Psyllid ID: psy15152

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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--
Protein Sequence
MNARFRLKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCVI
Secondary Structure (PSIPRED)
cccHHHcccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEEcEEEcccccccccccccccccccccccHHcccccHHHHHHHHccccccccccEEEEEEc
Secondary Structure Prediction (SSPRO)
cccEEEEHcHHHHHHHHccccccccccccccccccccccccccccccccccEccEccEEEEEEEcccccccHHHHHHHHHHHccEEEEEccEccccccEccEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEcEEcccccccccccccccccccccccccHHHHHHHHHHHHHccHHHHHHHHHcEEEcc
Coil and Loop (DISEMBL)
MNARFRLKGIARLKEKARKkkgrgfgtetstrneireyesmetdvgdeepgpqrsveGWILFVTGVheeaqeddMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTvdwcfvkgpkkvageqkvgpeggvkvLFPVIMYSTetsmsttlynapwifKTMHITILCVI
Flexible Loop (DISEMBL)
mnarfrlkgiarlkekarkkkgrgfgtetstrneireyesmetdvgdeepgpqrsVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPkkvageqkvgpeggvkvLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCVI
Low Complexity Region (SEG)
MNARFRLKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCVI
Disordered region (IsUnstruct)
*******************************************************VEGWILFVTGVHE*********KFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCV*
Disordered Region (DISOPRED)
**********************************************************WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD******************************************NAPWIFKTMHITILCVI
Disordered Region (DISEMBL)
MNARFRLKGIARLK**************TSTRNEIREYE*************QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCVI
Disordered Region (DISPRO)
*NARFRLKGIARLKEK**********************************GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG*****************VLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCVI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNARFRLKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMYSTETSMSTTLYNAPWIFKTMHITILCVI
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	192	2.2.26 [Sep-21-2011]
Q9V535	165	RNA-binding protein 8A OS	yes	N/A	0.734	0.854	0.669	5e-53
B5DGI7	175	RNA-binding protein 8A OS	N/A	N/A	0.671	0.737	0.689	1e-48
Q5D018	174	RNA-binding protein 8A OS	yes	N/A	0.609	0.672	0.708	3e-45
Q6PH90	174	RNA-binding protein 8A-B	N/A	N/A	0.619	0.683	0.721	9e-45
Q28BZ1	174	RNA-binding protein 8A OS	yes	N/A	0.619	0.683	0.713	1e-44
Q9DF42	174	RNA-binding protein 8A-A	N/A	N/A	0.619	0.683	0.713	2e-44
Q27W01	174	RNA-binding protein 8A OS	yes	N/A	0.593	0.655	0.709	2e-43
Q9Y5S9	174	RNA-binding protein 8A OS	yes	N/A	0.593	0.655	0.709	2e-43
Q3ZCE8	174	RNA-binding protein 8A OS	yes	N/A	0.593	0.655	0.709	2e-43
Q9CWZ3	174	RNA-binding protein 8A OS	yes	N/A	0.593	0.655	0.700	6e-43

>sp|Q9V535|RBM8A_DROME RNA-binding protein 8A OS=Drosophila melanogaster GN=tsu PE=1 SV=1

 Score =  207 bits (526), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 95/142 (66%), Positives = 119/142 (83%), Gaps = 1/142 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDE-EPGPQRSVEGWILFVTGV 66
           +GI RLKEKA+ +KGRGFG++++TR  I  YE +  +  DE EPGPQRSVEGWILFVT +
Sbjct: 21  QGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI 80

Query: 67  HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
           HEEAQED++ EKF +YGEIKN+HLNLDRRTGF KGYALVEY+++K+A AA++ALNG  I+
Sbjct: 81  HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM 140

Query: 127 GQTVTVDWCFVKGPKKVAGEQK 148
           GQT+ VDWCFVKGPK+V   +K
Sbjct: 141 GQTIQVDWCFVKGPKRVKKSEK 162

Involved in mRNA quality control via the nonsense-mediated mRNA decay (NMD) pathway. Also involved in localization of osk (oskar) mRNA in the posterior pole of oocytes via its interaction with mago.
Drosophila melanogaster (taxid: 7227)

>sp|B5DGI7|RBM8A_SALSA RNA-binding protein 8A OS=Salmo salar GN=rbm8a PE=2 SV=1

 Score =  192 bits (488), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 91/132 (68%), Positives = 115/132 (87%), Gaps = 3/132 (2%)

Query: 10  IARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHE 68
           I +LKEKA+++KGRGFG+E   R+ +RE Y+++E D GDE PGPQRSVEGWILFVTGVHE
Sbjct: 25  IHKLKEKAKRRKGRGFGSEEGARSRVREDYDTVEQD-GDE-PGPQRSVEGWILFVTGVHE 82

Query: 69  EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ 128
           EA E+D+H+KF+E+GEIKNLHLNLDRRTG+LKGYALVEY++YKEA AA + LNG  ++GQ
Sbjct: 83  EATEEDIHDKFAEFGEIKNLHLNLDRRTGYLKGYALVEYETYKEAQAAMEGLNGQDMMGQ 142

Query: 129 TVTVDWCFVKGP 140
            ++VDW FV+GP
Sbjct: 143 PISVDWGFVRGP 154

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Salmo salar (taxid: 8030)

>sp|Q5D018|RBM8A_DANRE RNA-binding protein 8A OS=Danio rerio GN=rbm8a PE=2 SV=1

 Score =  181 bits (459), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 85/120 (70%), Positives = 105/120 (87%), Gaps = 3/120 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG+E   R+ +RE Y+++E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+
Sbjct: 37  GRGFGSEEGARSRVREDYDTVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDVHDKFA 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           E+GEIKNLHLNLDRRTG+LKGYALVEY++YKEA AA + LNG  ++GQ ++VDWCFV+GP
Sbjct: 95  EFGEIKNLHLNLDRRTGYLKGYALVEYETYKEAQAAMEGLNGQELMGQPISVDWCFVRGP 154

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Danio rerio (taxid: 7955)

>sp|Q6PH90|RB8AB_XENLA RNA-binding protein 8A-B OS=Xenopus laevis GN=rbm8a-b PE=2 SV=1

 Score =  179 bits (454), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 88/122 (72%), Positives = 103/122 (84%), Gaps = 3/122 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG +  TR  IRE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF 
Sbjct: 37  GRGFGADEGTRTRIREDYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFG 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           E+GEIKN+HLNLDRRTGFLKGYALVEY++YKEA AA + LNG  ++GQ V+VDW FV+GP
Sbjct: 95  EFGEIKNIHLNLDRRTGFLKGYALVEYETYKEALAAMEGLNGQDLMGQPVSVDWGFVRGP 154

Query: 141 KK 142
            K
Sbjct: 155 PK 156

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Xenopus laevis (taxid: 8355)

>sp|Q28BZ1|RBM8A_XENTR RNA-binding protein 8A OS=Xenopus tropicalis GN=rbm8a PE=2 SV=1

 Score =  179 bits (453), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 87/122 (71%), Positives = 103/122 (84%), Gaps = 3/122 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG +  TR  IRE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF 
Sbjct: 37  GRGFGADEGTRARIREDYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFG 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           E+GEIKN+HLNLDRRTGFLKGYALVEY++YKEA AA + LNG  ++GQ ++VDW FV+GP
Sbjct: 95  EFGEIKNIHLNLDRRTGFLKGYALVEYETYKEALAAMEGLNGQDLMGQPISVDWGFVRGP 154

Query: 141 KK 142
            K
Sbjct: 155 PK 156

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Xenopus tropicalis (taxid: 8364)

>sp|Q9DF42|RB8AA_XENLA RNA-binding protein 8A-A OS=Xenopus laevis GN=rbm8a-a PE=2 SV=1

 Score =  178 bits (451), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 87/122 (71%), Positives = 103/122 (84%), Gaps = 3/122 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG +  T+  IRE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF 
Sbjct: 37  GRGFGADEGTKTRIREVYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFG 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           E+GEIKN+HLNLDRRTGFLKGYALVEY++YKEA AA + LNG  ++GQ V+VDW FV+GP
Sbjct: 95  EFGEIKNIHLNLDRRTGFLKGYALVEYETYKEALAAMEGLNGQDLMGQPVSVDWGFVRGP 154

Query: 141 KK 142
            K
Sbjct: 155 PK 156

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Xenopus laevis (taxid: 8355)

>sp|Q27W01|RBM8A_RAT RNA-binding protein 8A OS=Rattus norvegicus GN=Rbm8a PE=2 SV=1

 Score =  175 bits (443), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 83/117 (70%), Positives = 101/117 (86%), Gaps = 3/117 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+
Sbjct: 37  GRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFA 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV 137
           EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV
Sbjct: 95  EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 151

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Rattus norvegicus (taxid: 10116)

>sp|Q9Y5S9|RBM8A_HUMAN RNA-binding protein 8A OS=Homo sapiens GN=RBM8A PE=1 SV=1

 Score =  175 bits (443), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 83/117 (70%), Positives = 101/117 (86%), Gaps = 3/117 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+
Sbjct: 37  GRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFA 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV 137
           EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV
Sbjct: 95  EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 151

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Homo sapiens (taxid: 9606)

>sp|Q3ZCE8|RBM8A_BOVIN RNA-binding protein 8A OS=Bos taurus GN=RBM8A PE=2 SV=2

 Score =  175 bits (443), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 83/117 (70%), Positives = 101/117 (86%), Gaps = 3/117 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+
Sbjct: 37  GRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFA 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV 137
           EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV
Sbjct: 95  EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 151

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Bos taurus (taxid: 9913)

>sp|Q9CWZ3|RBM8A_MOUSE RNA-binding protein 8A OS=Mus musculus GN=Rbm8a PE=1 SV=3

 Score =  173 bits (438), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 82/117 (70%), Positives = 101/117 (86%), Gaps = 3/117 (2%)

Query: 22  GRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS 80
           GRGFG++  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+
Sbjct: 37  GRGFGSKEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFA 94

Query: 81  EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV 137
           EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV
Sbjct: 95  EYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 151

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	192
156553815	165	PREDICTED: RNA-binding protein 8A-like [	0.708	0.824	0.751	2e-55
442751093	171	Putative rna binding motif protein 8a [I	0.687	0.771	0.744	4e-54
242015830	160	RNA-binding protein 8A, putative [Pedicu	0.697	0.837	0.731	6e-54
66558056	166	PREDICTED: RNA-binding protein 8A [Apis	0.708	0.819	0.724	7e-54
340709557	166	PREDICTED: RNA-binding protein 8A-like [	0.708	0.819	0.724	8e-54
118787932	164	AGAP006365-PA [Anopheles gambiae str. PE	0.703	0.823	0.720	3e-53
307190290	166	RNA-binding protein 8A [Camponotus flori	0.708	0.819	0.717	4e-53
332019400	157	RNA-binding protein 8A [Acromyrmex echin	0.703	0.859	0.729	5e-53
312385484	165	hypothetical protein AND_00716 [Anophele	0.703	0.818	0.720	5e-53
157114117	165	ss-DNA binding protein 12RNP2 precursor,	0.703	0.818	0.720	6e-53

>gi|156553815|ref|XP_001604863.1| PREDICTED: RNA-binding protein 8A-like [Nasonia vitripennis]

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 103/137 (75%), Positives = 120/137 (87%), Gaps = 1/137 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTE-TSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGV 66
           +GIARLKEKA+K+KGRG G E  STR+++  YESM     D EPGPQRSVEGWILF+T V
Sbjct: 21  QGIARLKEKAKKRKGRGHGAELVSTRDDVGHYESMHVVEDDNEPGPQRSVEGWILFITSV 80

Query: 67  HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
           HEEAQEDD+H+KFSE+G+IKNLHLNLDRRTGFLKGYALVEY+++KEA AA+DALNG+ IL
Sbjct: 81  HEEAQEDDIHDKFSEFGQIKNLHLNLDRRTGFLKGYALVEYETFKEAQAAKDALNGSEIL 140

Query: 127 GQTVTVDWCFVKGPKKV 143
           GQ V VDWCFVKGPKK+
Sbjct: 141 GQAVGVDWCFVKGPKKL 157

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442751093|gb|JAA67706.1| Putative rna binding motif protein 8a [Ixodes ricinus]

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 99/133 (74%), Positives = 119/133 (89%), Gaps = 1/133 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVH 67
           + + +LKE+ARK+KGRGFG + + R +I+EYE+M+TD  DE PGPQRSVEGWIL+VTGVH
Sbjct: 21  QSVQKLKERARKRKGRGFGADGTAREDIQEYEAMDTDENDE-PGPQRSVEGWILYVTGVH 79

Query: 68  EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG 127
           EEAQEDD++EKF+EYGEIKNLHLNLDRRTGFLKGYALVEY+++KEA AA DALNG  IL 
Sbjct: 80  EEAQEDDIYEKFAEYGEIKNLHLNLDRRTGFLKGYALVEYETFKEAQAAIDALNGAKILD 139

Query: 128 QTVTVDWCFVKGP 140
           QT++VDWCFVKGP
Sbjct: 140 QTISVDWCFVKGP 152

Source: Ixodes ricinus

Species: Ixodes ricinus

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242015830|ref|XP_002428550.1| RNA-binding protein 8A, putative [Pediculus humanus corporis] gi|212513184|gb|EEB15812.1| RNA-binding protein 8A, putative [Pediculus humanus corporis]

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 98/134 (73%), Positives = 116/134 (86%)

Query: 7   LKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGV 66
            +GI RLKEKA+K+KGRGFG+E S R +I++YESM+ D G EEPGPQRSVEGWILFVT +
Sbjct: 12  FEGIERLKEKAKKRKGRGFGSENSAREDIQDYESMDLDGGGEEPGPQRSVEGWILFVTSI 71

Query: 67  HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
           HEEAQEDD+HE FSE+GEIKNLHLNLDRRTG+LKGYALVEY++Y+EA  A++ALNG  IL
Sbjct: 72  HEEAQEDDIHETFSEHGEIKNLHLNLDRRTGYLKGYALVEYETYEEALQAKEALNGAKIL 131

