK   89 (98)
T ss_dssp             CEEEETTSCC
T ss_pred             EEEEECCCCC
Confidence            9999986543

>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=99.70  E-value=1e-17  Score=123.51  Aligned_cols=81  Identities=16%  Similarity=0.387  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554           13 ERVKLFVGQVPKHMTEAQLLA----MFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~----~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ++++|||+|||++++++||++    +|++||+|.+|++.+   +++++|||||+|.+.++|.+|++.+|+.. +.+  +.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~-~~g--~~   75 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFP-FYD--KP   75 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCE-ETT--EE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCE-ECC--EE
Confidence            578999999999999999865    589999999988755   46789999999999999999999998866 555  89


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|.|++.+.+
T Consensus        76 l~v~~ak~~~~   86 (91)
T d1nu4a_          76 MRIQYAKTDSD   86 (91)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEeCCCch
Confidence            99999986543

>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=2.5e-17  Score=122.96  Aligned_cols=75  Identities=32%  Similarity=0.534  Sum_probs=66.4

Q ss_pred             cccceEEEecCC-CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          100 RLEHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~-~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ...++|||+||+ ..+++++|+++|++||.|++|+|.       ||||||+|++.++|.+||+.|||+. +.|  +.|+|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~-~~g--~~l~V   82 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRM-IAG--QVLDI   82 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCE-ETT--EECEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            335789999996 678899999999999999999994       8999999999999999999999987 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +|++..
T Consensus        83 ~~a~~~   88 (98)
T d1wf2a_          83 NLAAEP   88 (98)
T ss_dssp             EETTSC
T ss_pred             EECCCC
Confidence            998653

>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=99.69  E-value=2.8e-18  Score=129.54  Aligned_cols=83  Identities=27%  Similarity=0.414  Sum_probs=74.8

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      .+++|||+|||.++++++|+++|++||.|..+.+..+ .++.+++||||+|.+.++|.+|++.|||.. +.|  +.|+|+
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~V~   93 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYK-LYG--KILVIE   93 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCB-CSS--CBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCE-ECC--EEEEEE
Confidence            4679999999999999999999999999999988877 578899999999999999999999999976 566  689999


Q ss_pred             ecCChHH
Q 018554          180 WADTEKE  186 (354)
Q Consensus       180 ~a~~~~~  186 (354)
                      ||+++++
T Consensus        94 ~ak~k~~  100 (102)
T d2cpxa1          94 FGKNKKQ  100 (102)
T ss_dssp             ECCCCSC
T ss_pred             eCCCccc
Confidence            9987643

>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=99.69  E-value=5.7e-17  Score=118.71  Aligned_cols=83  Identities=20%  Similarity=0.321  Sum_probs=71.5

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCC-ccCCCCC
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNK-KTLPGAS   86 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~-~~~~g~~   86 (354)
                      +.+..++++|||+|||.++++++|+++|++||.|.++++.+++      |||||+|.+.++|++|++.+++. ..+.|  
T Consensus         2 ~~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~------~~afV~f~~~e~A~~a~~~~~~~~~~~~g--   73 (88)
T d2cq1a1           2 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNYYSAVTPHLRN--   73 (88)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCEETT--
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc------eEEEEEeCCHHHHHHHHHHHccCCCccCC--
Confidence            4567899999999999999999999999999999999988654      69999999999999999987543 33444  


Q ss_pred             ccceeecccccc
Q 018554           87 SPLQVKYADGEL   98 (354)
Q Consensus        87 ~~l~v~~~~~~~   98 (354)
                      +.|+|.|++.+.
T Consensus        74 ~~l~v~~sk~~~   85 (88)
T d2cq1a1          74 QPIYIQYSNHKE   85 (88)
T ss_dssp             EECEEEECSCSS
T ss_pred             CEEEEEECCCCC
Confidence            899999987654

>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=99.69  E-value=3e-17  Score=124.97  Aligned_cols=79  Identities=16%  Similarity=0.247  Sum_probs=70.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ..+|||+||++++|+++|+++|++||.|++|.|++++   ++|+|||+|++.++|++|++.|||..+ .+..+.|+|.|+
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l-~~~~~~l~v~~s   82 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNI-YNACCTLRIDFS   82 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCS-STTCCCCEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEe-ccCCcEEEEEec
Confidence            4579999999999999999999999999999999864   389999999999999999999999874 444578999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus        83 ~~~   85 (108)
T d2adba1          83 KLT   85 (108)
T ss_dssp             SSC
T ss_pred             CCc
Confidence            754

>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=99.68  E-value=7.1e-17  Score=117.66  Aligned_cols=75  Identities=24%  Similarity=0.363  Sum_probs=67.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+|||.++|+++|+++|++||.|..+.+.+.     +|||||+|.+.++|.+|++.|||.. ++|  +.|.|+||
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~-----rg~afV~f~~~~~A~~Ai~~l~~~~-i~g--~~i~V~~a   79 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALNGKV-LDG--SPIEVTLA   79 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHSSEE-ETT--EEEEEECC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc-----cEEEEEEeCCHHHHHHHHHHcCCCE-ECC--EEEEEEec
Confidence            468999999999999999999999999888887654     8899999999999999999999976 565  78999999


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      ++.
T Consensus        80 kP~   82 (86)
T d2cpda1          80 KPV   82 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.68  E-value=5e-17  Score=121.30  Aligned_cols=79  Identities=14%  Similarity=0.151  Sum_probs=67.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      .....++|||+|||++++++||+++|++||+|++|.|.+       +|||||+|.+.++|++||+.||+.. +.+  +.|
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~-~~g--~~i   80 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTK-FRS--HEG   80 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEE-EEC--TTS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCE-eCC--eEE
Confidence            345677899999999999999999999999999999864       3799999999999999999998876 544  677


Q ss_pred             eeecccccc
Q 018554           90 QVKYADGEL   98 (354)
Q Consensus        90 ~v~~~~~~~   98 (354)
                      +|.+.+.+.
T Consensus        81 ~v~~~~~~~   89 (98)
T d1wg4a_          81 ETSYIRVYP   89 (98)
T ss_dssp             CEEEEEEEC
T ss_pred             EEEEEecCC
Confidence            877765543

>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=99.68  E-value=3.6e-17  Score=123.21  Aligned_cols=84  Identities=13%  Similarity=0.095  Sum_probs=70.6

Q ss_pred             ccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCc
Q 018554            8 KKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASS   87 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~   87 (354)
                      ..+.....+|||+|||+++||+||+++|+.||. .+|.++++.. ++++|||||+|.+.++|++|++ +|+.. +.+  +
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~-g~~~G~afVeF~~~~~a~~Al~-~~~~~-i~g--R   82 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPD-GRVTGEADVEFATHEDAVAAMA-KDKAN-MQH--R   82 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSS-SCEEEEEEEECSSSHHHHHHHT-TSSCC-SSS--S
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecC-CcceEEEEEEECCHHHHHHHHH-cCCCE-ECC--E
Confidence            445567789999999999999999999999984 5788888864 8899999999999999999986 76655 655  7