Query: 127 GQTVTVDWCFVKGP 140
            Q + VDWCF KGP
Sbjct: 132 DQQIGVDWCFAKGP 145

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66558056|ref|XP_395245.2| PREDICTED: RNA-binding protein 8A [Apis mellifera] gi|380027468|ref|XP_003697445.1| PREDICTED: RNA-binding protein 8A-like [Apis florea]

 Score =  215 bits (548), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 100/138 (72%), Positives = 121/138 (87%), Gaps = 2/138 (1%)

Query: 8   KGIARLKEKARKKKGRGFGTE-TSTRNEIREYESMET-DVGDEEPGPQRSVEGWILFVTG 65
           +GIARLKEKA+++KGRG G E  STR+++  YESM   +  D+EPGPQRSVEGWILF+  
Sbjct: 21  QGIARLKEKAKRRKGRGHGAELVSTRDDVGHYESMNVVEEDDDEPGPQRSVEGWILFINS 80

Query: 66  VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI 125
           VHEEAQEDD+ +KFSE+G+IKNLHLNLDRRTGFLKGYALVEY+++KEA AA+DALNGT I
Sbjct: 81  VHEEAQEDDIQDKFSEFGQIKNLHLNLDRRTGFLKGYALVEYETFKEAQAAKDALNGTEI 140

Query: 126 LGQTVTVDWCFVKGPKKV 143
           LGQ ++VDWCFVKGPKK+
Sbjct: 141 LGQPISVDWCFVKGPKKI 158

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340709557|ref|XP_003393372.1| PREDICTED: RNA-binding protein 8A-like [Bombus terrestris] gi|350401131|ref|XP_003486057.1| PREDICTED: RNA-binding protein 8A-like [Bombus impatiens] gi|383852814|ref|XP_003701920.1| PREDICTED: RNA-binding protein 8A-like [Megachile rotundata]

 Score =  215 bits (547), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 100/138 (72%), Positives = 121/138 (87%), Gaps = 2/138 (1%)

Query: 8   KGIARLKEKARKKKGRGFGTE-TSTRNEIREYESME-TDVGDEEPGPQRSVEGWILFVTG 65
           +GIARLKEKA+++KGRG G E  STR+++  YESM   +  D+EPGPQRSVEGWILF+  
Sbjct: 21  QGIARLKEKAKRRKGRGHGAELVSTRDDVGHYESMNIVEEDDDEPGPQRSVEGWILFINS 80

Query: 66  VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI 125
           VHEEAQEDD+ +KFSE+G+IKNLHLNLDRRTGFLKGYALVEY+++KEA AA+DALNGT I
Sbjct: 81  VHEEAQEDDIQDKFSEFGQIKNLHLNLDRRTGFLKGYALVEYETFKEAQAAKDALNGTEI 140

Query: 126 LGQTVTVDWCFVKGPKKV 143
           LGQ ++VDWCFVKGPKK+
Sbjct: 141 LGQPISVDWCFVKGPKKI 158

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|118787932|ref|XP_316392.3| AGAP006365-PA [Anopheles gambiae str. PEST] gi|116127037|gb|EAA11513.3| AGAP006365-PA [Anopheles gambiae str. PEST]

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 98/136 (72%), Positives = 119/136 (87%), Gaps = 1/136 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVH 67
           +GIARLKEKARK+KGRGFG E+  R  I +YE ++ D  + EPGPQRSVEGWILFVT +H
Sbjct: 21  QGIARLKEKARKRKGRGFGNESIPRETI-DYERLQDDEEEAEPGPQRSVEGWILFVTAIH 79

Query: 68  EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG 127
           EEAQEDD+ EKF E+G+IKN+HLNLDRRTGFLKGYALVEY++YK+A AA++ALNG+ +LG
Sbjct: 80  EEAQEDDIQEKFCEFGDIKNIHLNLDRRTGFLKGYALVEYETYKQALAAKEALNGSEVLG 139

Query: 128 QTVTVDWCFVKGPKKV 143
           QT+ VDWCFVKGPKK+
Sbjct: 140 QTIAVDWCFVKGPKKL 155

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307190290|gb|EFN74382.1| RNA-binding protein 8A [Camponotus floridanus]

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 99/138 (71%), Positives = 120/138 (86%), Gaps = 2/138 (1%)

Query: 8   KGIARLKEKARKKKGRGFGTE-TSTRNEIREYESMET-DVGDEEPGPQRSVEGWILFVTG 65
           +GIARLKEKA+++KGRG G E  STR+++  YESM   +  D EPGPQRSVEGWILF+  
Sbjct: 21  QGIARLKEKAKRRKGRGHGAELVSTRDDVGHYESMNVVEEDDNEPGPQRSVEGWILFINS 80

Query: 66  VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI 125
           VHEEAQEDD+ +KFSE+G+IKNLHLNLDRRTGFLKGYALVEY+++KEA AA++ALNGT I
Sbjct: 81  VHEEAQEDDIQDKFSEFGQIKNLHLNLDRRTGFLKGYALVEYETFKEAQAAKEALNGTEI 140

Query: 126 LGQTVTVDWCFVKGPKKV 143
           LGQ ++VDWCFVKGPKK+
Sbjct: 141 LGQAISVDWCFVKGPKKI 158

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332019400|gb|EGI59886.1| RNA-binding protein 8A [Acromyrmex echinatior]

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 100/137 (72%), Positives = 119/137 (86%), Gaps = 2/137 (1%)

Query: 8   KGIARLKEKARKKKGRGFGTE-TSTRNEIREYESME-TDVGDEEPGPQRSVEGWILFVTG 65
           +GIARLKEKA+K+KGRG G E  STR+++  YESM   +  D EPGPQRSVEGWILF+  
Sbjct: 21  QGIARLKEKAKKRKGRGHGAELVSTRDDVGHYESMNLIEEDDNEPGPQRSVEGWILFINS 80

Query: 66  VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI 125
           VHEEAQEDD+ +KFSE+G+IKNLHLNLDRRTGFLKGYALVEY+++KEA AA++ALNGT I
Sbjct: 81  VHEEAQEDDIQDKFSEFGQIKNLHLNLDRRTGFLKGYALVEYETFKEAQAAKEALNGTEI 140

Query: 126 LGQTVTVDWCFVKGPKK 142
           LGQ ++VDWCFVKGPKK
Sbjct: 141 LGQAISVDWCFVKGPKK 157

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312385484|gb|EFR29970.1| hypothetical protein AND_00716 [Anopheles darlingi]

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 98/136 (72%), Positives = 118/136 (86%), Gaps = 1/136 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVH 67
           +GIARLKEKAR +KGRGFG E+  R  I +YE ++ D  + EPGPQRSVEGWILFVT +H
Sbjct: 21  QGIARLKEKARHRKGRGFGNESIPRESI-DYERLQDDEEEAEPGPQRSVEGWILFVTSIH 79

Query: 68  EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG 127
           EEAQEDD+ EKF E+G+IKN+HLNLDRRTGFLKGYALVEY++YK+A AA++ALNG+ ILG
Sbjct: 80  EEAQEDDIQEKFCEFGDIKNIHLNLDRRTGFLKGYALVEYETYKQAMAAKEALNGSEILG 139

Query: 128 QTVTVDWCFVKGPKKV 143
           QT+ VDWCFVKGPKK+
Sbjct: 140 QTIAVDWCFVKGPKKL 155

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157114117|ref|XP_001652167.1| ss-DNA binding protein 12RNP2 precursor, putative [Aedes aegypti] gi|108877401|gb|EAT41626.1| AAEL006748-PA [Aedes aegypti]

 Score =  212 bits (539), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 98/136 (72%), Positives = 118/136 (86%), Gaps = 1/136 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVH 67
           +GIARLKEKARK+KGRGFG E+  R  I +YE ++ D  + EPGPQRSVEGWILFVT +H
Sbjct: 21  QGIARLKEKARKRKGRGFGNESIPREAI-DYERLQDDEEEAEPGPQRSVEGWILFVTSIH 79

Query: 68  EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG 127
           EEAQEDD+ EKF E+G+IKN+HLNLDRRTGFLKGYALVEY++YK+A AA++ALN + ILG
Sbjct: 80  EEAQEDDIQEKFCEFGDIKNIHLNLDRRTGFLKGYALVEYETYKQALAAKEALNASEILG 139

Query: 128 QTVTVDWCFVKGPKKV 143
           QT+ VDWCFVKGPKK+
Sbjct: 140 QTIAVDWCFVKGPKKL 155

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	192
FB|FBgn0033378	165	tsu "tsunagi" [Drosophila mela	0.734	0.854	0.669	1.1e-50
UNIPROTKB|I3LI59	177	RBM8A "Uncharacterized protein	0.729	0.790	0.668	7.4e-50
ZFIN|ZDB-GENE-050306-51	174	rbm8a "RNA binding motif prote	0.692	0.764	0.691	1.5e-49
UNIPROTKB|Q3ZCE8	174	RBM8A "RNA-binding protein 8A"	0.723	0.798	0.666	2e-49
UNIPROTKB|E2QV85	177	RBM8A "Uncharacterized protein	0.723	0.785	0.666	2e-49
UNIPROTKB|F6XAE9	174	RBM8A "Uncharacterized protein	0.723	0.798	0.666	2e-49
UNIPROTKB|Q9Y5S9	174	RBM8A "RNA-binding protein 8A"	0.723	0.798	0.666	2e-49
RGD|1310099	174	Rbm8a "RNA binding motif prote	0.723	0.798	0.666	2e-49
WB|WBGene00004387	142	rnp-4 [Caenorhabditis elegans	0.677	0.915	0.587	1.5e-37
TAIR|locus:2033888	202	Y14 [Arabidopsis thaliana (tax	0.687	0.653	0.539	2.5e-33

FB|FBgn0033378 tsu "tsunagi" [Drosophila melanogaster (taxid:7227)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 95/142 (66%), Positives = 119/142 (83%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDE-EPGPQRSVEGWILFVTGV 66
             +GI RLKEKA+ +KGRGFG++++TR  I  YE +  +  DE EPGPQRSVEGWILFVT +
Sbjct:    21 QGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI 80

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEAQED++ EKF +YGEIKN+HLNLDRRTGF KGYALVEY+++K+A AA++ALNG  I+
Sbjct:    81 HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM 140

Query:   127 GQTVTVDWCFVKGPKKVAGEQK 148
             GQT+ VDWCFVKGPK+V   +K
Sbjct:   141 GQTIQVDWCFVKGPKRVKKSEK 162

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

GO:0007310 "oocyte dorsal/ventral axis specification" evidence=IMP

GO:0007314 "oocyte anterior/posterior axis specification" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0000226 "microtubule cytoskeleton organization" evidence=IMP

GO:0007312 "oocyte nucleus migration involved in oocyte dorsal/ventral axis specification" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0007317 "regulation of pole plasm oskar mRNA localization" evidence=IMP;IPI

GO:0006406 "mRNA export from nucleus" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0045451 "pole plasm oskar mRNA localization" evidence=TAS

GO:0046595 "establishment of pole plasm mRNA localization" evidence=TAS

GO:0006396 "RNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007294 "germarium-derived oocyte fate determination" evidence=IMP

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

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0035145 "exon-exon junction complex" evidence=IPI

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=IMP

UNIPROTKB|I3LI59 RBM8A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 519 (187.8 bits), Expect = 7.4e-50, P = 7.4e-50
 Identities = 97/145 (66%), Positives = 123/145 (84%)

Query:     7 LKGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTG 65
             L+ I +LKEKA+K+KGRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTG
Sbjct:    25 LESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTG 82

Query:    66 VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI 125
             VHEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  +
Sbjct:    83 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 142

Query:   126 LGQTVTVDWCFVKGPKKVAGEQKVG 150
             +GQ ++VDWCFV+GP K  G+++ G
Sbjct:   143 MGQPISVDWCFVRGPPK--GKRRGG 165

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

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

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-050306-51 rbm8a "RNA binding motif protein 8A" [Danio rerio (taxid:7955)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 94/136 (69%), Positives = 118/136 (86%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGV 66
             + I +LKEKA+K+KGRGFG+E   R+ +RE Y+++E D GDE PGPQRSVEGWILFVTGV
Sbjct:    23 ESIHKLKEKAKKRKGRGFGSEEGARSRVREDYDTVEQD-GDE-PGPQRSVEGWILFVTGV 80

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEA E+D+H+KF+E+GEIKNLHLNLDRRTG+LKGYALVEY++YKEA AA + LNG  ++
Sbjct:    81 HEEATEEDVHDKFAEFGEIKNLHLNLDRRTGYLKGYALVEYETYKEAQAAMEGLNGQELM 140

Query:   127 GQTVTVDWCFVKGPKK 142
             GQ ++VDWCFV+GP K
Sbjct:   141 GQPISVDWCFVRGPPK 156

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006417 "regulation of translation" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|Q3ZCE8 RBM8A "RNA-binding protein 8A" [Bos taurus (taxid:9913)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 96/144 (66%), Positives = 122/144 (84%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGV 66
             + I +LKEKA+K+KGRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGV
Sbjct:    23 ESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGV 80

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++
Sbjct:    81 HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 140

Query:   127 GQTVTVDWCFVKGPKKVAGEQKVG 150
             GQ ++VDWCFV+GP K  G+++ G
Sbjct:   141 GQPISVDWCFVRGPPK--GKRRGG 162

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

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

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QV85 RBM8A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 96/144 (66%), Positives = 122/144 (84%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGV 66
             + I +LKEKA+K+KGRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGV
Sbjct:    26 ESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGV 83

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++
Sbjct:    84 HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 143

Query:   127 GQTVTVDWCFVKGPKKVAGEQKVG 150
             GQ ++VDWCFV+GP K  G+++ G
Sbjct:   144 GQPISVDWCFVRGPPK--GKRRGG 165

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

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

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F6XAE9 RBM8A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 96/144 (66%), Positives = 122/144 (84%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGV 66
             + I +LKEKA+K+KGRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGV
Sbjct:    23 ESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGV 80

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++
Sbjct:    81 HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 140

Query:   127 GQTVTVDWCFVKGPKKVAGEQKVG 150
             GQ ++VDWCFV+GP K  G+++ G
Sbjct:   141 GQPISVDWCFVRGPPK--GKRRGG 162

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9Y5S9 RBM8A "RNA-binding protein 8A" [Homo sapiens (taxid:9606)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 96/144 (66%), Positives = 122/144 (84%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGV 66
             + I +LKEKA+K+KGRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGV
Sbjct:    23 ESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGV 80

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++
Sbjct:    81 HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 140

Query:   127 GQTVTVDWCFVKGPKKVAGEQKVG 150
             GQ ++VDWCFV+GP K  G+++ G
Sbjct:   141 GQPISVDWCFVRGPPK--GKRRGG 162

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0005737 "cytoplasm" evidence=NAS

GO:0003729 "mRNA binding" evidence=NAS

GO:0003723 "RNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0035145 "exon-exon junction complex" evidence=IDA

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

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

RGD|1310099 Rbm8a "RNA binding motif protein 8A" [Rattus norvegicus (taxid:10116)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 96/144 (66%), Positives = 122/144 (84%)

Query:     8 KGIARLKEKARKKKGRGFGTETSTRNEIRE-YESMETDVGDEEPGPQRSVEGWILFVTGV 66
             + I +LKEKA+K+KGRGFG+E  +R  +RE Y+S+E D GDE PGPQRSVEGWILFVTGV
Sbjct:    23 ESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD-GDE-PGPQRSVEGWILFVTGV 80

Query:    67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
             HEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YKEA AA + LNG  ++
Sbjct:    81 HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 140

Query:   127 GQTVTVDWCFVKGPKKVAGEQKVG 150
             GQ ++VDWCFV+GP K  G+++ G
Sbjct:   141 GQPISVDWCFVRGPPK--GKRRGG 162

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA;ISO

GO:0051028 "mRNA transport" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

WB|WBGene00004387 rnp-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 77/131 (58%), Positives = 96/131 (73%)

Query:    17 ARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMH 76
             A  ++ RG G   S   E   Y+ ++ +       PQRSVEGWI+FVT +HEEA EDD+H
Sbjct:    13 ANAERSRGRGLAQSRNRERITYDVVDEESSATSGAPQRSVEGWIVFVTNIHEEATEDDVH 72

Query:    77 EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF 136
             +KFSEYG+IKN+HLNLDRRTGFLKGYALVEY++ KEA+ A D  N T +LGQ V VDWCF
Sbjct:    73 DKFSEYGKIKNIHLNLDRRTGFLKGYALVEYETQKEANEAIDQSNDTDLLGQNVKVDWCF 132

Query:   137 VKGPKKVAGEQ 147
             VKG KK +G++
Sbjct:   133 VKG-KKTSGKR 142

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

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

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

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

TAIR|locus:2033888 Y14 [Arabidopsis thaliana (taxid:3702)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 76/141 (53%), Positives = 99/141 (70%)

Query:     6 RLKG-IARLK-EKARKKKGRGFGTETST----RNEIREYESMETDVGDEEPGPQRSVEGW 59
             RLK  IA    E A+K KGRGF  E  +    R   R++ES+ +D G   PGPQRSVEGW
Sbjct:    39 RLKSAIAGANGESAKKTKGRGFREEKDSDRQRRLSSRDFESLGSD-G--RPGPQRSVEGW 95

Query:    60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
             I+ V+GVHEE QE+D+   F ++GEIKNL+LNLDRR+G++KGYAL+EY+  +EA +A  A
Sbjct:    96 IILVSGVHEETQEEDITNAFGDFGEIKNLNLNLDRRSGYVKGYALIEYEKKEEAQSAISA 155

Query:   120 LNGTTILGQTVTVDWCFVKGP 140
             +NG  +L Q V+VDW F  GP
Sbjct:   156 MNGAELLTQNVSVDWAFSSGP 176

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0016604 "nuclear body" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0035145 "exon-exon junction complex" evidence=IPI

GO:0010628 "positive regulation of gene expression" evidence=IEP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q27W01	RBM8A_RAT	No assigned EC number	0.7094	0.5937	0.6551	yes	N/A
Q5D018	RBM8A_DANRE	No assigned EC number	0.7083	0.6093	0.6724	yes	N/A
Q3ZCE8	RBM8A_BOVIN	No assigned EC number	0.7094	0.5937	0.6551	yes	N/A
Q6PH90	RB8AB_XENLA	No assigned EC number	0.7213	0.6197	0.6839	N/A	N/A
Q9V535	RBM8A_DROME	No assigned EC number	0.6690	0.7343	0.8545	yes	N/A
Q9CWZ3	RBM8A_MOUSE	No assigned EC number	0.7008	0.5937	0.6551	yes	N/A
Q28BZ1	RBM8A_XENTR	No assigned EC number	0.7131	0.6197	0.6839	yes	N/A
Q9Y5S9	RBM8A_HUMAN	No assigned EC number	0.7094	0.5937	0.6551	yes	N/A
Q9DF42	RB8AA_XENLA	No assigned EC number	0.7131	0.6197	0.6839	N/A	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	192
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-61
smart00360	73	smart00360, RRM, RNA recognition motif	4e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-15
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-13
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-13
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-12
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-12
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-11
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-11
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-11
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-10
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-09
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	8e-09
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-08
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	3e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-07
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-07
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	8e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-07
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	9e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	9e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	1e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-06
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	3e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	4e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	5e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	5e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	5e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	5e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	5e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	6e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-06
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	9e-06
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	9e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	1e-05
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	1e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-05
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-05
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	4e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	4e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	4e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	5e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	5e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	7e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	7e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	7e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-05
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	8e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	9e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	9e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	1e-04
cd12668	98	cd12668, RRM3_RAVER2, RNA recognition motif 3 foun	1e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-04
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	4e-04
cd12434	75	cd12434, RRM_RCAN_like, RNA recognition motif in r	4e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	4e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	4e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-04
PLN03121	243	PLN03121, PLN03121, nucleic acid binding protein;	5e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	6e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	6e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	6e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	6e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	7e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	7e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	8e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	8e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	8e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	9e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.001
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.001
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.001
cd12480	80	cd12480, RRM2_U1A, RNA recognition motif 2 found i	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.001
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	0.002
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.002
cd12541	76	cd12541, RRM2_La, RNA recognition motif 2 in La au	0.002
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.002
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.002
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.002
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.002
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.002
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.002
PLN03120	260	PLN03120, PLN03120, nucleic acid binding protein;	0.002
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.002
cd12667	92	cd12667, RRM3_RAVER1, RNA recognition motif 3 in v	0.003
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.003
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.004
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.004
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.004
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.004
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.004
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.004
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.004
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.004
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.004
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	0.004

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

 Score =  183 bits (468), Expect = 5e-61
 Identities = 67/88 (76%), Positives = 81/88 (92%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
           QRSVEGWI+FVTGVHEEAQE+D+H+KF+E+GEIKNLHLNLDRRTGF+KGYAL+EY++ KE
Sbjct: 1   QRSVEGWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKE 60

Query: 113 ASAARDALNGTTILGQTVTVDWCFVKGP 140
           A AA + LNG  +LGQT++VDW FVKGP
Sbjct: 61  AQAAIEGLNGKELLGQTISVDWAFVKGP 88

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

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

 Score = 74.2 bits (183), Expect = 4e-18
 Identities = 26/72 (36%), Positives = 48/72 (66%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  E+++ E FS++G+++++ L  D+ TG  KG+A VE++S ++A  A +AL
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

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

 Score = 66.5 bits (163), Expect = 4e-15
 Identities = 24/71 (33%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  E+D+ + FS++G I+++ +  D  TG  KG+A VE++  ++A  A +AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 121 NGTTILGQTVT 131
           NG  + G+ + 
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 65.8 bits (161), Expect = 7e-15
 Identities = 27/73 (36%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  E+D+ E FS++GEI+++ +  D+  G  KG+A VE++S ++A  A +AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 121 NGTTILGQTVTVD 133
           NG  + G+ + V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 64.5 bits (158), Expect = 3e-14
 Identities = 25/61 (40%), Positives = 38/61 (62%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           +D + E FS YG +K++ L +DR     +GYA VE++S ++A  A   ++G  I GQ VT
Sbjct: 12  KDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVT 71

Query: 132 V 132
           V
Sbjct: 72  V 72

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

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

 Score = 67.3 bits (163), Expect = 1e-13
 Identities = 29/111 (26%), Positives = 50/111 (45%), Gaps = 1/111 (0%)

Query: 33  NEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNL 92
                 E +       +   +   E   LFV  +  +  E+D+ E F ++G +K + L  
Sbjct: 90  YTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVR 149

Query: 93  DRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW-CFVKGPKK 142
           DR TG  +G+A VE++S + A  A + LNG  + G+ + V        P+ 
Sbjct: 150 DRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRS 200

Length = 306

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

 Score = 61.2 bits (149), Expect = 5e-13
 Identities = 33/73 (45%), Positives = 46/73 (63%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +A ED ++E F EYGEI ++ L  D  +G  KG+  VE+ S + A AA DAL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 121 NGTTILGQTVTVD 133
            GT +LG+ V +D
Sbjct: 61  GGTDLLGRPVRLD 73

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

>gnl|CDD|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 = 60.3 bits (147), Expect = 9e-13
 Identities = 26/73 (35%), Positives = 40/73 (54%)

Query: 62  FVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN 121
           FV  +  +A E+ + E FSE G + +  L  DR TG  KGY   E++  + A++A   LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 122 GTTILGQTVTVDW 134
           G    G+ + VD+
Sbjct: 62  GYEFNGRALRVDF 74

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

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 29/78 (37%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           +I ++ G+  E  E D+   FS+YGEI +++L  D++TG  KG+A + Y+  +    A D
Sbjct: 11  YI-YIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVD 69

Query: 119 ALNGTTILGQTVTVDWCF 136
            LNG  +LG+T+ VD   
Sbjct: 70  NLNGIKLLGRTIRVDHVR 87

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

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 29/73 (39%), Positives = 40/73 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  E+ + E FS YG+I+ L L  D  TGF KGYA VEY+  ++A  A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 121 NGTTILGQTVTVD 133
           +   I G  + VD
Sbjct: 66  HKLVIDGSEIFVD 78

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|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 = 59.9 bits (146), Expect = 2e-12
 Identities = 23/73 (31%), Positives = 42/73 (57%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV+G+     E ++   FS++G ++ + L  D  TG  +G+  V ++S ++A AA   L
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 121 NGTTILGQTVTVD 133
           NG  + G+ + V+
Sbjct: 64  NGKELEGRVIKVE 76

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|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 = 59.6 bits (145), Expect = 2e-12
 Identities = 23/72 (31%), Positives = 34/72 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+ G+     ED + E    +G++K  +L  D  TG  KGYA  EY        A   L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 121 NGTTILGQTVTV 132
           NG  +  + +TV
Sbjct: 63  NGMQLGDKKLTV 74

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

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

 Score = 56.8 bits (138), Expect = 2e-11
 Identities = 26/72 (36%), Positives = 46/72 (63%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V G+ EE  E  +H  F  +G+IK++ + LD  T   +G+A VE++  ++A+AA D +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 121 NGTTILGQTVTV 132
           N + + G+T+ V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 56.5 bits (137), Expect = 3e-11
 Identities = 23/64 (35%), Positives = 40/64 (62%)

Query: 71  QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV 130
            E D+ E FS YG I+ + +  D++TG  +G+  V ++S ++A  A++ LNG  I G+ +
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71

Query: 131 TVDW 134
            VD+
Sbjct: 72  RVDY 75

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

 Score = 56.4 bits (137), Expect = 3e-11
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
            L+V  +H +  E  ++E FS  G + ++ +  D  T    GYA V + +  +A  A D 
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 120 LNGTTILGQTVTVDW 134
           LN   I G+ + + W
Sbjct: 61  LNFDVIKGKPIRIMW 75

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

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

 Score = 55.7 bits (135), Expect = 6e-11
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +     E+D+ + F ++GE+ +  +  DR TG  +G+  VE ++ +EA+AA + L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 121 NGTTILGQTVTV 132
           NGT   G+T+TV
Sbjct: 62  NGTDFGGRTLTV 73

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

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

 Score = 55.5 bits (134), Expect = 9e-11
 Identities = 21/74 (28%), Positives = 42/74 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  V +  + DD+   F +YG I ++++ LD  T   +G+A V+++  ++A  A   L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 121 NGTTILGQTVTVDW 134
           + T  LG+ + + +
Sbjct: 63  DRTRFLGREIEIQF 76

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

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

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 25/74 (33%), Positives = 36/74 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +  E  ++   E  S +G ++   L     TG  KGY  VEY S   A  A++ L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 121 NGTTILGQTVTVDW 134
           +G  I G+ + VDW
Sbjct: 62  DGKQIGGRKLQVDW 75

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|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 = 54.6 bits (132), Expect = 2e-10
 Identities = 24/72 (33%), Positives = 38/72 (52%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +     E+++ E F  +GEI  +HL LD+ T   KG+A V +   + A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 121 NGTTILGQTVTV 132
           +G+   G+ + V
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 53.9 bits (130), Expect = 3e-10
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           GW +FV  +  +A E  + + FS +G + N+ +  D  T   KGY  V   +Y+EA +A 
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 118 DALNGTTILGQTVTV 132
            +LNG  + G+ + V
Sbjct: 61  ASLNGYRLGGRVLQV 75

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

>gnl|CDD|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 = 53.0 bits (128), Expect = 5e-10
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +     E+++   FS +G I+ + +  D      KGYA V +D+++ A+ A  A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 121 NGTTILGQTVTVDW 134
           NGT+I GQTV   W
Sbjct: 57  NGTSINGQTVKCSW 70

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

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

 Score = 53.4 bits (128), Expect = 6e-10
 Identities = 28/69 (40%), Positives = 39/69 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+VT +  +  ED++ + F  YG I   +L  D+ TG  +G A V YD  +EA AA  +L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 121 NGTTILGQT 129
           NGT   G T
Sbjct: 63  NGTIPPGST 71

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|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 = 52.9 bits (128), Expect = 7e-10
 Identities = 25/66 (37%), Positives = 39/66 (59%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  + + A E+D+   F EYG I+ + +  D+ TG  KG A V++ S +EA  A +AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 121 NGTTIL 126
           +G   +
Sbjct: 62  HGKVTM 67