Q ss_pred             cceeeccccc
Q 018554           88 PLQVKYADGE   97 (354)
Q Consensus        88 ~l~v~~~~~~   97 (354)
                      .|+|.++...
T Consensus        83 ~I~V~~s~~~   92 (102)
T d1weza_          83 YVELFLNSTA   92 (102)
T ss_dssp             CCEEEEECCC
T ss_pred             EEEEEEcCCC
Confidence            7888876654

>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=99.68  E-value=5.2e-17  Score=118.39  Aligned_cols=77  Identities=18%  Similarity=0.270  Sum_probs=69.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..+|||+|||++++++||+++|+.||.|.+ +.+..+.++.++|+|||+|++.++|++|++.||++. +.|  ++|+|++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~-l~g--r~i~v~l   85 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP-IGS--RKVKLVL   85 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCE-ETT--EECEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCE-ECC--EEEEEEE
Confidence            467999999999999999999999999876 577777899999999999999999999999999988 555  7888887


Q ss_pred             c
Q 018554          181 A  181 (354)
Q Consensus       181 a  181 (354)
                      |
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.68  E-value=2.6e-17  Score=121.28  Aligned_cols=82  Identities=24%  Similarity=0.485  Sum_probs=70.5

Q ss_pred             ccceEEEecCCCCCCHHHHHH----hhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSA----LFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~----~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      ++++|||+||+.+++++||++    +|++||+|.+|++.+  ++.++|||||+|++.++|.+|++.+||.. ++|  +.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~-~~g--~~l   76 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFP-FYD--KPM   76 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCE-ETT--EEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCE-ECC--EEE
Confidence            357899999999999999864    689999999998764  45568999999999999999999999977 565  789


Q ss_pred             EEEecCChHHH
Q 018554          177 VVKWADTEKER  187 (354)
Q Consensus       177 ~v~~a~~~~~~  187 (354)
                      +|.||+++.+.
T Consensus        77 ~v~~ak~~~~~   87 (91)
T d1nu4a_          77 RIQYAKTDSDI   87 (91)
T ss_dssp             EEEECSSCCTH
T ss_pred             EEEEeCCCchh
Confidence            99999876443

>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=99.68  E-value=4.9e-17  Score=124.11  Aligned_cols=75  Identities=24%  Similarity=0.467  Sum_probs=67.0

Q ss_pred             cceEEEecCC-CCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLP-KNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~-~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      +++|||+||+ ..+|+++|+++|+.||.|++|+|++++    +|||||+|++.++|.+|++.|||.. +.|  +.|+|+|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~-l~g--~~l~v~~   74 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHK-LHG--KPIRITL   74 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCB-CSS--SBCEEEC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEE
Confidence            4689999995 569999999999999999999999874    7899999999999999999999987 666  5889999


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      ++.
T Consensus        75 s~~   77 (109)
T d2adca1          75 SKH   77 (109)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            853

>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=99.67  E-value=5.5e-17  Score=120.78  Aligned_cols=79  Identities=22%  Similarity=0.357  Sum_probs=69.0

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      .+..++|||+||+.++|++||+++|++||.|..+..    ++.+++||||+|.+.++|++|++.||+.. ++|  +.|+|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~-~~g--r~i~V   85 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAE-IDG--RSVSL   85 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEE-ETT--EEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCE-ECC--EEEEE
Confidence            344689999999999999999999999998876542    46679999999999999999999999976 666  79999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .|++++
T Consensus        86 ~~a~~k   91 (96)
T d1fjca_          86 YYTGEK   91 (96)
T ss_dssp             EECSSS
T ss_pred             EEeCCC
Confidence            999865

>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=7e-17  Score=114.32  Aligned_cols=73  Identities=14%  Similarity=0.162  Sum_probs=63.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeec
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKY   93 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~   93 (354)
                      ++|||+|||+++++++|+++|+.||.|.+|++.+|+.+  .++||||+|.+.++|++|++ ++++. +.+  +.|.|..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~-i~g--~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKV-VGQ--NEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCE-ETT--EECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcE-ECC--EEEEEEE
Confidence            58999999999999999999999999999999999863  45799999999999999995 66664 666  6666653

>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=99.67  E-value=6.1e-17  Score=118.69  Aligned_cols=75  Identities=23%  Similarity=0.427  Sum_probs=65.0

Q ss_pred             cceEEEecCCCCCCHHHH---HHhhccCCCeeEEEEeeCC-CCC---cceEEEEEeCCHHHHHHHHHHhCCCcccCCCce
Q 018554          102 EHKLFIGMLPKNVSEAEV---SALFSIYGTIKDLQILRGS-QQT---SKGCAFLKYETKEQALAALEAINGKHKMEGSSV  174 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l---~~~F~~~G~v~~i~i~~~~-~~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~  174 (354)
                      .++|||+|||++++++||   +++|++||.|++|.|++++ ++.   .+|||||+|++.++|.+|++.|||.. ++|  +
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~-~~g--r   84 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV-VDG--R   84 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE-ETT--E
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCE-ECC--E
Confidence            357999999999999999   6789999999999999884 333   34899999999999999999999976 666  6


Q ss_pred             eEEEE
Q 018554          175 PLVVK  179 (354)
Q Consensus       175 ~l~v~  179 (354)
                      .|+|+
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            77764

>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=99.67  E-value=1.6e-17  Score=121.64  Aligned_cols=78  Identities=24%  Similarity=0.346  Sum_probs=66.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ..+++|||+|||+++||++|+++|++||+|.+|++..     +++|||||+|.+.++|++|+.  ++ ..+.+  +.|+|
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~-~~i~g--~~l~v   72 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--ED-LIIKG--ISVHI   72 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CE-EEETT--EEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CC-CEECC--EEeEE
Confidence            4688999999999999999999999999999987643     467899999999999999985  33 44666  88999


Q ss_pred             eccccccc
Q 018554           92 KYADGELE   99 (354)
Q Consensus        92 ~~~~~~~~   99 (354)
                      ++++++..
T Consensus        73 ~~a~~k~~   80 (88)
T d1wf0a_          73 SNAEPKHN   80 (88)
T ss_dssp             ECCCCCCC
T ss_pred             EeCCCCCC
Confidence            99876544

>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=99.67  E-value=1.1e-16  Score=114.69  Aligned_cols=75  Identities=24%  Similarity=0.347  Sum_probs=66.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ...++|||+||+  +||++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|++.||+.. +.|  +.|+|
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~-~~g--~~l~V   71 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQ-VES--VQLKV   71 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCB-CSS--CBCEE
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            467899999995  999999999999999999998754      4699999999999999999998876 555  88999


Q ss_pred             eccccc
Q 018554           92 KYADGE   97 (354)
Q Consensus        92 ~~~~~~   97 (354)
                      .|++++
T Consensus        72 ~~a~~~   77 (79)
T d2bz2a1          72 NIARKQ   77 (79)
T ss_dssp             EECCSS
T ss_pred             EEecCC
Confidence            998754

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=3.5e-17  Score=115.14  Aligned_cols=67  Identities=19%  Similarity=0.406  Sum_probs=62.6

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCC
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG-SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGS  172 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~-~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~  172 (354)
                      |||+|||.++|+++|+++|++||.|..+++.++ .++.++|+|||+|.+.++|++|++.|||+. ++|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~-~~Gr   68 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG-VQAQ   68 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT-CCEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCE-ECCE
Confidence            799999999999999999999999999999988 478899999999999999999999999976 6663