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 52.2 bits (126), Expect = 9e-10
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +     E+D+ E FS YG+++ + L  ++     +G+A VE+ S ++A AA   L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRP--RGFAFVEFASPEDAEAALKKL 58

Query: 121 NGTTILGQTV 130
           NG  + G+T+
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 52.3 bits (126), Expect = 1e-09
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 70  AQEDDMHEKFSEYGEIKNLHLNLDR-RTGFLKGYALVEYDSYKEASAARDALNGTTILGQ 128
             E D+ + FS +G +    + + R   G  KG+A V++ S  +A  A   +NG  I G+
Sbjct: 11  CTEADLKKLFSPFGFV--WEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68

Query: 129 TVTVDWC 135
            V VDW 
Sbjct: 69  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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 52.3 bits (126), Expect = 1e-09
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           ++++   F   G I++  +  DR TG   GY  V+Y    +A  A + LNG  I  + + 
Sbjct: 14  QEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLK 73

Query: 132 V 132
           V
Sbjct: 74  V 74

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

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

 Score = 51.7 bits (124), Expect = 2e-09
 Identities = 27/73 (36%), Positives = 39/73 (53%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  EA E+ + + FSE G + +  L  DR TG  KGY   EY   + A +A   L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 121 NGTTILGQTVTVD 133
           NG  + G+ + VD
Sbjct: 61  NGYELNGRQLRVD 73

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

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

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++ +  E  +  +F EYG IK + L  D++TG  +GYA +E++  ++  AA    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 121 NGTTILGQTVTVD 133
           +G  I G+ V VD
Sbjct: 64  DGKKIDGRRVLVD 76

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

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

 Score = 51.1 bits (123), Expect = 4e-09
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEI-KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           LF+  +  E  E  +++ FS +G I +   +  D  TG  KG+A + YDS++ + AA +A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 120 LNGTTILGQTVTVDWCFVK 138
           +NG  +  + +TV + F K
Sbjct: 64  MNGQYLCNRPITVSYAFKK 82

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

 Score = 50.9 bits (122), Expect = 5e-09
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +    +EDD+ + FS++GE+  +H+ +D+++G  KG+A V +   ++A  A   L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 121 NGTTILGQ 128
           +G    G+
Sbjct: 65  DGKVFQGR 72

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

 Score = 50.3 bits (121), Expect = 5e-09
 Identities = 24/72 (33%), Positives = 39/72 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H    EDD+   F  +GEI+ + L  D  TG  KGY  +++   ++A  A + L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 49.8 bits (120), Expect = 8e-09
 Identities = 23/60 (38%), Positives = 37/60 (61%)

Query: 63  VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
           VT + E+A EDD+ E F  +G I  ++L  D+ TG  +G+A V + + ++A  A + LNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

 Score = 50.1 bits (120), Expect = 9e-09
 Identities = 23/72 (31%), Positives = 41/72 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +  E  ED + + FS +G IK++ ++ D  T   KG+A VEY+  + A  A + +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 63  NGVMLGGRNIKV 74

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

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

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 24/72 (33%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV+G+     ++++ + F ++G +K++ L +  R+G  KG A VEY++   AS A   +
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRL-VTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 121 NGTTILGQTVTV 132
           +GT I  +T++V
Sbjct: 64  DGTEIKEKTISV 75

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

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 21/73 (28%), Positives = 39/73 (53%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +      DD+   F +YGE+ ++++  DR T   +G+A V +   ++A  A DA+
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 121 NGTTILGQTVTVD 133
           +G  + G+ + V 
Sbjct: 61  DGKELDGRELRVQ 73

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

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

 Score = 53.4 bits (128), Expect = 1e-08
 Identities = 22/93 (23%), Positives = 45/93 (48%), Gaps = 6/93 (6%)

Query: 40  SMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL 99
              T    + P   +      L+V  +H    E ++ + F  +G+I+++ L+ D  TG  
Sbjct: 174 KAATHQPGDIPNFLK------LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRS 227

Query: 100 KGYALVEYDSYKEASAARDALNGTTILGQTVTV 132
           KG+  +++   +EA  A + +NG  + G+ + V
Sbjct: 228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 260

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

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

 Score = 49.0 bits (118), Expect = 1e-08
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 5/56 (8%)

Query: 79  FSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           FS +G ++ + L   +      G+A VE+ + + A  A   LNG    G+ + VD+
Sbjct: 5   FSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  VH +  EDD+   F  +G+IK+  L  D  TG  KGY  +EY++ + A  A  ++
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 121 NGTTILGQTVTV 132
           N   + GQ + V
Sbjct: 63  NLFDLGGQQLRV 74

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

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

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV G+ E+  E+ + E F   G I    +  DR TG  KG+  V++ S ++A AA++A+
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 121 NGTTILGQTVTVDWCFVKG 139
               I G  VT+D+   KG
Sbjct: 60  EDGEIDGNKVTLDFAKPKG 78

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

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

 Score = 47.5 bits (114), Expect = 6e-08
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           E+ ++E FS  G+IK + + LDR T    G+  VEY + ++A  A   LNGT +  + + 
Sbjct: 12  EEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIR 71

Query: 132 VDW 134
           VDW
Sbjct: 72  VDW 74

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

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

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 5/60 (8%)

Query: 79  FSEYGEIKNLHLNLDRRTGFLKG----YALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           FS+YG+IK     L  ++G LKG    Y  V +++ +EA  A  +LNG T LG+ + V W
Sbjct: 20  FSKYGKIKKFDF-LFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRW 78

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

 Score = 50.3 bits (120), Expect = 1e-07
 Identities = 22/82 (26%), Positives = 39/82 (47%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
                  G+ +FV  +  +  E  + + F  +G ++N+ +  D  T   KGY  V   +Y
Sbjct: 262 IAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNY 321

Query: 111 KEASAARDALNGTTILGQTVTV 132
            EA+ A  +LNG T+  + + V
Sbjct: 322 DEAAMAILSLNGYTLGNRVLQV 343

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

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 5/68 (7%)

Query: 69  EAQEDDMHEKFSEYGEIKNLHL--NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
           EA + D+   FS YG++K++ +    D+     +G+A VE+ + KEA  A +AL  T +L
Sbjct: 11  EATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAMNALKDTHLL 67

Query: 127 GQTVTVDW 134
           G+ + + +
Sbjct: 68  GRRLVLQY 75

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

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 23/66 (34%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++++A E ++ E FS YG ++++++  D      +G A V+Y S + A AA  AL
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60

Query: 121 NGTTIL 126
           NG   +
Sbjct: 61  NGVYTM 66

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  E++  E FS+YGE+  + LN +      KG+  +  D+   A  A+  L
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 121 NGTTILGQTVTV 132
           +G    G+ + V
Sbjct: 58  DGIMRKGRQLRV 69

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

>gnl|CDD|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 = 46.8 bits (111), Expect = 2e-07
 Identities = 22/73 (30%), Positives = 42/73 (57%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+  +  E  + + FS+YG+I  + +  DR T   +G+  V +++  +A  A  A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 121 NGTTILGQTVTVD 133
           NG ++ G+ + VD
Sbjct: 63  NGKSVDGRQIRVD 75

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

 Score = 46.3 bits (110), Expect = 2e-07
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V     +  E  + E FS YG +K + +        +  +A VE++S + A  A+D++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDSV 53

Query: 121 NGTTILGQTVTV 132
           +G  +    + V
Sbjct: 54  HGKVLNNNPLYV 65

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

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

 Score = 46.1 bits (109), Expect = 3e-07
 Identities = 20/69 (28%), Positives = 35/69 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + ++ + FS+YG I    +  D+ TG  +G   + +D   EA  A   L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 121 NGTTILGQT 129
           NG    G +
Sbjct: 63  NGQKPEGAS 71

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 21/63 (33%), Positives = 34/63 (53%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           +D++   FS  GEI++  L  D+ TG   GY  V Y   ++A  A + LNG  +  +T+ 
Sbjct: 15  QDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIK 74

Query: 132 VDW 134
           V +
Sbjct: 75  VSY 77

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

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 20/50 (40%), Positives = 34/50 (68%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           LFV G+ E+  E+D+ E FS+YG ++++ +  D+ TG  +G+A V +D Y
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY 51

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|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 = 45.9 bits (109), Expect = 4e-07
 Identities = 21/66 (31%), Positives = 34/66 (51%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +    +E D+   F ++G+I  L +  D+ TG  KG A + Y + + A  A+ AL
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 121 NGTTIL 126
           +    L
Sbjct: 68  HEQKTL 73

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|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 = 45.3 bits (108), Expect = 4e-07
 Identities = 20/66 (30%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 69  EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ 128
           EA + ++ E FS +G++K++ L   +  G  +G+A VE+ + +EA  A +AL  T + G+
Sbjct: 11  EATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGR 69

Query: 129 TVTVDW 134
            + +++
Sbjct: 70  HLVLEY 75

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

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 20/58 (34%), Positives = 35/58 (60%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT 129
           EDD+ E F+ +GEI+++ +  D++T   KG A V++     A+ A + +NG  + G T
Sbjct: 16  EDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 44.9 bits (107), Expect = 6e-07
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 8/60 (13%)

Query: 73  DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV 132
           +D+ E FS+YG+I  + L+        KGY  V++D+ ++A AA    NG  I GQ + +
Sbjct: 16  EDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAAVAGENGREIAGQKLDI 67

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 45.0 bits (107), Expect = 8e-07
 Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYD--------SYKE 112
           + +TG+        +   F  +GEI+   L LD RTG   G   V +         +++ 
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 113 ASAARDALNGTTILGQTVTVD 133
           A AA D LNG  I G+ V V+
Sbjct: 61  AKAAVDGLNGRRIGGKRVRVE 81

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

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

 Score = 44.7 bits (106), Expect = 9e-07
 Identities = 19/73 (26%), Positives = 41/73 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +     ++ +  +F ++G +    +  DR TG  +G+  V+++S ++A  A +A+
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 121 NGTTILGQTVTVD 133
           +G  + G+ + VD
Sbjct: 62  DGKELDGRPINVD 74

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

 Score = 44.7 bits (106), Expect = 9e-07
 Identities = 20/74 (27%), Positives = 38/74 (51%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  E   + +   F+ +GEI +  +  D +TG  KGY  V +   ++A  A  ++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ +  +W
Sbjct: 62  NGQWLGGRAIRTNW 75

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

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

 Score = 44.6 bits (105), Expect = 9e-07
 Identities = 22/69 (31%), Positives = 36/69 (52%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + +M + FS+YG I    + +D+ TG  +G   + +D   EA  A   L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 121 NGTTILGQT 129
           NG   LG  
Sbjct: 64  NGQKPLGAA 72

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

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 21/66 (31%), Positives = 32/66 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  V     E ++   F E+G +  + +  D+RTG  +G   V+Y +  EA  A  AL
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 121 NGTTIL 126
           +    L
Sbjct: 62  HNQRTL 67

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + ++   FS YG I    +  D  TG  +G   + +D   EA  A  AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 121 NGTTILGQT--VTV 132
           NGT   G T  +TV
Sbjct: 63  NGTIPPGATEPITV 76

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 75  MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           + + FS+ G+     L +    G  +G+A VEY + ++A  A+ ALNG ++ G  + V +
Sbjct: 20  LRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSF 78

Query: 135 C 135
            
Sbjct: 79  G 79

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 17/54 (31%), Positives = 32/54 (59%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI 125
           E  ++  F+E GE+ ++ +  +++TG   GY  VE+ +++ A  A  +LNG  I
Sbjct: 13  EAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66

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

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 63  VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
           V G+     E D+ E FS YG +  +++  D+RTG  +G+A V ++   ++  A +  NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 123 TTILGQTVTVDWCFVK 138
             + G+ + VD+   K
Sbjct: 64  MELDGRRIRVDYSITK 79

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

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

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 19/69 (27%), Positives = 37/69 (53%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++ G+     ++D+ +    +G+I +    LD++T   KGY  V++DS + A  A + L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 121 NGTTILGQT 129
           NG  +  Q 
Sbjct: 63  NGRGVQAQF 71

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 19/76 (25%), Positives = 42/76 (55%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +LFV  ++    ++D+   FS +G+IK+  +  D++TG    YA +E+++ ++   A   
Sbjct: 5   VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64

Query: 120 LNGTTILGQTVTVDWC 135
           ++   I  + + VD+ 
Sbjct: 65  MDNVLIDDRRIHVDFS 80

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +     ED + E FS+ G IK+  L  +        YA VEY  ++ A+AA   +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGN---DPYAFVEYYDHRSAAAALQTM 57

Query: 121 NGTTILGQTVTVDW 134
           NG  ILGQ + V+W
Sbjct: 58  NGRLILGQEIKVNW 71

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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 9/75 (12%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVE-YDSYKEASAARD 118
           L V  +     + ++   FS++GE+K++     R    F      VE YD  + A AA D
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKF------VEFYDI-RAAEAALD 56

Query: 119 ALNGTTILGQTVTVD 133
           ALNG   LG  + V 
Sbjct: 57  ALNGRPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|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 = 43.8 bits (104), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 41/72 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+  +  E  + D+++ F+ +G + +  + +D+ TG  K +  V YD+ + A AA  A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 61  NGFQVGGKRLKV 72

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

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V+ +H +  E+D+ E F   GE+K + +N D R+G  +G A V ++  ++A  A    
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQF 61

Query: 121 NGTTILGQ 128
           NG  + GQ
Sbjct: 62  NGVLLDGQ 69

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

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 23/78 (29%), Positives = 44/78 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V G+     E D+ E FS+YG I ++ +  D+++   +G+A V +++  +A  A++  
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 121 NGTTILGQTVTVDWCFVK 138
           NG  + G+ + VD+   K
Sbjct: 72  NGMELDGRRIRVDFSITK 89

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

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

 Score = 43.0 bits (102), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 8/77 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLK---GYALVEYDSYKEASAAR 117
           ++V  +  +  EDD+   FS++GE++++ +   +     +   G+A V    +K+AS+A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVT---FKDASSAE 59

Query: 118 DAL--NGTTILGQTVTV 132
           +AL  NGT + G+ ++V
Sbjct: 60  NALQLNGTELGGRKISV 76

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

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           LFV G+ E+ +E  + + F EYG+I  + +  DR++G  +G+  V +D +
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDH 52

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 22/65 (33%), Positives = 34/65 (52%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           GW +FV  +  EA E  + + F  +G + N+ +  D  T   KG+  V   +Y EA+ A 
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 118 DALNG 122
            +LNG
Sbjct: 61  ASLNG 65

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|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 = 42.8 bits (101), Expect = 4e-06
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 61  LFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           LFV G      +E+D+ + F  +G +    +   R+T     +A VE++  ++A+ A +A
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI---RKT-----FAFVEFEDSEDATKALEA 53

Query: 120 LNGTTILGQTVTVDW 134
           L+G+ I G  +TV++
Sbjct: 54  LHGSRIDGSVLTVEF 68

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

 Score = 43.1 bits (101), Expect = 4e-06
 Identities = 20/65 (30%), Positives = 36/65 (55%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           GW +F+  + ++A E  + + F  +G + N+ +  D  T   KG+  V   +Y+EA+ A 
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 118 DALNG 122
            +LNG
Sbjct: 61  ASLNG 65

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

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

 Score = 42.6 bits (101), Expect = 4e-06
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+     +D + + FS++GEI+   +  DR+TG  +GY  V    +K+  +A  A 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVT---FKDKESAERAC 59

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

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 15/73 (20%), Positives = 42/73 (57%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ++++  +     E ++ + FS++G +KN+ +   ++TG  K Y  +++ + + A+ A  +
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 120 LNGTTILGQTVTV 132
           +N   ++G+ + V
Sbjct: 61  MNNYLLMGKVLQV 73

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

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 42.3 bits (100), Expect = 4e-06
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++  +   A+E D+   F  YG I+ ++L          G+  VE++  ++A  A   L
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLK--------NGFGFVEFEDPRDADDAVYEL 53

Query: 121 NGTTILGQTVTVD 133
           NG  + G+ V V+
Sbjct: 54  NGKELCGERVIVE 66

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

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 23/82 (28%), Positives = 40/82 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + ++ + FS+YG I    + +D+ TG  +G   + +D   EA  A   L
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG    G T  +   F   P +
Sbjct: 68  NGQKPPGATEPITVKFANNPSQ 89

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

 Score = 42.8 bits (101), Expect = 5e-06
 Identities = 23/68 (33%), Positives = 37/68 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+  +     E+D+ + FS+YG +  +HL +D+ T   KG+A V Y   + A  A   L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 121 NGTTILGQ 128
           +GT   G+
Sbjct: 65  DGTVFQGR 72

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

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

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 22/82 (26%), Positives = 40/82 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+++G+     + D+ + FS +G I N  + +D+ TG  +G A + +D   EA  A  + 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG    G +  +   F   P +
Sbjct: 63  NGHKPPGSSEPITVKFAANPNQ 84

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 16/50 (32%), Positives = 32/50 (64%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +D +
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 52

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 11/79 (13%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHL-----NLDRRTGFLKGYALVEYDSYKEAS 114
            L+VT       + D+ + F +YGEI ++       N  RR      +  V++ S + A+
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR------FCYVQFTSPESAA 55

Query: 115 AARDALNGTTILGQTVTVD 133
           AA   LNG    G  + V 
Sbjct: 56  AAVALLNGKLGEGYKLVVK 74

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

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

 Score = 42.6 bits (100), Expect = 5e-06
 Identities = 22/82 (26%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  + ++ + +D+  +F  YG I ++++ LD  T   +G+A V+++  ++A  A   L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           +   I G+ + +   F +G +K
Sbjct: 63  DRKWICGRQIEIQ--FAQGDRK 82

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

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

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
           E ++ + FS++G +  L L+  ++TG  KGYA VE++S + A    + +N 
Sbjct: 13  EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNN 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 45.4 bits (107), Expect = 6e-06
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +  E +ED +   F  +G IK+++++ D  TG  KG+A VEY+  + A  A + +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 170 NGQMLGGRNIKV 181

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

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

 Score = 42.2 bits (100), Expect = 6e-06
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +   A + ++ ++F +YG ++++ +   R      G+A VE++  ++A  A  AL
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVA--RNP---PGFAFVEFEDPRDAEDAVRAL 56

Query: 121 NGTTILGQTVTV 132
           +G  I G  V V
Sbjct: 57  DGRRICGNRVRV 68

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

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

 Score = 42.8 bits (100), Expect = 6e-06
 Identities = 21/65 (32%), Positives = 34/65 (52%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           GW +FV  +  +A E  + + F  +G + N+ +  D  T   KG+  V   +Y EA+ A 
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 118 DALNG 122
            +LNG
Sbjct: 63  ASLNG 67

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

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 42.3 bits (99), Expect = 7e-06
 Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 2/82 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  V +  + +D+  +F  YG I ++++ LD  T   +G+A ++++  ++A  A   L
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           N   + G+ + +   F +G +K
Sbjct: 63  NRKWVCGRQIEIQ--FAQGDRK 82

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 41.9 bits (98), Expect = 9e-06
 Identities = 21/69 (30%), Positives = 37/69 (53%)

Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           EG  LF+  + +E  + D+ + F  +G + +  + +D++T   K +  V YD+   A AA
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 117 RDALNGTTI 125
             A+NG  I
Sbjct: 63  IQAMNGFQI 71

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 42.2 bits (99), Expect = 9e-06
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 8/82 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYALVEYDSYKE 112
           +FV G+ E+   + + + F + G IK         ++L  DR TG LKG A V +D    
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 113 ASAARDALNGTTILGQTVTVDW 134
           A AA D  +G    G  + V +
Sbjct: 65  AKAAIDWFDGKEFSGNPIKVSF 86

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

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

 Score = 41.4 bits (97), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 8/75 (10%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           W +FV  V      D++   F E+G +    +  D+    +K YA V  +  +EA AA +
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRV----VECDK----VKDYAFVHMEREEEALAAIE 52

Query: 119 ALNGTTILGQTVTVD 133
           ALNG  + G+ + V+
Sbjct: 53  ALNGKEVKGRRINVE 67

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

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 61  LFVTGVHEEAQEDD----MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           +FV G      EDD    + E FS  GEI  + +  DR TG  KG+A +E+ S      A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 117 RDALNGTTILGQTVTVD 133
            + L+G+ + G  + VD
Sbjct: 62  LE-LDGSDLGGGNLVVD 77

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

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  + E+  ++ + E F +YG+I +  +  D   G  KG+  V +++++ A  A + L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 63  NGKEVNGKKLYV 74

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

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

 Score = 41.4 bits (98), Expect = 1e-05
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 62  FVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN 121
           FV  +  + +E D++E FS+ G+++++ +  DR +   KG A VE+   +    A   L 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLT 61

Query: 122 GTTILGQTVTV 132
           G  +LGQ + V
Sbjct: 62  GQRLLGQPIMV 72

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

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

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +  +  E  + + FS+ G  K+  + +D  T     Y  VE+  ++ A+A+  A+
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 121 NGTTILGQTVTVDW 134
           NG  I+G+ V V+W
Sbjct: 60  NGRKIMGKEVKVNW 73

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 8/72 (11%)

Query: 63  VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA--L 120
           VT +  +A E D+++ FS  G+I+ + +   +R+G     +   Y ++K+  A   A  L
Sbjct: 3   VTNLSPKATERDIYDFFSFSGDIEYVEI---QRSGE---QSQTAYVTFKDPQAQETALLL 56

Query: 121 NGTTILGQTVTV 132
           +G TI+ Q+VT+
Sbjct: 57  SGATIVDQSVTI 68

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

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

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 20/65 (30%), Positives = 34/65 (52%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           GW +FV  +  ++ E  + + F  +G + N+ +  D  T   KG+  V   +Y EA+ A 
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 118 DALNG 122
            +LNG
Sbjct: 63  ASLNG 67

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

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

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  + +    +++   F +YG +       D     +K Y  V  +  ++A  A  AL
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDV----VKNYGFVHMEEEEDAEDAIKAL 53

Query: 121 NGTTILGQTVTV 132
           NG   +G+ + V
Sbjct: 54  NGYEFMGKRINV 65

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           G  L+V G      E+ + + FS +G I N+ +  ++  GF      V ++  + A  A 
Sbjct: 4   GNTLYVHGY--GLTEEILKKAFSPFGNIINISMEKEKNCGF------VTFEKMESADRAI 55

Query: 118 DALNGTTILGQTVTVD 133
             LNGTT+ G  + V 
Sbjct: 56  AELNGTTVQGVQLKVS 71

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

 Score = 41.4 bits (98), Expect = 1e-05
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           IL+V  +  +   +++++ F +YG I+ + +   + T   +G A V Y+   +A  A D 
Sbjct: 4   ILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDH 60

Query: 120 LNGTTILGQTVTV 132
           L+G  +  + + V
Sbjct: 61  LSGFNVANRYLVV 73

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

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR--D 118
           LFV G+     E D+ E+FS +G + ++ +   +  G  +G+A ++  +  EA   +   
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRT-SEAQLKKCKS 60

Query: 119 ALNGTTILGQTVTVD 133
            LNGT   G  + ++
Sbjct: 61  TLNGTKWKGSVLKIE 75

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

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V G+       ++  +F  +G I+ +    D   G  + YA +EY+S + A AA++AL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI----DYDPG--RNYAYIEYESIEAAQAAKEAL 54

Query: 121 NGTTI--LGQTVTVD 133
            G  +   G+ + VD
Sbjct: 55  RGFPLGGPGRRLRVD 69

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

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 62  FVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA-- 119
           FV  V      +++ E F   G I  + +  D+ TG  KG+A +E+    + S+  +A  
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFL---DKSSVENALL 59

Query: 120 LNGTTILGQTVTV 132
           LN +   G+ + V
Sbjct: 60  LNESEFRGRQIKV 72

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

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V G+  +  E D+ + FS +GE+  + +  D +TG  KG+  V +  Y++        
Sbjct: 2   LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQV------ 55

Query: 121 NGTTILGQTVTVD--WCFVKGPKK 142
               +L Q   +D  WC VK P  
Sbjct: 56  ---KVLSQRHMIDGRWCDVKIPNS 76

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 12/78 (15%)

Query: 63  VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
             GV  E     +   F +YG +++L +      G  K Y  V Y S ++A+AA DALNG
Sbjct: 12  GNGVSREE----LLRVFEKYGTVEDLVM----PPG--KPYCFVSYSSIEDAAAAYDALNG 61

Query: 123 T--TILGQTVTVDWCFVK 138
               +  Q   +   +V+
Sbjct: 62  KELELPQQNKPLYLSYVE 79

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

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +     ED + + F   G ++N+ +  D+    +  Y  VEY    +A  A   L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVN-YGFVEYHQSHDAEIALQTL 59

Query: 121 NGTTILGQTVTVDW 134
           NG  I    + V+W
Sbjct: 60  NGRQIENNEIRVNW 73

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

 Score = 43.0 bits (101), Expect = 3e-05
 Identities = 27/86 (31%), Positives = 42/86 (48%)

Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           S++G  L+V+G+ +   + ++   FS +G+I    +  D  TG  KG   + +D   EA 
Sbjct: 86  SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEAD 145

Query: 115 AARDALNGTTILGQTVTVDWCFVKGP 140
            A   LNGTT  G T  +   F   P
Sbjct: 146 RAIKTLNGTTPSGCTEPITVKFANNP 171

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 17/56 (30%), Positives = 33/56 (58%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASA 115
            +F+  +  +A E+++ E FS++GE+K   +  D+ TG  KG A V++ + + A  
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK 57

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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++  GV     E  M + FS +G+I  + +  D      KGY+ V ++S++ A+ A  ++
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56

Query: 121 NGTTILGQTVTVDW 134
           NGTTI G  V   W
Sbjct: 57  NGTTIEGHVVKCYW 70

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 18/61 (29%), Positives = 35/61 (57%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  + + A  + +   FS+YG +  + L   + TG +KG+A +E+++ +EA  A   L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 121 N 121
           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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 40.3 bits (95), Expect = 3e-05
 Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
            LFV  ++   +++++   F ++G+I+ L+     R     G+ +V Y   + A  A+ A
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHR-----GFIMVSYYDIRAARRAKRA 57

Query: 120 LNGTTILGQTVTVDWCFVK 138
           L GT + G+ + + +   K
Sbjct: 58  LQGTELGGRKLDIHFSIPK 76

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 40.2 bits (95), Expect = 3e-05
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ILF+  + EE  ++ +   F+++   K + L + RR     G A VE+++ ++A+ A  A
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEVRL-VPRR-----GIAFVEFETEEQATVALQA 57

Query: 120 LNGTTIL-GQTVTV 132
           L G  I  G  + +
Sbjct: 58  LQGFKITPGHAMKI 71

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

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +   A++DD+ E F E GE+ ++ +  D   G  KG+  VE+ + + A  A    
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKAL-EK 59

Query: 121 NGTTILGQTVTVD 133
           +G  +LG+ + VD
Sbjct: 60  SGEELLGREIRVD 72

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

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 4/60 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV+ +     ED++ + FS+ GEI ++ L  + + G  KGYA VE   ++   + ++AL
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVE---FENEESVQEAL 57

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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 6/79 (7%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGE-IKNLHL--NLDRRTGFLKGYALVEYDSYKEASAAR 117
           LFV G+ +   ++++ E+FS+  E + ++ +  + D +    +G+A VEY+S++ A+ AR
Sbjct: 4   LFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKN-RGFAFVEYESHRAAAMAR 62

Query: 118 DAL-NGTTIL-GQTVTVDW 134
             L  G  +L G  V VDW
Sbjct: 63  RKLVPGRILLWGHEVAVDW 81

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 22/74 (29%), Positives = 38/74 (51%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + +   +D++   FS  GE+++  L  D+  G   GY  V Y + K+A  A + L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 121 NGTTILGQTVTVDW 134
           NG  +  +T+ V +
Sbjct: 64  NGLRLQSKTIKVSY 77

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

 Score = 40.2 bits (94), Expect = 4e-05
 Identities = 16/74 (21%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  E  +  +   FS +    +  +  D ++G  +GY  V + S ++A  A + +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 121 NGTTILGQTVTVDW 134
           NG  +  + +  +W
Sbjct: 62  NGKWLGSRPIRCNW 75