>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=99.66  E-value=2.7e-17  Score=124.19  Aligned_cols=81  Identities=17%  Similarity=0.253  Sum_probs=68.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccce
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQ   90 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~   90 (354)
                      .....+|||+|||+++|++||+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++||+ +|+.. +.+  +.|.
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~-i~g--r~i~   80 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKK-LNG--REAF   80 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEE-ETT--EEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCe-ECC--cEEE
Confidence            3456789999999999999999999999998876666666689999999999999999999996 77654 655  6777


Q ss_pred             eeccc
Q 018554           91 VKYAD   95 (354)
Q Consensus        91 v~~~~   95 (354)
                      |.++.
T Consensus        81 V~~~~   85 (103)
T d2cpya1          81 VHVVT   85 (103)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            77654

>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=99.66  E-value=2.9e-16  Score=118.52  Aligned_cols=84  Identities=12%  Similarity=0.137  Sum_probs=71.0

Q ss_pred             cccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc-cCCCC
Q 018554            7 EKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK-TLPGA   85 (354)
Q Consensus         7 ~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~-~~~g~   85 (354)
                      ......++++|||+|||.++||+||+++|++||.|.+|++.++      +|||||+|.+.++|+.|++.+++.. .+.  
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~--   79 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIA--   79 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSS--
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEe--
Confidence            3445678899999999999999999999999999999999764      4699999999999999999886543 233  


Q ss_pred             Cccceeecccccc
Q 018554           86 SSPLQVKYADGEL   98 (354)
Q Consensus        86 ~~~l~v~~~~~~~   98 (354)
                      .+.|+|.|++.+.
T Consensus        80 g~~l~v~~s~~~~   92 (104)
T d1wexa_          80 GQQAFFNYSTSKR   92 (104)
T ss_dssp             SSBCEEEECSSSS
T ss_pred             eEEEEEEEcCCCc
Confidence            4889999987643

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.1e-16  Score=116.98  Aligned_cols=74  Identities=26%  Similarity=0.363  Sum_probs=63.2

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+|||++++++||+++|++|| ++.+.+.+     +++||||+|++.++|++|++.||+.. ++|  ++|+|+|+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~-----~kg~afV~f~~~~~A~~Ai~~ln~~~-~~G--~~l~V~~a   75 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-----NKRTAFVTLLNGEQAQNAIQMFHQYS-FRG--KDLIVQLQ   75 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG-----GGTEEEECCSCHHHHHHHHHHHTTEE-ETT--EEEEEEEC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec-----cCCceEEEECCHHHHHHHHHHhCCCE-ECC--EEEEEEEc
Confidence            46899999999999999999999999 33344433     48999999999999999999999987 566  78999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +.+
T Consensus        76 ~~~   78 (88)
T d1wg1a_          76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=1.4e-16  Score=120.21  Aligned_cols=82  Identities=13%  Similarity=0.219  Sum_probs=70.4

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVK  179 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~  179 (354)
                      ...+|||+|||+++|+++|+++|+.||.|.. +.+..+.++.++|+|||+|.+.++|++|++ ||+.. ++|  +.|.|.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~-i~g--r~i~V~   82 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKK-LNG--REAFVH   82 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEE-ETT--EEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCe-ECC--cEEEEE
Confidence            3567999999999999999999999999876 566666889999999999999999999996 89876 666  689998


Q ss_pred             ecCChHH
Q 018554          180 WADTEKE  186 (354)
Q Consensus       180 ~a~~~~~  186 (354)
                      ++.....
T Consensus        83 ~~~~~~~   89 (103)
T d2cpya1          83 VVTLEDM   89 (103)
T ss_dssp             EECHHHH
T ss_pred             ECCHHHh
Confidence            8865433

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.5e-17  Score=119.70  Aligned_cols=77  Identities=16%  Similarity=0.307  Sum_probs=64.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcccee
Q 018554           12 EERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQV   91 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v   91 (354)
                      ..+++|||+|||.+++++||+++|++||. ..+.+      ++++|||||+|.+.++|++|++.||+.. +.+  +.|+|
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~-~~G--~~l~V   72 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYS-FRG--KDLIV   72 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEE-ETT--EEEEE
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCE-ECC--EEEEE
Confidence            35689999999999999999999999992 23333      4578899999999999999999999876 555  89999


Q ss_pred             ecccccc
Q 018554           92 KYADGEL   98 (354)
Q Consensus        92 ~~~~~~~   98 (354)
                      ++++.+.
T Consensus        73 ~~a~~~~   79 (88)
T d1wg1a_          73 QLQPTDA   79 (88)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9886543

>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=99.65  E-value=4.5e-17  Score=124.77  Aligned_cols=87  Identities=15%  Similarity=0.245  Sum_probs=72.4

Q ss_pred             ccccCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            6 KEKKSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         6 ~~~~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      +.+......++|||+|||+++|++||+++|+.||.|.++.++.+..+|+++|||||+|.+.++|++|++ +|+.. +.+ 
T Consensus        10 ~~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~-i~g-   86 (112)
T d1wela1          10 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQY-MGN-   86 (112)
T ss_dssp             CCSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBC-STT-
T ss_pred             CCCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCc-CCC-
Confidence            344456677899999999999999999999999999887777777789999999999999999999996 77655 655 


Q ss_pred             Cccceeecccc
Q 018554           86 SSPLQVKYADG   96 (354)
Q Consensus        86 ~~~l~v~~~~~   96 (354)
                       +.|.|..+..
T Consensus        87 -R~i~V~~~~~   96 (112)
T d1wela1          87 -RFIQVHPITK   96 (112)
T ss_dssp             -SCBEEEEECH
T ss_pred             -EEEEEEEcCh
Confidence             6777766543

>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=99.65  E-value=2.4e-16  Score=115.28  Aligned_cols=79  Identities=27%  Similarity=0.459  Sum_probs=68.2

Q ss_pred             ccccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-cccCCCceeEE
Q 018554           99 ERLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGK-HKMEGSSVPLV  177 (354)
Q Consensus        99 ~~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~~g~~~~l~  177 (354)
                      ...+++|||+||+.++++++|+++|++||.|.++++.++     ++||||+|++.++|++|++.+++. ..+.|  ++|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g--~~l~   77 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRN--QPIY   77 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETT--EECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCC--CEEE
Confidence            345789999999999999999999999999999999976     789999999999999999876533 23555  7899


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |.|++.+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9998754

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2e-16  Score=119.53  Aligned_cols=79  Identities=24%  Similarity=0.420  Sum_probs=68.1

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeC--CCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEE
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRG--SQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVV  178 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~--~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v  178 (354)
                      ..++|||+||++++|+++|+++|+.|| |+++.++.+  .++.++|||||+|.+.++|++|+ .||+.. ++|  +.|+|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~-~~g--r~l~V   88 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEES-LGN--KRIRV   88 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCE-ETT--EECEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCE-ECC--EEEEE
Confidence            357999999999999999999999999 778887766  36788999999999999998666 699976 565  78999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      +||+.+
T Consensus        89 ~~a~~~   94 (104)
T d1wi8a_          89 DVADQA   94 (104)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            998765

>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=99.65  E-value=5.8e-17  Score=118.34  Aligned_cols=71  Identities=13%  Similarity=0.225  Sum_probs=62.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      ++|||+|||+++++++|+++|++||.|.+++|.+      +|||||+|++.++|++||+.|||.. +.|+  .|+|.+++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~-~~g~--~i~v~~~~   71 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTK-FRSH--EGETAYIR   71 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCB-CCCT--TSCCCBCE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCE-ECCc--EeEEeEEe
Confidence            4799999999999999999999999999999875      4899999999999999999999987 6664  45555553

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.65  E-value=3.8e-16  Score=110.48  Aligned_cols=74  Identities=19%  Similarity=0.278  Sum_probs=65.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .+|||+|||+++++++|+++|+.||.|.++++.++..+. +++|||+|+++++|.+|++ +|++. ++|  +.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKV-VGQ--NEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCE-ETT--EECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcE-ECC--EEEEEEEC
Confidence            479999999999999999999999999999999987655 5799999999999999985 79986 676  67888754

>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=99.65  E-value=1.8e-16  Score=119.33  Aligned_cols=79  Identities=22%  Similarity=0.255  Sum_probs=69.0

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...+|||+|||+++|++||+++|+.|| +.++.++.+.++.++|||||+|++.++|++|++ +|++. ++|  +.|+|.|
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~-i~g--R~I~V~~   88 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKAN-MQH--RYVELFL   88 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCC-SSS--SCCEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCE-ECC--EEEEEEE
Confidence            357899999999999999999999997 568888888889999999999999999999986 89976 666  5678887


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +...
T Consensus        89 s~~~   92 (102)
T d1weza_          89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             cCCC
Confidence            7644

>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=99.64  E-value=2.3e-16  Score=111.61  Aligned_cols=72  Identities=17%  Similarity=0.383  Sum_probs=61.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecccc
Q 018554           17 LFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYADG   96 (354)
Q Consensus        17 lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~~   96 (354)
                      |||+|||.+++++||+++|++|| +..+.+      ++++|||||+|.+.++|++|++.||+.. +.|  +.|+|+++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~-~~g--~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSR-LRE--RELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEE-SSS--CEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCcc-CCC--CEEEEEEeCC
Confidence            79999999999999999999999 444443      4578899999999999999999998866 555  8899998865


Q ss_pred             cc
Q 018554           97 EL   98 (354)
Q Consensus        97 ~~   98 (354)
                      +.
T Consensus        71 d~   72 (75)
T d1wi6a1          71 DA   72 (75)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.64  E-value=5.1e-16  Score=109.80  Aligned_cols=71  Identities=31%  Similarity=0.400  Sum_probs=62.0

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecCCh
Q 018554          105 LFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWADTE  184 (354)
Q Consensus       105 l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~~~  184 (354)
                      |||+|||.+++++||+++|++|| +..+.+.+     ++|||||+|.+.++|++|++.|||.. ++|  +.|+|+|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~-----~~g~afv~f~~~~~A~~Ai~~ln~~~-~~g--~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK-----YKGTAFVTLLNGEQAEAAINTFHQSR-LRE--RELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEE-SSS--CEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc-----cceeEEEEECCHHHHHHHHHHhCCcc-CCC--CEEEEEEeCCC
Confidence            79999999999999999999999 55555543     48999999999999999999999976 666  68999998654

>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=99.63  E-value=1.1e-16  Score=117.08  Aligned_cols=74  Identities=20%  Similarity=0.407  Sum_probs=64.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .++|||+|||+++|+++|+++|++||.|.+|++..+    +++||||+|++.++|++|++  ++. .++|  +.|+|++|
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~-~i~g--~~l~v~~a   75 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDL-IIKG--ISVHISNA   75 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEE-EETT--EEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCC-EECC--EEeEEEeC
Confidence            579999999999999999999999999999987643    47899999999999999985  554 4776  78999998


Q ss_pred             CCh
Q 018554          182 DTE  184 (354)
Q Consensus       182 ~~~  184 (354)
                      +++
T Consensus        76 ~~k   78 (88)
T d1wf0a_          76 EPK   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.6e-16  Score=117.29  Aligned_cols=74  Identities=14%  Similarity=0.223  Sum_probs=65.2

Q ss_pred             ccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          101 LEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       101 ~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ...+|||+|||++++++||+++|++||+|++++|.+      +|||||+|.+.++|++||+.|||.. ++|+  .|+|.+
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~-~~g~--~i~v~~   84 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTK-FRSH--EGETSY   84 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEE-EECT--TSCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCE-eCCe--EEEEEE
Confidence            457899999999999999999999999999999875      6899999999999999999999987 6664  566676


Q ss_pred             cCC
Q 018554          181 ADT  183 (354)
Q Consensus       181 a~~  183 (354)
                      ++.
T Consensus        85 ~~~   87 (98)
T d1wg4a_          85 IRV   87 (98)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            643

>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=4.3e-16  Score=113.97  Aligned_cols=82  Identities=18%  Similarity=0.275  Sum_probs=69.5

Q ss_pred             ccCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCc-cCCCC
Q 018554            8 KKSSEERVKLFVGQVPKH-MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKK-TLPGA   85 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~-~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~-~~~g~   85 (354)
                      +...+.+++|||+|||.. +|++||.++|+.||.|.+|.+++++      ++|||+|++.++|.+|++.++... .+.| 
T Consensus         2 ~~~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~g-   74 (89)
T d1x4da1           2 KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFG-   74 (89)
T ss_dssp             CCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETT-
T ss_pred             CCCCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCC-
Confidence            346678999999999986 8899999999999999999998765      489999999999999999875322 2444 


Q ss_pred             Cccceeeccccc
Q 018554           86 SSPLQVKYADGE   97 (354)
Q Consensus        86 ~~~l~v~~~~~~   97 (354)
                       ++|+|+|++..
T Consensus        75 -r~l~V~~s~~~   85 (89)
T d1x4da1          75 -KPVRVHLSQKY   85 (89)
T ss_dssp             -EECEEEEECCC
T ss_pred             -ceEEEEECCCc
Confidence             89999998754

>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=99.62  E-value=6.7e-16  Score=128.75  Aligned_cols=87  Identities=23%  Similarity=0.376  Sum_probs=76.8

Q ss_pred             cCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCcc
Q 018554            9 KSSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSP   88 (354)
Q Consensus         9 ~~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~   88 (354)
                      ......++|||+|||+++|+++|+++|+.||.|..+.|+.|..+++++|||||+|.+.++|++||+ +++.. +.|  +.
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~-~~G--~~  167 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHT-VNG--HN  167 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEE-ETT--EE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCe-ECC--EE
Confidence            345677899999999999999999999999999999999999999999999999999999999997 45544 555  78


Q ss_pred             ceeeccccccc
Q 018554           89 LQVKYADGELE   99 (354)
Q Consensus        89 l~v~~~~~~~~   99 (354)
                      |+|+++.++.+
T Consensus       168 i~V~~A~~k~e  178 (183)
T d1u1qa_         168 CEVRKALSKQE  178 (183)
T ss_dssp             EEEEECCCHHH
T ss_pred             EEEEecCCccc
Confidence            99998876654

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=6.7e-16  Score=116.52  Aligned_cols=78  Identities=15%  Similarity=0.225  Sum_probs=67.7