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 40.0 bits (94), Expect = 4e-05
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V G+   + ED++   FS  GEI+ L L     TG  +G A + + + +EA+    AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT-EEAAKRALAL 59

Query: 121 NGTTILGQTVTV 132
           +G  + G+ + V
Sbjct: 60  DGEDMGGRFLKV 71

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

>gnl|CDD|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 = 4e-05
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V  +     E+ + E FSEYGE++        R   +K YA V ++   +A  A + 
Sbjct: 3   VLYVRNLPLSTTEEQLRELFSEYGEVE--------RVKKIKDYAFVHFEERDDAVKAMEE 54

Query: 120 LNGTTILGQTVTVDW 134
           +NG  + G  + V  
Sbjct: 55  MNGKELEGSPIEVSL 69

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

 Score = 40.1 bits (93), Expect = 4e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + ++ + FS+YG I    + +D+ TG  +G   + +D   EA  A   L
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 121 NGTTILGQT 129
           NG    G  
Sbjct: 65  NGQKPSGAA 73

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

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 16/72 (22%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  +  +++++E+FS +G+I    +NL +R      +A ++++  + A+ A ++ 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILE--VNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 121 NGTTILGQTVTV 132
           N + +  +T+ V
Sbjct: 64  NHSMLKNKTMHV 75

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

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 40.1 bits (93), Expect = 5e-05
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +  +  E  + + FS+ G  K+  +  +  +     Y  VE+  +++A+AA  A+
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 59

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG  ILG+ V V+W      +K
Sbjct: 60  NGRKILGKEVKVNWATTPSSQK 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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 21/69 (30%), Positives = 37/69 (53%)

Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           EG  LF+  + +E  + D+ + F  +G + +  + +D++T   K +  V YD+   A AA
Sbjct: 6   EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65

Query: 117 RDALNGTTI 125
             A+NG  I
Sbjct: 66  IQAMNGFQI 74

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 39.8 bits (94), Expect = 6e-05
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 72  EDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG---TTIL 126
           E+D+ +  S      IK++ L  D+ TG  +G+A VE+ S ++A+   DALN      I 
Sbjct: 16  EEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVID 75

Query: 127 GQTVTVDWC 135
           G+ V V + 
Sbjct: 76  GRVVRVSYA 84

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

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 39.7 bits (93), Expect = 7e-05
 Identities = 27/80 (33%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRTGFLKGYALVEYDSYKE 112
           +FV+ +     E D+ E F   G IK         + L  D+ TG  KG A V YD    
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 113 ASAARDALNGTTILGQTVTV 132
           ASAA +  N    +G T+ V
Sbjct: 61  ASAAIEWFNNKDFMGNTIKV 80

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.2 bits (92), Expect = 7e-05
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 11/67 (16%)

Query: 61  LFVTGVHEEAQEDDMHEKFS-----EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASA 115
           LFV  V +   ++ +H  F      EY ++K      D  TG  KG+A V Y +   A  
Sbjct: 3   LFVV-VSKSVTQEQLHRLFDIIPGLEYCDLK-----RDPYTGKSKGFAYVTYSNPASAIY 56

Query: 116 ARDALNG 122
           A++ LNG
Sbjct: 57  AKEKLNG 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 39.6 bits (92), Expect = 7e-05
 Identities = 16/50 (32%), Positives = 33/50 (66%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           +FV G+ E+ +E  + + F +YG+I+ + +  DR++G  +G+A V +D +
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDH 52

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 39.5 bits (92), Expect = 8e-05
 Identities = 17/56 (30%), Positives = 32/56 (57%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           LFV G+  +  E D+ E FS++G ++   +  D++TG  +G+  V + ++  A  A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 39.1 bits (91), Expect = 8e-05
 Identities = 14/62 (22%), Positives = 33/62 (53%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V+G  +   E+ + E+F +  +++ + L  D  +G    Y  +++   + A+AA D +
Sbjct: 1   IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 121 NG 122
            G
Sbjct: 61  TG 62

This subfamily corresponds to the RRM2 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.8 bits (98), Expect = 9e-05
 Identities = 31/128 (24%), Positives = 53/128 (41%), Gaps = 19/128 (14%)

Query: 12  RLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGP-------QRSVEGWILFVT 64
           R + ++R                 R Y   +   G     P        R+V     FV 
Sbjct: 47  RGRSRSRSPNRY------YRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTV-----FVL 95

Query: 65  GVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT 124
            +  +A+E D++E FS+ G+++++    DR +   KG A VE+   +    A  AL G  
Sbjct: 96  QLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQM 154

Query: 125 ILGQTVTV 132
           +LG+ + V
Sbjct: 155 LLGRPIIV 162

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

 Score = 42.0 bits (98), Expect = 9e-05
 Identities = 22/75 (29%), Positives = 35/75 (46%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  VH +  E D+   F  +GEI    L         KGY  +EY++ +  S A  ++
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 121 NGTTILGQTVTVDWC 135
           N   + GQ + V  C
Sbjct: 267 NLFDLGGQYLRVGKC 281

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.4 bits (91), Expect = 9e-05
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++ G+H    + D+ +    YG+I +    LD+ T   KGY  V++DS   A  A  AL
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

Query: 121 NGTTILGQ 128
             + +  Q
Sbjct: 64  KASGVQAQ 71

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 41.7 bits (98), Expect = 9e-05
 Identities = 15/74 (20%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +  +  E  +++ F  +G + ++ +  D  T    GY  V + +  +A  A + +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 121 NGTTILGQTVTVDW 134
           N   + G+ + + W
Sbjct: 63  NFKRLGGKPIRIMW 76

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

 Score = 38.9 bits (91), Expect = 9e-05
 Identities = 15/49 (30%), Positives = 29/49 (59%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           +FV G+  E  E+ + E F ++G I  + L +D++T   +G+  + +DS
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDS 50

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

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +     ED + E F+++GEI +  +  D  +G  +G+A V ++ +++A+ A + +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 121 NGTTI 125
           NG  I
Sbjct: 240 NGKKI 244

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 76  HEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           H+ FS YG ++ +   +  +   ++  ALV++DS + A  A+ ALNG  I     T+D
Sbjct: 19  HQVFSPYGAVEKI--LIFEKNTGVQ--ALVQFDSVESAENAKKALNGRNIYDGCCTLD 72

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

>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 13/39 (33%), Positives = 26/39 (66%)

Query: 97  GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC 135
             + G+A+VEY++ ++A   + A++GTTI G  + + +C
Sbjct: 41  SCVGGFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFC 79

This subgroup corresponds to the RRM3 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 98

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           +++    F   G +KN  +  D+RTG+  G+  V+Y S ++A  A   LNG  +  + + 
Sbjct: 14  DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIK 73

Query: 132 V 132
           V
Sbjct: 74  V 74

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

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 19/74 (25%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +     ++D+ + FS+   IK+  +  D  TG  +GY  V +   ++A  A   L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 121 NGTTILGQTVTVDW 134
               + G+ + +D 
Sbjct: 62  KNKKLHGRILRLDI 75

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 39/72 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  + E+  E+ + E F + G + N+H+  DR T   +GY  VE+ S ++A  A   +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 121 NGTTILGQTVTV 132
           N   + G+ + V
Sbjct: 61  NMIKLYGKPIRV 72

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

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 31/49 (63%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           +FV G+     EDD+ + FS++G++++  L  D++T   +G+  V ++S
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFES 50

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+  +  E+ + E FS+YGE+ +  +  D  TG  +G+  V   ++ + S+    L
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFV---TFADPSSVDKVL 57

Query: 121 N 121
            
Sbjct: 58  A 58

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           ED + + F  +G I ++ L   +  G  + +  V Y + +EA  A    N + I    +T
Sbjct: 14  EDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKIT 72

Query: 132 VDWC 135
           V+ C
Sbjct: 73  VEIC 76

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

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++  G+     E  M + FS +G+I      ++ R    KGY+ + + +++ A+ A  ++
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQI------MEIRVFPEKGYSFIRFSTHESAAHAIVSV 56

Query: 121 NGTTILGQTVTVDW 134
           NGTTI G  V   W
Sbjct: 57  NGTTIEGHVVKCYW 70

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 39.8 bits (93), Expect = 4e-04
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  + +   ++ + E FSE GEI +  + LD   G  +G+  V + + +EA+ A   +
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 121 NGTTILGQTVTV 132
           +G  + G+ + V
Sbjct: 347 HGRMLGGKPLYV 358

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

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+  + +      +++ FS +G I +  +  D   G  KGY  V +++ + A  A + +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 121 NGTTILGQTVTV 132
           NG  +  + V V
Sbjct: 64  NGMLLNDKKVFV 75

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

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

 Score = 39.9 bits (93), Expect = 4e-04
 Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++  +     ED + E    +G++K  +L  D  TG  KGYA  EY        A  AL
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 121 NGTTILGQTVTVDW-CFVKGPKKVAGEQKVGP 151
           NG       + V   C       +     + P
Sbjct: 358 NGKDTGDNKLHVQRACVGANQATIDTSNGMAP 389

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

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 7/72 (9%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           W++ +  +  +     +     ++G +   HLNL        G AL+ Y S +EA+ A+ 
Sbjct: 3   WLV-LRNLTPQIDGSTLRTLCMQHGPLLTFHLNLR------HGNALIRYSSKEEAAKAQS 55

Query: 119 ALNGTTILGQTV 130
           ALN   +   T+
Sbjct: 56  ALNNCVLGNTTL 67

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

>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of calcineurin (RCANs) and similar proteins

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 15/79 (18%)

Query: 61  LFVTGVHEEA-QEDDMHEK----FSEYGEIKNLHLNLDRRTGFLKGY--ALVEYDSYKEA 113
           L VT V  E     ++       FS YGEI            +L  +  A V + S +EA
Sbjct: 1   LIVTNVPSEVFTNAELKAALESLFSSYGEIATFV--------YLPSFRRARVVFSSPEEA 52

Query: 114 SAARDALNGTTILGQTVTV 132
           + AR  L+GT   G  + V
Sbjct: 53  ALARIELHGTVFEGSVLRV 71

This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic subunit. Overexpressed RCANs may bind and inhibit calcineurin. In contrast, low levels of phosphorylated RCANs may stimulate the calcineurin signaling. RCANs are characterized by harboring a central short, unique serine-proline motif containing FLIISPPxSPP box, which is strongly conserved from yeast to human but is absent in bacteria. They consist of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. . Length = 75

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 22/74 (29%), Positives = 37/74 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + +   ++++   F   GEI++  L  D+ TG   GY  V Y   K+A  A + L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 121 NGTTILGQTVTVDW 134
           NG  +  +T+ V +
Sbjct: 67  NGLRLQTKTIKVSY 80

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 21/74 (28%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + +   +++    F   GEI++  L  D+ TG   GY  V Y    +A  A + L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 121 NGTTILGQTVTVDW 134
           NG  +  +T+ V +
Sbjct: 66  NGLKLQTKTIKVSY 79

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

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 71  QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV 130
              D+   F   G ++ + +           +A + +++ + A  A + LNG ++ G  +
Sbjct: 12  CLSDVKRLFETCGPVRKVTMLSRTVQP----HAFITFENLEAAQLAIETLNGASVDGNCI 67

Query: 131 TV 132
            V
Sbjct: 68  KV 69

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

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 10/82 (12%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++  +  +A+E D+   F  YG+I  + L          GY  VE+D  ++A  A   L
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEVDLK--------NGYGFVEFDDLRDADDAVYEL 53

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG  + G+ V V+    +GP++
Sbjct: 54  NGKDLCGERVIVE--HARGPRR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|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 = 36.9 bits (86), Expect = 5e-04
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+     ED++   F  +GEI  + +   +  GF      V++     A AA   L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGF------VQFVHRAAAEAAIQQL 57

Query: 121 NGTTILGQTVTVDW 134
            GT I G  + + W
Sbjct: 58  QGTIIGGSRIRLSW 71

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

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 18/53 (33%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
           +FV G+  +  E+D+ + FS+YG +K + +  D R G  KGY  V +++ ++A
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDA 56

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 8/75 (10%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           G+   VT +  +A E D+++ FS  G I+++ +    R+G    YA   Y ++K+A A  
Sbjct: 5   GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEII---RSG---EYACTAYVTFKDAYALE 58

Query: 118 DA--LNGTTILGQTV 130
            A  L+G TI+ Q V
Sbjct: 59  TAVLLSGATIVDQRV 73

Length = 243

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

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 17/73 (23%), Positives = 40/73 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +  + + F+ +G++ +  + +DR TG  +G+  V ++    A+AA   +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 121 NGTTILGQTVTVD 133
           +G  + G+ + V+
Sbjct: 97  DGKELNGRHIRVN 109

Length = 144

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 37.0 bits (85), Expect = 6e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + +   +++    F   GEI++  L  D+ TG   GY  V Y   K+A  A + L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 121 NGTTILGQTVTVDW 134
           NG  +  +T+ V +
Sbjct: 65  NGLRLQTKTIKVSY 78

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

 Score = 36.7 bits (85), Expect = 6e-04
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 5/55 (9%)

Query: 79  FSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           F  YG++K L     R T   +    VE+   ++A+ A  A+NG  I G+ V ++
Sbjct: 22  FQVYGDVKEL-----RETPCKREQRFVEFFDVRDAAKALRAMNGKEISGKPVVIE 71

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

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

 Score = 36.6 bits (85), Expect = 6e-04
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 69  EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ 128
           +  EDD+ E F    EI ++ L  D+ TG  KG+  V++   +E+  A   L+GT + G+
Sbjct: 10  DITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFAD-EESLDAALKLDGTVLCGR 67

Query: 129 TVTVD 133
            + + 
Sbjct: 68  PIRIA 72

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

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.1 bits (85), Expect = 7e-04
 Identities = 20/68 (29%), Positives = 33/68 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++ G+     + D+ +    YG+I +    LD+ T   KGY  V++DS   A  A  AL
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 121 NGTTILGQ 128
             + +  Q
Sbjct: 70  KASGVQAQ 77