Q ss_pred             cccceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-ccCCCceeEEE
Q 018554          100 RLEHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH-KMEGSSVPLVV  178 (354)
Q Consensus       100 ~~~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~~g~~~~l~v  178 (354)
                      ..+++|||+|||.++|++||+++|++||.|+++.+.++     |++|||+|++.++|++|++.+++.. .+.|  ++|+|
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g--~~l~v   85 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAG--QQAFF   85 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSS--SBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEee--EEEEE
Confidence            34678999999999999999999999999999999876     7899999999999999999886443 3455  68999


Q ss_pred             EecCCh
Q 018554          179 KWADTE  184 (354)
Q Consensus       179 ~~a~~~  184 (354)
                      .|++.+
T Consensus        86 ~~s~~~   91 (104)
T d1wexa_          86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            998654

>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=99.61  E-value=6.1e-16  Score=116.77  Aligned_cols=79  Identities=19%  Similarity=0.188  Sum_probs=67.3

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEE-EEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDL-QILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i-~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      ..+|||+|||+++|++||+++|+.+|.|..+ .++.+.++.++|+|||+|+++++|++|++ +|+.. |.|  +.|+|.+
T Consensus        15 ~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~-i~g--R~i~V~~   90 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKER-IGH--RYIEIFK   90 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCC-SSS--SCCEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCE-Ecc--eEEEEEE
Confidence            4579999999999999999999999988774 45555788999999999999999999996 88876 666  5788887


Q ss_pred             cCCh
Q 018554          181 ADTE  184 (354)
Q Consensus       181 a~~~  184 (354)
                      +...
T Consensus        91 ~~~~   94 (104)
T d1wg5a_          91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            7654

>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=99.61  E-value=8.1e-16  Score=114.86  Aligned_cols=82  Identities=13%  Similarity=0.295  Sum_probs=67.7

Q ss_pred             ccCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHh--cCCccCCC
Q 018554            8 KKSSEERVKLFVGQVPKH-MTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNAC--HNKKTLPG   84 (354)
Q Consensus         8 ~~~~~~~~~lfVg~Lp~~-~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l--~~~~~~~g   84 (354)
                      .......++|||+|||.+ +|+++|+++|++||.|.+|.+++++      |||||+|.+.++|.+|++.+  ++.. +.|
T Consensus        12 ~~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k------~~afV~f~~~~~A~~Ai~~~~~~~~~-~~g   84 (99)
T d1x4fa1          12 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVDHCLKKALW-FQG   84 (99)
T ss_dssp             CCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT------TEEEEECSSHHHHHHHHHHHHHSCCC-SSS
T ss_pred             ccCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC------CcEEEEecchHHHHHHHHHHhcCCce-ECC
Confidence            344567789999999985 8999999999999999999998754      69999999999999999854  4323 444


Q ss_pred             CCccceeecccccc
Q 018554           85 ASSPLQVKYADGEL   98 (354)
Q Consensus        85 ~~~~l~v~~~~~~~   98 (354)
                        +.|+|.+++.+.
T Consensus        85 --r~l~V~~s~~~~   96 (99)
T d1x4fa1          85 --RCVKVDLSEKYK   96 (99)
T ss_dssp             --SCCEEEEECSCS
T ss_pred             --EEEEEEEcCCcc
Confidence              889999886543

>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=99.59  E-value=2.5e-17  Score=121.15  Aligned_cols=77  Identities=17%  Similarity=0.319  Sum_probs=65.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----eCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNII-----KDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~-----~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ++|||+|||.++||++|+++|++||.|..+.+.     .+..+++++|||||+|.+.++|++|++ ||+.. +.|  +.|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~-~~G--r~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGII-FQG--QSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCC-SSS--SCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcE-ECC--EEE
Confidence            789999999999999999999999988776654     455678899999999999999999985 88877 445  788


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      +|+.++
T Consensus        78 ~V~r~k   83 (90)
T d1u2fa_          78 KIRRPH   83 (90)
T ss_dssp             CCBCTT
T ss_pred             EECCCC
Confidence            887554

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.7e-15  Score=115.87  Aligned_cols=82  Identities=17%  Similarity=0.217  Sum_probs=69.8

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeE-EEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKD-LQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~-i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .++|||+|||+++|++||+++|+.||.|.. +.+..+.+|.++|+|||+|.+.++|++|++ ||+.. |+|  +.|.|..
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~-i~g--R~i~V~~   93 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQY-MGN--RFIQVHP   93 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBC-STT--SCBEEEE
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCc-CCC--EEEEEEE
Confidence            568999999999999999999999999876 455566789999999999999999999996 89976 666  5778888


Q ss_pred             cCChHHH
Q 018554          181 ADTEKER  187 (354)
Q Consensus       181 a~~~~~~  187 (354)
                      +......
T Consensus        94 ~~~~~~~  100 (112)
T d1wela1          94 ITKKGML  100 (112)
T ss_dssp             ECHHHHH
T ss_pred             cChHHHH
Confidence            7665543

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=2.2e-15  Score=110.16  Aligned_cols=78  Identities=21%  Similarity=0.227  Sum_probs=66.5

Q ss_pred             cccceEEEecCCCC-CCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-ccCCCceeEE
Q 018554          100 RLEHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKH-KMEGSSVPLV  177 (354)
Q Consensus       100 ~~~~~l~V~~l~~~-~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~~g~~~~l~  177 (354)
                      +.+++|||+||+.. +|++||+++|+.||.|.+|.++++     +++|||+|++.++|.+|++.|++.. .+.|  ++|+
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~g--r~l~   78 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFG--KPVR   78 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETT--EECE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCC--ceEE
Confidence            34678999999985 889999999999999999999976     6799999999999999999774322 2555  7999


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+||+..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999754

>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=99.57  E-value=1.5e-15  Score=113.40  Aligned_cols=76  Identities=28%  Similarity=0.425  Sum_probs=65.3

Q ss_pred             ccceEEEecCCCC-CCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHH--hCCCcccCCCceeEE
Q 018554          101 LEHKLFIGMLPKN-VSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEA--INGKHKMEGSSVPLV  177 (354)
Q Consensus       101 ~~~~l~V~~l~~~-~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~--l~g~~~~~g~~~~l~  177 (354)
                      ..++|||+|||.+ +|+++|+++|+.||.|.++.++++     +++|||+|++.++|.+|++.  +++.. ++|  +.|.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~-~~g--r~l~   88 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALW-FQG--RCVK   88 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCC-SSS--SCCE
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCce-ECC--EEEE
Confidence            3678999999975 899999999999999999999976     78999999999999999984  56644 566  6788


Q ss_pred             EEecCCh
Q 018554          178 VKWADTE  184 (354)
Q Consensus       178 v~~a~~~  184 (354)
                      |+|++..
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            8998654

>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=99.57  E-value=6.3e-15  Score=112.69  Aligned_cols=79  Identities=22%  Similarity=0.314  Sum_probs=67.2

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCH-HHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          104 KLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETK-EQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       104 ~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~-~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      .+|||||++++|+++|+++|++||+|.+|+|+++     ++||||+|.+. ++|.+|+..+|+.. +.++...|.+.+..
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~-l~~~~~~v~~~~~~   86 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGN-LQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSC-BCTTSSSEEEEECC
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCc-eecCceEEEEeecc
Confidence            4599999999999999999999999999999976     89999999985 78999999999977 55566777777766


Q ss_pred             ChHHHH
Q 018554          183 TEKERQ  188 (354)
Q Consensus       183 ~~~~~~  188 (354)
                      ...++.
T Consensus        87 ~~~e~~   92 (113)
T d1owxa_          87 GEVEKE   92 (113)
T ss_dssp             HHHHHH
T ss_pred             chhhHH
Confidence            555443

>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=99.57  E-value=1.1e-15  Score=114.36  Aligned_cols=75  Identities=19%  Similarity=0.278  Sum_probs=64.3

Q ss_pred             ccCCCCCCeEEE--cCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554            8 KKSSEERVKLFV--GQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus         8 ~~~~~~~~~lfV--g~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      .....+.++|||  |||+.++||++|+++|++||.|++|+++++      +|||||+|.+.++|.+|++.|||+.+..+.
T Consensus        12 ~~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~~   85 (101)
T d2cq2a1          12 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (101)
T ss_dssp             CCCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             ccCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCCC
Confidence            345667889999  559999999999999999999999988765      469999999999999999999998877664


Q ss_pred             Ccc
Q 018554           86 SSP   88 (354)
Q Consensus        86 ~~~   88 (354)
                      ...
T Consensus        86 ~~~   88 (101)
T d2cq2a1          86 GQK   88 (101)
T ss_dssp             SCE
T ss_pred             CcE
Confidence            333

>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=99.56  E-value=2.2e-15  Score=112.73  Aligned_cols=77  Identities=19%  Similarity=0.353  Sum_probs=66.0

Q ss_pred             ccceEEEec--CCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE--
Q 018554          101 LEHKLFIGM--LPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL--  176 (354)
Q Consensus       101 ~~~~l~V~~--l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l--  176 (354)
                      ..++|||.|  |+.++|+++|+++|++||.|++|.+.++     ++||||+|++.++|.+|++.|||+.+.++....+  
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i~~   91 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL   91 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEEC
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEEEE
Confidence            457888855  9999999999999999999999999876     7899999999999999999999999877754444  


Q ss_pred             EEEecC
Q 018554          177 VVKWAD  182 (354)
Q Consensus       177 ~v~~a~  182 (354)
                      .+.|.+
T Consensus        92 ~~~~~~   97 (101)
T d2cq2a1          92 YLNFVE   97 (101)
T ss_dssp             EEEEES
T ss_pred             EEEeee
Confidence            445544

>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=99.54  E-value=2e-15  Score=113.55  Aligned_cols=75  Identities=16%  Similarity=0.184  Sum_probs=65.6

Q ss_pred             cceEEEecCCCCCCH-----HHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          102 EHKLFIGMLPKNVSE-----AEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~-----~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      .++|||+||+.++.+     ++|+++|++||.|+++++++.     ++||||+|++.++|.+|++.|||.. ++|  +.|
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~lng~~-~~g--~~l   76 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTE-FLG--KEM   76 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSE-ETT--EEC
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhcccc-cCC--CEe
Confidence            578999999987633     569999999999999999964     7899999999999999999999987 555  789


Q ss_pred             EEEecCCh
Q 018554          177 VVKWADTE  184 (354)
Q Consensus       177 ~v~~a~~~  184 (354)
                      +|.||+..
T Consensus        77 ~v~~a~~~   84 (104)
T d1weya_          77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEeecccC
Confidence            99999654

>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=99.52  E-value=6.2e-16  Score=116.40  Aligned_cols=76  Identities=14%  Similarity=0.286  Sum_probs=68.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      .+++|.++..+++||+|+++|++||+|++|+|+++.++.++|||||+|++.++|.+|++.|||+. ++|  +.|+|+|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~-~~g--r~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW-FNG--QPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCE-ECC--EEEEEEEC
Confidence            35778888888999999999999999999999999899999999999999999999999999987 666  68888774

>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=99.50  E-value=1.6e-15  Score=114.15  Aligned_cols=76  Identities=18%  Similarity=0.284  Sum_probs=67.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeecc
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYA   94 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~   94 (354)
                      ..++|.++..+++|++|+++|++||+|++|+|+++. +++++|||||+|.+.++|.+|++.|||+. +.|  +.|+|.+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~-~~g--r~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRW-FNG--QPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCE-ETT--EECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCE-ECC--EEEEEEEC
Confidence            457888888899999999999999999999998775 79999999999999999999999999876 555  77777653

>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=99.50  E-value=7e-15  Score=110.51  Aligned_cols=79  Identities=13%  Similarity=0.127  Sum_probs=67.1

Q ss_pred             CCCCeEEEcCCCCCC-C----HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 018554           12 EERVKLFVGQVPKHM-T----EAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGAS   86 (354)
Q Consensus        12 ~~~~~lfVg~Lp~~~-t----e~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~   86 (354)
                      ...++|||+||+.++ +    +++|+++|+.||.|.++++++      ++|||||+|.+.++|.+|++.||+.. +.+  
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~-~~g--   73 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTE-FLG--   73 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSE-ETT--
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccc-cCC--
Confidence            467899999999876 3    357999999999999999975      45699999999999999999999876 555  


Q ss_pred             ccceeeccccccc
Q 018554           87 SPLQVKYADGELE   99 (354)
Q Consensus        87 ~~l~v~~~~~~~~   99 (354)
                      +.|+|.|++....
T Consensus        74 ~~l~v~~a~~~~~   86 (104)
T d1weya_          74 KEMKLYFAQTLHI   86 (104)
T ss_dssp             EECEEECCCCSSC
T ss_pred             CEeEEeecccCCC
Confidence            8999999876543

>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=99.47  E-value=5.4e-16  Score=113.89  Aligned_cols=75  Identities=19%  Similarity=0.400  Sum_probs=62.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEee------CCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILR------GSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPL  176 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~------~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l  176 (354)
                      ++|||+|||.++|+++|+++|+.||.|..+.+..      ..++.++|||||+|++.++|++|++ |||.. +.|  +.|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~-~~G--r~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGII-FQG--QSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCC-SSS--SCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcE-ECC--EEE
Confidence            5799999999999999999999999877665532      2456789999999999999999985 99987 666  567


Q ss_pred             EEEec
Q 018554          177 VVKWA  181 (354)
Q Consensus       177 ~v~~a  181 (354)
                      +|+.+
T Consensus        78 ~V~r~   82 (90)
T d1u2fa_          78 KIRRP   82 (90)
T ss_dssp             CCBCT
T ss_pred             EECCC
Confidence            77643

>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=8e-14  Score=106.43  Aligned_cols=78  Identities=9%  Similarity=0.147  Sum_probs=62.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCH-HHHHHHHHHhcCCccCCCCCccc
Q 018554           11 SEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSR-QEADKAVNACHNKKTLPGASSPL   89 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~-~~A~~Ai~~l~~~~~~~g~~~~l   89 (354)
                      ......+||||||.++|+++|+++|++||+|.+|.|+++      +|||||.|.+. ++|.+|+..+++..+ .+....+
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l-~~~~~~v   80 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNL-QLRNKEV   80 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCB-CTTSSSE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCce-ecCceEE
Confidence            334556699999999999999999999999999999865      57999999985 789999999988764 4434555