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 3/57 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           LFV  + +   E+D+ EKF E+G+I+ + +  D+ TG  KG+  V++  +K + AA 
Sbjct: 4   LFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF--HKPSQAAV 57

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD-A 119
           +FV G+  +  E++  E FS++G++ +  L  D  TG  +G+  V +DS  E++  R  +
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS--ESAVERVFS 59

Query: 120 LNGTTILGQTVTV 132
                + G+ V V
Sbjct: 60  AGMLELGGKQVEV 72

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

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

 Score = 36.5 bits (85), Expect = 8e-04
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +       ++ E FS++G++K+ ++  D+ TG  KGY  V + S       RD L
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSS-------RDGL 54

Query: 121 N 121
            
Sbjct: 55  E 55

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 75  MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           + + F  YG+++   +   R  G L G+A V     K A  A +  NG  I G+ V VDW
Sbjct: 18  LKKIFGRYGKVREATIPRKR-GGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76

Query: 135 CFVK 138
              K
Sbjct: 77  AVQK 80

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 36.5 bits (84), Expect = 8e-04
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           +FV G+  +  E+ + E F  +GEI+N+ L +D +T   +G+  V Y
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTY 48

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 36.6 bits (84), Expect = 9e-04
 Identities = 19/74 (25%), Positives = 36/74 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  E   +D+   F+ +G+I +  +  D  TG  KGY  V + +  +A  A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 121 NGTTILGQTVTVDW 134
            G  + G+ +  +W
Sbjct: 64  GGQWLGGRQIRTNW 77

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

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

 Score = 36.5 bits (85), Expect = 9e-04
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
            +D+H+ FS+YG++  + +  D+ T   KG A + +   ++A     ALN   + G+T+ 
Sbjct: 15  NNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLK 74

Query: 132 V 132
            
Sbjct: 75  C 75

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

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

 Score = 38.8 bits (90), Expect = 0.001
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           ++++   F+  GEI++  L  D+ TG   GY  V Y   ++A  A ++LNG  +  +T+ 
Sbjct: 17  QEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIK 76

Query: 132 V 132
           V
Sbjct: 77  V 77

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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 20/69 (28%), Positives = 36/69 (52%)

Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           EG  LF+  + +E  + ++ + F  +G + +  + +DR T   K +  V +D+   A AA
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 117 RDALNGTTI 125
             A+NG  I
Sbjct: 63  IQAMNGFQI 71

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 18/57 (31%), Positives = 30/57 (52%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           ILFV  +  +   +D+   F   G   ++ L  D++TG  KG A VE+D+ +  + A
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 24/75 (32%), Positives = 31/75 (41%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L VT +      ++  E    YG I+   L     TG  KGY  VEY     AS AR  
Sbjct: 1   LLCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60

Query: 120 LNGTTILGQTVTVDW 134
           L G  +   T+   W
Sbjct: 61  LLGKQLGESTLFAQW 75

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

>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A)

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 5/66 (7%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ILF+T + EE  E  +   F+++   K + L   R        A VE+D+  +A AAR+A
Sbjct: 7   ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAAREA 61

Query: 120 LNGTTI 125
           L G  I
Sbjct: 62  LQGFKI 67

This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), 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. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 80

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G++ EA E+ + E F E+GEI+ + L +D +T   +G+  +   ++KE    +  L
Sbjct: 7   IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFI---TFKEEDPVKKVL 63

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L V  +   A ED + E F +   I+     + +  G  KGYA VE++S ++A  A ++
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIR-----IPQNNGRPKGYAFVEFESAEDAKEALNS 57

Query: 120 LNGTTILGQTVTVDW 134
            N T I G+++ +++
Sbjct: 58  CNNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|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 = 35.9 bits (83), Expect = 0.002
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  + ++  EDD+   F  +G I+   + L    G  KG A V++ S+ EA AA +AL
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTI-LRGPDGNSKGCAFVKFSSHAEAQAAINAL 62

Query: 121 NGTTIL 126
           +G+  +
Sbjct: 63  HGSQTM 68

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           LFV  +  +  ED++ E F E+G +  + +N     G L  +  V +D 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD 54

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|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
           G +L  +GV E+   +D+ E F E+GE+  +     +  G+++     E ++ KEA    
Sbjct: 1   GCVLHFSGVGEQTSREDLKEAFEEFGEVAWVDFARGQTEGYVR---FKEENAAKEALEKL 57

Query: 118 DALNGTTILGQTVTV 132
                  I G  VTV
Sbjct: 58  KEAKNLKIKGSEVTV 72

This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 76

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 73  DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV 132
            DM +K+ E  E+K        +T    G A V +DS K A    + LN T+++G+ + V
Sbjct: 20  KDMCKKYGEVEEVKIYF---HPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKV 76

Query: 133 DWCFVKGPK 141
            +   KG  
Sbjct: 77  -FLDPKGEI 84

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>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 = 35.6 bits (83), Expect = 0.002
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 73  DDMHEKFSEYGEIKNLHL---NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT 129
           +D+ E+  +YG++ ++ +     +       G   VE+   ++A  A+ AL G    G+T
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRT 85

Query: 130 V 130
           V
Sbjct: 86  V 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|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 35.2 bits (82), Expect = 0.002
 Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 11/57 (19%)

Query: 79  FSEYGEIKNLHLNLDRRTGFLK---GYALVEYDSYKEASAARDALNGTTILGQTVTV 132
           F  YG   N+      R  FLK   G A+V+    + A  A + LNG  + GQ + V
Sbjct: 21  FCLYG---NVL-----RIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEV 69

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +      DD+H+ F  YGEIK +     R T   + +  +E+   + A AA  AL
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAALKAL 58

Query: 121 NGTTILGQTVTVD 133
           N + I G+ + ++
Sbjct: 59  NRSEIAGKRIKLE 71

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

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

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 6/102 (5%)

Query: 25  FGTETSTRNEIREYESMET-----DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKF 79
           FG+E  ++  I+    +        V    PG + S++   L+VT +     +D +   F
Sbjct: 156 FGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE-SIKDTNLYVTNLPRTITDDQLDTIF 214

Query: 80  SEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN 121
            +YG+I   ++  D+ TG  +G A V ++  +EA  A  ALN
Sbjct: 215 GKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 60  ILFVTGVHEEAQEDDMHEK----FSEYG---EIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
            L+V G+  +  E++++E     FS++G    +K +  N    T     YA V++ S + 
Sbjct: 2   TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVK-VFPNAAVATPGF--YAFVKFYSARA 58

Query: 113 ASAARDALNGTTILG 127
           AS A+ A NG  +  
Sbjct: 59  ASRAQKACNGKWLFQ 73

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 63  VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA--L 120
           V+ V  +A E D+ E FS  G+I+ + +   +        A V   ++K+   A  A  L
Sbjct: 9   VSNVSLKATERDIKEFFSFSGDIEYVEM---QSENERSQIAYV---TFKDPQGAETALLL 62

Query: 121 NGTTILGQTVTV 132
           +G TI+ Q+VT+
Sbjct: 63  SGATIVDQSVTI 74

Length = 260

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 18/73 (24%), Positives = 35/73 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  ++ + E FSE G IK   +  D+ +   +G+  V +   ++A  A +  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 121 NGTTILGQTVTVD 133
             T   G+ + V+
Sbjct: 62  KKTKFGGRKIHVE 74

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|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 13/39 (33%), Positives = 24/39 (61%)

Query: 97  GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC 135
           G LKG+A++EY+S + A   +   +G ++ G  + V +C
Sbjct: 41  GQLKGFAVLEYESAEMAEMVQQQADGLSLAGSHIRVSFC 79

This subgroup corresponds to the RRM3 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 92

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 34.7 bits (79), Expect = 0.003
 Identities = 20/74 (27%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  E   DD+   F+ +G I +  +  D  TG  KGY  V + +  +A  A   +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 121 NGTTILGQTVTVDW 134
            G  + G+ +  +W
Sbjct: 64  GGQWLGGRQIRTNW 77

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 3/47 (6%)

Query: 78  KFSEYGEIK--NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
            FS++G  K   +++ +D  TG  KGYA VE+ + +EA  A  ALNG
Sbjct: 27  IFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNG 72

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 34.8 bits (79), Expect = 0.004
 Identities = 19/68 (27%), Positives = 32/68 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++ G+     + D+ +    YG+I +    LD+ T   KGY  V++DS   A  A  +L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 121 NGTTILGQ 128
               +  Q
Sbjct: 67  KANGVQAQ 74

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|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 = 34.8 bits (80), Expect = 0.004
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL--KGYALVEYDSYKEASAARD 118
           +FV  +     E D+ E F +YG +  +++  DR       KG   V + + K A  A++
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 119 ALNGTTIL 126
           AL+    L
Sbjct: 64  ALHNMKTL 71

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

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V+ +    ++ D+ + F ++G I ++ +  + R    KG+  V + +  +A  AR+ L
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS--KGFGFVTFANSADADRAREKL 60

Query: 121 NGTTILGQTVTVD 133
           +GT + G+ + V+
Sbjct: 61  HGTVVEGRKIEVN 73

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

 Score = 34.6 bits (80), Expect = 0.004
 Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 62  FVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           FV G+  +  E+++ + FS +G +K++ +  DR  G  KGY  V +++ ++A     
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILA 61

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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V+ +     +DD+ E F+E+G +K   ++ D R+G   G A V ++   +A  A    
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQY 61

Query: 121 NGTTILGQ 128
           NG  + G+
Sbjct: 62  NGVPLDGR 69

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

 Score = 34.6 bits (80), Expect = 0.004
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +     E+ ++E F + G ++ + +  D   G  K +A V +        A   L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 121 NGTTILGQTVTVD 133
           NG  + G+ + + 
Sbjct: 63  NGIRLFGRELRIK 75

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

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+  ++  A+E D+   F  YG I+++ L         +G+  VE+D  ++A  A   L
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAVYEL 53

Query: 121 NGTTILGQTVTVD 133
           +G  +  + VT++
Sbjct: 54  DGKELCNERVTIE 66

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 34.7 bits (80), Expect = 0.004
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 69  EAQEDDMHEKFSEYGEIKNLHL-NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL- 126
           EA   ++ E FS +GE+K + L      TG  +G+  V++ + ++A  A  AL  +T L 
Sbjct: 11  EATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLY 70

Query: 127 GQTVTVDW 134
           G+ + ++W
Sbjct: 71  GRRLVLEW 78

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|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA--- 116
           ++ V+ +  +  E+D+    +E+G I N+ +         K  ALVE+ + ++A+ A   
Sbjct: 9   MIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNG----KKQALVEFATEEQATEALAC 64

Query: 117 --RDALNGTTI 125
               +LNG+TI
Sbjct: 65  KHASSLNGSTI 75

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	192
KOG0130|consensus	170		99.91
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.91
KOG0148|consensus	321		99.9
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.89
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.89
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.87
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.86
KOG0144|consensus	510		99.85
KOG0145|consensus	360		99.84
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.84
KOG0117|consensus	506		99.83
KOG0131|consensus	203		99.81
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.81
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.8
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.8
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.77
KOG0117|consensus	506		99.77
KOG0122|consensus	270		99.76
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.76
KOG0127|consensus	678		99.76
KOG0149|consensus	247		99.75
KOG0124|consensus	544		99.75
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.73
KOG0121|consensus	153		99.73
KOG0147|consensus	549		99.73
KOG0145|consensus	360		99.72
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.71
KOG4205|consensus	311		99.68
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.68
KOG0148|consensus	321		99.68
KOG0107|consensus	195		99.67
KOG0113|consensus	335		99.67
KOG0111|consensus	298		99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.66
KOG0125|consensus	376		99.65
KOG4207|consensus	256		99.64
PLN03213	759	repressor of silencing 3; Provisional	99.64
KOG0123|consensus	369		99.64
KOG0126|consensus	219		99.64
smart00362	72	RRM_2 RNA recognition motif.	99.61
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.61
KOG0114|consensus	124		99.61
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.6
KOG0110|consensus	725		99.6
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.6
PLN03121	243	nucleic acid binding protein; Provisional	99.59
KOG0108|consensus	435		99.59
smart00360	71	RRM RNA recognition motif.	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
KOG0131|consensus	203		99.56
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.54
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.54
KOG0146|consensus	371		99.53
KOG0144|consensus	510		99.52
KOG0415|consensus	479		99.5
KOG0105|consensus	241		99.48
KOG0124|consensus	544		99.47
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
smart00361	70	RRM_1 RNA recognition motif.	99.46
KOG0123|consensus	369		99.45
KOG0127|consensus	678		99.44
KOG0109|consensus	346		99.41
KOG4208|consensus	214		99.37
KOG0109|consensus	346		99.32
KOG4212|consensus	608		99.31
KOG4206|consensus	221		99.28
KOG0146|consensus	371		99.26
KOG0153|consensus	377		99.25
KOG0132|consensus	894		99.22
KOG4205|consensus	311		99.22
KOG4661|consensus	940		99.14
KOG4212|consensus	608		99.13
KOG0533|consensus	243		99.12
KOG0110|consensus	725		99.11
KOG0116|consensus	419		99.1
KOG4209|consensus	231		99.07
KOG0226|consensus	290		99.03
KOG1457|consensus	284		99.0
KOG4211|consensus	510		98.92
KOG0106|consensus	216		98.89
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.88
KOG0151|consensus	877		98.78
KOG4660|consensus	549		98.74
KOG1548|consensus	382		98.68
KOG4211|consensus	510		98.67
KOG1190|consensus	492		98.67
KOG4454|consensus	267		98.61
KOG0120|consensus	500		98.55
KOG0106|consensus	216		98.5
KOG1456|consensus	494		98.42
KOG4206|consensus	221		98.42
KOG0147|consensus	549		98.35
KOG0105|consensus	241		98.35
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.32
KOG4210|consensus	285		98.3
KOG1995|consensus	351		98.3
KOG0128|consensus	881		98.23
KOG4849|consensus	498		98.18
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.16
KOG1457|consensus	284		98.15
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.98
KOG2314|consensus	698		97.93
KOG1365|consensus	508		97.79
KOG4307|consensus	944		97.79
KOG0112|consensus	975		97.77
KOG1190|consensus	492		97.74
KOG3152|consensus	278		97.69
KOG1365|consensus	508		97.69
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.66
KOG0129|consensus	520		97.65
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.61
KOG1456|consensus	494		97.6
KOG0120|consensus	500		97.51
KOG2416|consensus	718		97.41
KOG1855|consensus	484		97.41
KOG4307|consensus	944		97.29
KOG0129|consensus	520		97.26
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.2
KOG2193|consensus	584		97.2
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.16
KOG1548|consensus	382		97.15
KOG0149|consensus	247		96.98
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.94
KOG0128|consensus	881		96.78
KOG2202|consensus	260		96.72
KOG0115|consensus	275		96.6
COG0724	306	RNA-binding proteins (RRM domain) [General functio	96.55
KOG2068|consensus	327		96.33
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.25
KOG4208|consensus	214		96.22
KOG0122|consensus	270		96.17
KOG0111|consensus	298		96.17
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.03
KOG2193|consensus	584		95.88
KOG1996|consensus	378		95.85
KOG4676|consensus	479		95.85
KOG2135|consensus	526		95.81
KOG0113|consensus	335		95.7
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.6
KOG4207|consensus	256		95.56
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	95.5
KOG4454|consensus	267		95.49
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.3
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.22
KOG0226|consensus	290		95.0
smart00361	70	RRM_1 RNA recognition motif.	94.94
KOG0112|consensus	975		94.88
KOG4660|consensus	549		94.81
KOG4210|consensus	285		94.77
KOG0126|consensus	219		94.27
KOG2253|consensus	668		94.18
KOG4285|consensus	350		93.96
KOG4574|consensus	1007		93.2
KOG0125|consensus	376		92.64
KOG2591|consensus	684		91.86
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	90.43
KOG0804|consensus	493		88.59
smart00360	71	RRM RNA recognition motif.	87.51
KOG2318|consensus	650		86.82
KOG0108|consensus	435		86.18
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	83.63
KOG4483|consensus	528		82.67