Q ss_pred             eeeccc
Q 018554           90 QVKYAD   95 (354)
Q Consensus        90 ~v~~~~   95 (354)
                      .+.+..
T Consensus        81 ~~~~~~   86 (113)
T d1owxa_          81 TWEVLE   86 (113)
T ss_dssp             EEEECC
T ss_pred             EEeecc
Confidence            555443

>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=99.40  E-value=4e-13  Score=95.71  Aligned_cols=75  Identities=20%  Similarity=0.229  Sum_probs=62.6

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEec
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWA  181 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a  181 (354)
                      ++.|+|+++|.+.+++.| ++|++||+|.++++.++     ++||||+|+++++|++|++ +||.. ++|+ +.|.|+.+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al~-~nG~~-~~g~-~~vgV~~~   74 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KDGRI-FGES-IMIGVKPC   74 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHT-TTTCE-ETTT-EECEEEEC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHHh-cCCCe-ECCc-EEEEEEeC
Confidence            467999999999887655 57999999999998755     7899999999999999995 89976 6664 45678877


Q ss_pred             CChH
Q 018554          182 DTEK  185 (354)
Q Consensus       182 ~~~~  185 (354)
                      ..+.
T Consensus        75 ~~k~   78 (81)
T d1wwha1          75 IDKN   78 (81)
T ss_dssp             CCHH
T ss_pred             CChh
Confidence            6653

>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=99.36  E-value=4.7e-13  Score=95.34  Aligned_cols=73  Identities=15%  Similarity=0.098  Sum_probs=57.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceee
Q 018554           13 ERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVK   92 (354)
Q Consensus        13 ~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~   92 (354)
                      +.+.|+|+|||++++++.| ++|++||+|.++++.      +++|||||+|.+.++|++||+ +|+.. +.+ ...+.|+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~-~~g-~~~vgV~   72 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRI-FGE-SIMIGVK   72 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCE-ETT-TEECEEE
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCe-ECC-cEEEEEE
Confidence            5678999999999987655 579999999999874      356799999999999999995 77765 444 2344566


Q ss_pred             ccc
Q 018554           93 YAD   95 (354)
Q Consensus        93 ~~~   95 (354)
                      ...
T Consensus        73 ~~~   75 (81)
T d1wwha1          73 PCI   75 (81)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            544

>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=99.34  E-value=9e-13  Score=97.89  Aligned_cols=83  Identities=13%  Similarity=0.231  Sum_probs=68.7

Q ss_pred             cCCCCCCeEEEcCC--CCCC---------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554            9 KSSEERVKLFVGQV--PKHM---------TEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus         9 ~~~~~~~~lfVg~L--p~~~---------te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      .+...+++|+|.||  +.++         .++||++.|++||.|.+|.+..+    +.+|||||+|.+.++|.+|++.||
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC
Confidence            45678899999999  5443         23689999999999999988765    367999999999999999999998


Q ss_pred             CCccCCCCCccceeecccccc
Q 018554           78 NKKTLPGASSPLQVKYADGEL   98 (354)
Q Consensus        78 ~~~~~~g~~~~l~v~~~~~~~   98 (354)
                      +.. +.|  +.|+|.+.+++.
T Consensus        79 g~~-~~g--r~i~v~~~~g~~   96 (99)
T d2dita1          79 GRW-FGG--RQITAQAWDGTT   96 (99)
T ss_dssp             TCE-ETT--EECEEEECCSCC
T ss_pred             CcE-ECC--EEEEEEEeCCcC
Confidence            877 555  899999877643

>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=99.34  E-value=1.4e-12  Score=96.85  Aligned_cols=79  Identities=19%  Similarity=0.358  Sum_probs=65.9

Q ss_pred             cccceEEEecC--CCCC---------CHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          100 RLEHKLFIGML--PKNV---------SEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       100 ~~~~~l~V~~l--~~~~---------t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      +.+++|+|.||  +.++         .++||++.|++||.|..|.+..+.   .+|++||+|++.++|.+|++.|||.. 
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~---~~G~~fV~f~~~e~A~~A~~~lng~~-   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH---PDGVASVSFRDPEEADYCIQTLDGRW-   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC---TTCEEEEECSCHHHHHHHHHHSTTCE-
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC---CccEEEEEECCHHHHHHHHHHhCCcE-
Confidence            44678999998  4432         236899999999999999988663   37999999999999999999999987 


Q ss_pred             cCCCceeEEEEecCCh
Q 018554          169 MEGSSVPLVVKWADTE  184 (354)
Q Consensus       169 ~~g~~~~l~v~~a~~~  184 (354)
                      ++|  +.|+|.+++.+
T Consensus        82 ~~g--r~i~v~~~~g~   95 (99)
T d2dita1          82 FGG--RQITAQAWDGT   95 (99)
T ss_dssp             ETT--EECEEEECCSC
T ss_pred             ECC--EEEEEEEeCCc
Confidence            666  79999998654

>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=99.27  E-value=2.7e-12  Score=96.17  Aligned_cols=82  Identities=18%  Similarity=0.257  Sum_probs=68.0

Q ss_pred             CCCCeEEEcCC--CCCC--------CHHHHHHHHhhcCCeeEEEEeeCCCCC--CcccEEEEEeCCHHHHHHHHHHhcCC
Q 018554           12 EERVKLFVGQV--PKHM--------TEAQLLAMFKEFALVDEVNIIKDKTTR--ASRGCCFVICPSRQEADKAVNACHNK   79 (354)
Q Consensus        12 ~~~~~lfVg~L--p~~~--------te~~L~~~F~~~G~v~~i~i~~d~~tg--~~~G~aFV~f~~~~~A~~Ai~~l~~~   79 (354)
                      .+++.|.|.||  +.++        ..+||++.|++||.|++|.|.++..+.  ..+|++||+|.+.++|.+|++.|||+
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            46788999999  5443        345799999999999999998877653  45689999999999999999999997


Q ss_pred             ccCCCCCccceeecccc
Q 018554           80 KTLPGASSPLQVKYADG   96 (354)
Q Consensus        80 ~~~~g~~~~l~v~~~~~   96 (354)
                      . +.|  +.|.+.+.+.
T Consensus        82 ~-f~g--R~v~v~f~~~   95 (104)
T d1o0pa_          82 K-FAN--RVVVTKYCDP   95 (104)
T ss_dssp             C-SSS--SCCEEEEECH
T ss_pred             E-ECC--eEEEEEEcCH
Confidence            7 555  8888888764

>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=99.24  E-value=5.1e-12  Score=94.67  Aligned_cols=80  Identities=20%  Similarity=0.376  Sum_probs=65.7

Q ss_pred             cceEEEecC--CCCC--------CHHHHHHhhccCCCeeEEEEeeCCCC---CcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 018554          102 EHKLFIGML--PKNV--------SEAEVSALFSIYGTIKDLQILRGSQQ---TSKGCAFLKYETKEQALAALEAINGKHK  168 (354)
Q Consensus       102 ~~~l~V~~l--~~~~--------t~~~l~~~F~~~G~v~~i~i~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~  168 (354)
                      ++.|.|.||  +..+        ..+||++.|++||.|++|.|.++..+   ..+|++||+|.+.++|.+|++.|||+. 
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~-   82 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK-   82 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC-
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE-
Confidence            567899998  4443        24579999999999999999887433   345899999999999999999999987 


Q ss_pred             cCCCceeEEEEecCCh
Q 018554          169 MEGSSVPLVVKWADTE  184 (354)
Q Consensus       169 ~~g~~~~l~v~~a~~~  184 (354)
                      ++|  +.|.|.+.+..
T Consensus        83 f~g--R~v~v~f~~~~   96 (104)
T d1o0pa_          83 FAN--RVVVTKYCDPD   96 (104)
T ss_dssp             SSS--SCCEEEEECHH
T ss_pred             ECC--eEEEEEEcCHH
Confidence            677  68899998743

>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=0.00011  Score=51.67  Aligned_cols=79  Identities=13%  Similarity=0.285  Sum_probs=64.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCC--CCCc-ceEEEEEeCCHHHHHHHHHHhCCCcccCCCce--eEE
Q 018554          103 HKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGS--QQTS-KGCAFLKYETKEQALAALEAINGKHKMEGSSV--PLV  177 (354)
Q Consensus       103 ~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~--~~~~-~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~--~l~  177 (354)
                      +||.|+.||..+||+++.+.+...|++........+  .+.+ -.-|+|.|.+.++.....+..+|+.++|.++.  .-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            579999999999999999999999999998888763  2222 26799999999999999999999988775433  345


Q ss_pred             EEec
Q 018554          178 VKWA  181 (354)
Q Consensus       178 v~~a  181 (354)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6665

>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=97.71  E-value=7e-05  Score=52.74  Aligned_cols=71  Identities=11%  Similarity=0.141  Sum_probs=59.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC-cc-cEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 018554           15 VKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRA-SR-GCCFVICPSRQEADKAVNACHNKKTLPGA   85 (354)
Q Consensus        15 ~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~-~~-G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~   85 (354)
                      ++|.|+.||+.+||+++.+.+...|++.......-+.+-+ ++ .-|+|.|.+.++.....+.+++..+.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~   74 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNK   74 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCC
Confidence            6899999999999999999999999988887776655432 22 45999999999999999999988776653

>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=97.27  E-value=0.00067  Score=44.45  Aligned_cols=60  Identities=15%  Similarity=0.244  Sum_probs=49.7

Q ss_pred             HHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEecC
Q 018554          118 EVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKWAD  182 (354)
Q Consensus       118 ~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~a~  182 (354)
                      .|.+.|.+++.|.++.|.....+.  -.|-|...+.++|.-|+..|+... ++.  ++|.|+++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~--~~A~V~v~~~q~A~~~v~~LhR~K-iG~--KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGAVNSLHRYK-IGS--KKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTT--CCEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCc--EEEEEEcCCHHHHHHHHHHHHHHh-cCC--eEEEEEEec
Confidence            456788999999999998765554  358899999999999999999976 544  789999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.0011  Score=45.70  Aligned_cols=53  Identities=23%  Similarity=0.443  Sum_probs=44.0

Q ss_pred             HHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcccCCCceeEEEEe
Q 018554          117 AEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAINGKHKMEGSSVPLVVKW  180 (354)
Q Consensus       117 ~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~~~l~v~~  180 (354)
                      .+|.+.|..||+|.-++++.|       -..|+|.+-++|.+|++ ++|.. +.|  +.|.|..
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~-v~G--~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMK-VKG--RAVKISG   91 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSE-ETT--EEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeE-Ecc--eEEEEec
Confidence            458889999999999999965       68999999999999996 79987 444  5677664

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.28  E-value=0.0069  Score=39.52  Aligned_cols=61  Identities=23%  Similarity=0.188  Sum_probs=46.7

Q ss_pred             HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCccCCCCCccceeeccc
Q 018554           29 AQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKTLPGASSPLQVKYAD   95 (354)
Q Consensus        29 ~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~~~g~~~~l~v~~~~   95 (354)
                      +-|.+.|.+++.|.++.+..-.+ +  .-.|-|...+..+|..|++.||..+ +..  +.|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g--~~~A~V~v~~~q~A~~~v~~LhR~K-iG~--KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-Y--QLKAVVQMENLQDAIGAVNSLHRYK-IGS--KKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEE-ETT--EEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHh-cCC--eEEEEEEec
Confidence            34567889999999998865432 2  2369999999999999999998777 444  777777654

>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=95.92  E-value=0.016  Score=40.42  Aligned_cols=60  Identities=22%  Similarity=0.337  Sum_probs=48.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhc
Q 018554           10 SSEERVKLFVGQVPKHMTEAQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACH   77 (354)
Q Consensus        10 ~~~~~~~lfVg~Lp~~~te~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~   77 (354)
                      .......||.-.+|..+...||.++|+.||-|.- ..+.|.       -|||.-.+.+.|+.++..+.
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCceEE-EEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            3445567899999999999999999999998743 444543       69999999999999887653

>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=95.41  E-value=0.0087  Score=41.10  Aligned_cols=70  Identities=13%  Similarity=0.218  Sum_probs=49.2

Q ss_pred             CCCCCeEEEcCCCCCCCH---------HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEeCCHHHHHHHHHHhcCCcc
Q 018554           11 SEERVKLFVGQVPKHMTE---------AQLLAMFKEFALVDEVNIIKDKTTRASRGCCFVICPSRQEADKAVNACHNKKT   81 (354)
Q Consensus        11 ~~~~~~lfVg~Lp~~~te---------~~L~~~F~~~G~v~~i~i~~d~~tg~~~G~aFV~f~~~~~A~~Ai~~l~~~~~   81 (354)
                      -...-||.|.=...+..+         ++|.+.|..||+|.-|+++.|        -..|+|.|-++|-+|++. ++.+ 
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l-~g~~-   81 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDV-DGMK-   81 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHG-GGSE-
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhcc-CCeE-
Confidence            345567777433323222         378888999999999999887        479999999999999864 4555 


Q ss_pred             CCCCCccceee
Q 018554           82 LPGASSPLQVK   92 (354)
Q Consensus        82 ~~g~~~~l~v~   92 (354)
                      +.+  +.+++.
T Consensus        82 v~G--~~l~It   90 (95)
T d1ufwa_          82 VKG--RAVKIS   90 (95)
T ss_dssp             ETT--EEEEEE
T ss_pred             Ecc--eEEEEe
Confidence            444  455554

>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=93.70  E-value=0.13  Score=35.72  Aligned_cols=56  Identities=23%  Similarity=0.344  Sum_probs=45.0

Q ss_pred             cceEEEecCCCCCCHHHHHHhhccCCCeeEEEEeeCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 018554          102 EHKLFIGMLPKNVSEAEVSALFSIYGTIKDLQILRGSQQTSKGCAFLKYETKEQALAALEAIN  164 (354)
Q Consensus       102 ~~~l~V~~l~~~~t~~~l~~~F~~~G~v~~i~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~  164 (354)
                      ..-+|.-..|..+...||.++|+.||.|.=--| .|      --|||...++++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC------ceEEEEecCHHHHHHHHHHhc
Confidence            456888899999999999999999997643333 32      269999999999998887654