>KOG0130|consensus

Probab=99.91  E-value=7.3e-25  Score=152.17  Aligned_cols=133  Identities=67%  Similarity=1.173  Sum_probs=117.5

Q ss_pred             EeeccCcCCCCCCccCCCCC-hhHHHhhhcccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEE
Q psy15152         12 RLKEKARKKKGRGFGTETST-RNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHL   90 (192)
Q Consensus        12 ~~~d~~~~~k~rG~gfv~f~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i   90 (192)
                      ..+.++.++|+||||..+-. ......|+..+.+++...|+|+++.+++.|||.+++...+++++.+.|..||+|+.+.+
T Consensus        25 ~~~e~Akk~kGRGf~~e~~sr~r~r~~yd~vee~~s~~~pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihL  104 (170)
T KOG0130|consen   25 GLKEKAKKRKGRGFGSEKDSRRRRRLSYDDVEEDGSDMRPGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHL  104 (170)
T ss_pred             HHHHHHHhhcCCCcccccchHHHhhhhhhhHhhcccccCCCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceee
Confidence            34466777789999987663 33344577778888778999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCCCCC
Q psy15152         91 NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVA  144 (192)
Q Consensus        91 ~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~~~~  144 (192)
                      ..|+.||..+|||+|+|.+.++|++|+..|||..|.|+.|.|.|+..+++.+..
T Consensus       105 NLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~gp~~g~  158 (170)
T KOG0130|consen  105 NLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKGPERGK  158 (170)
T ss_pred             ccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecCCccCc
Confidence            999999999999999999999999999999999999999999999987765444

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.91  E-value=1.6e-23  Score=171.67  Aligned_cols=133  Identities=21%  Similarity=0.273  Sum_probs=106.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCC---CCCCCCC----CCCCCCCcEEEEcCCCCCCcHHHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETD---VGDEEPG----PQRSVEGWILFVTGVHEEAQEDDMHE   77 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~---~~~~~~~----~~~~~~~~~l~V~nLp~~~t~~~L~~   77 (192)
                      +++|++++|+.+++ +|||+||+|..++  ..++..++..   +......    .......++|||+|||+++++++|++
T Consensus       134 V~~v~i~~d~~tg~-srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~  212 (346)
T TIGR01659       134 INTCRIMRDYKTGY-SFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDT  212 (346)
T ss_pred             EEEEEEEecCCCCc-cCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccccccccccceeEEeCCCCcccHHHHHH
Confidence            57899999999996 9999999994433  3333333322   1111110    11223467899999999999999999


Q ss_pred             hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEecccCCC
Q psy15152         78 KFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVDWCFVKGP  140 (192)
Q Consensus        78 ~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a~~~~~  140 (192)
                      +|++||.|..+.++.|+.+|+++|||||+|.+.++|++||+.||+..+.+  ++|+|+++.....
T Consensus       213 ~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       213 IFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             HHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            99999999999999999999999999999999999999999999999876  7999999986544

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

>KOG0148|consensus

Probab=99.90  E-value=5.1e-23  Score=158.04  Aligned_cols=127  Identities=22%  Similarity=0.347  Sum_probs=107.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCC--ChhHHHhhhcccCC--------CCCCCCC---------------CCCCCCCcEE
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETS--TRNEIREYESMETD--------VGDEEPG---------------PQRSVEGWIL   61 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f--~~~~~~~~~~~~~~--------~~~~~~~---------------~~~~~~~~~l   61 (192)
                      +.+.++++|..|+ ||+|||||+|  ..++..++..+++.        -+|...+               .+.+.+.++|
T Consensus        89 vS~akvirD~~T~-KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsV  167 (321)
T KOG0148|consen   89 VSDAKVIRDMNTG-KSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSV  167 (321)
T ss_pred             cccceEeecccCC-cccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceE
Confidence            4578899999999 7999999999  56666677776554        1111111               2456778999


Q ss_pred             EEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCC
Q psy15152         62 FVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP  140 (192)
Q Consensus        62 ~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~  140 (192)
                      ||||++..+++++|++.|++||.|.+|++..+      +||+||.|+++|+|..||..+|+..|.|+.+++.|.+....
T Consensus       168 Y~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  168 YVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             EeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            99999999999999999999999999999988      58999999999999999999999999999999999986554

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.89  E-value=1.5e-22  Score=166.93  Aligned_cols=81  Identities=27%  Similarity=0.445  Sum_probs=78.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      .+|||+|||+++++++|+++|++||.|.+++|+.|+.||.++|||||+|.+.++|.+|+..|||..|+|+.|+|.|+..+
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q psy15152        139 G  139 (192)
Q Consensus       139 ~  139 (192)
                      .
T Consensus       350 ~  350 (352)
T TIGR01661       350 A  350 (352)
T ss_pred             C
Confidence            4

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

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.89  E-value=1.3e-22  Score=175.14  Aligned_cols=134  Identities=25%  Similarity=0.325  Sum_probs=107.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccC---CCCCCCCC-----C----------CCCCCCcEEEEcCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMET---DVGDEEPG-----P----------QRSVEGWILFVTGV   66 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~---~~~~~~~~-----~----------~~~~~~~~l~V~nL   66 (192)
                      +.+|.+++|+.+++ +||||||+|...+  ..++..++.   .+......     +          ......++|||+||
T Consensus       134 I~sV~I~~D~~Tgk-skGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnL  212 (612)
T TIGR01645       134 IKSINMSWDPATGK-HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASV  212 (612)
T ss_pred             EEEEEEeecCCCCC-cCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecC
Confidence            56899999999995 9999999994443  333333322   12111000     0          01123478999999


Q ss_pred             CCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCC
Q psy15152         67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK  141 (192)
Q Consensus        67 p~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~  141 (192)
                      |+++++++|+++|+.||.|.++++..|+.+|+++|||||+|.+.++|.+|++.||+..|+|+.|+|.++.+++..
T Consensus       213 p~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       213 HPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             CCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccc
Confidence            999999999999999999999999999989999999999999999999999999999999999999999875543

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.

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

Probab=99.87  E-value=5.3e-21  Score=138.78  Aligned_cols=87  Identities=20%  Similarity=0.427  Sum_probs=81.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ...+++|||+|||+++++++|+++|++||.|.++.++.|+.+++++|||||+|.+.++|++|++.|++..|.|+.|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      +.++...
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9866543

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.86  E-value=9.4e-21  Score=161.44  Aligned_cols=131  Identities=18%  Similarity=0.376  Sum_probs=104.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCC-ChhHHHhhhcccCC---CCC----------------CCCCCCCCCCCcEEEEcC
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETS-TRNEIREYESMETD---VGD----------------EEPGPQRSVEGWILFVTG   65 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f-~~~~~~~~~~~~~~---~~~----------------~~~~~~~~~~~~~l~V~n   65 (192)
                      .+.+|.+++|+.++. ++|||||+| +.+.+..+..++..   +..                ............+|||+|
T Consensus       115 ~v~~v~i~~d~~~~~-skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~n  193 (457)
T TIGR01622       115 KVRDVQCIKDRNSRR-SKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGN  193 (457)
T ss_pred             CeeEEEEeecCCCCC-cceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcC
Confidence            357899999999995 999999999 33333222222211   100                000011112357899999


Q ss_pred             CCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         66 VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        66 Lp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ||..+++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|++.|+|..|.|+.|.|.|+..
T Consensus       194 l~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       194 LHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            999999999999999999999999999998999999999999999999999999999999999999999763

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.

>KOG0144|consensus

Probab=99.85  E-value=1.3e-21  Score=158.51  Aligned_cols=136  Identities=25%  Similarity=0.340  Sum_probs=108.3

Q ss_pred             eeeEEeeccCcCCCCCCccCCCC-C-hhHHHhhhcccC----CC-------CCCCCCCCCCCCCcEEEEcCCCCCCcHHH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETS-T-RNEIREYESMET----DV-------GDEEPGPQRSVEGWILFVTGVHEEAQEDD   74 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f-~-~~~~~~~~~~~~----~~-------~~~~~~~~~~~~~~~l~V~nLp~~~t~~~   74 (192)
                      -.|.+++|+.|+. ++|++||.| . .++..+..++..    .|       ...+....+-.+.++||||-|+..++|.+
T Consensus        62 ~einl~kDk~t~~-s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~e  140 (510)
T KOG0144|consen   62 YEINLIKDKSTGQ-SKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENE  140 (510)
T ss_pred             eEEEeecccccCc-ccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhccccchhhhhhhccccccHHH
Confidence            4789999999996 999999999 3 333333333311    11       11111122334578899999999999999


Q ss_pred             HHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe-eCC--eEEEEEecccCCCCCCCC
Q psy15152         75 MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT-ILG--QTVTVDWCFVKGPKKVAG  145 (192)
Q Consensus        75 L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~-~~g--~~l~v~~a~~~~~~~~~~  145 (192)
                      ++++|++||.|++|.|++|. .|.+||||||.|.+++.|..|++.|||.. +.|  .+|.|+||.++.++..+.
T Consensus       141 vr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~  213 (510)
T KOG0144|consen  141 VREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKR  213 (510)
T ss_pred             HHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchHHH
Confidence            99999999999999999996 89999999999999999999999999986 544  699999999987766553

>KOG0145|consensus

Probab=99.84  E-value=6.3e-21  Score=146.03  Aligned_cols=133  Identities=21%  Similarity=0.397  Sum_probs=109.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCCh--hHHHhhhcccCC--------CCCCCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTR--NEIREYESMETD--------VGDEEPGPQRSVEGWILFVTGVHEEAQEDDM   75 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~--~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L   75 (192)
                      +++++++++|+.++. |-|||||.|.+  ++..+...+++-        .+...|. .....+..|||++||..+|..+|
T Consensus        67 eiEScKLvRDKitGq-SLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPS-s~~Ik~aNLYvSGlPktMtqkel  144 (360)
T KOG0145|consen   67 EIESCKLVRDKITGQ-SLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPS-SDSIKDANLYVSGLPKTMTQKEL  144 (360)
T ss_pred             ceeeeeeeecccccc-ccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCC-hhhhcccceEEecCCccchHHHH
Confidence            478999999999997 99999999933  334444443322        2223333 33456678999999999999999


Q ss_pred             HHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEecccCCC
Q psy15152         76 HEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVDWCFVKGP  140 (192)
Q Consensus        76 ~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a~~~~~  140 (192)
                      +++|++||.|...+|+.|..||.+||.|||.|+.+++|+.||..|||..-.|  .+|.|+||.....
T Consensus       145 E~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  145 EQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             HHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence            9999999999999999999999999999999999999999999999998766  5899999976543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.84  E-value=4.3e-20  Score=152.33  Aligned_cols=131  Identities=25%  Similarity=0.412  Sum_probs=105.2

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCC---CCCC-----CCCCCCCCCCcEEEEcCCCCCCcHHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETD---VGDE-----EPGPQRSVEGWILFVTGVHEEAQEDDMH   76 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~---~~~~-----~~~~~~~~~~~~l~V~nLp~~~t~~~L~   76 (192)
                      +.+|.+++|+.+++ +||||||+|...+  ..++..++..   +...     .+ ........+|||+|||..+++++|+
T Consensus        30 i~~v~i~~d~~~g~-s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~-~~~~~~~~~l~v~~l~~~~~~~~l~  107 (352)
T TIGR01661        30 IESCKLVRDKVTGQ-SLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP-SSDSIKGANLYVSGLPKTMTQHELE  107 (352)
T ss_pred             EEEEEEEEcCCCCc-cceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc-cccccccceEEECCccccCCHHHHH
Confidence            57899999999995 9999999994433  3333333322   1111     11 1122346789999999999999999


Q ss_pred             HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEecccCC
Q psy15152         77 EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVDWCFVKG  139 (192)
Q Consensus        77 ~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a~~~~  139 (192)
                      ++|++||.|..+.++.+..+|.++|||||+|.+.++|+.|++.|||..+.|  .+|.|.|+....
T Consensus       108 ~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       108 SIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            999999999999999998889999999999999999999999999999887  678999887554

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

>KOG0117|consensus

Probab=99.83  E-value=1.4e-20  Score=153.14  Aligned_cols=130  Identities=21%  Similarity=0.305  Sum_probs=108.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHhhhcccCC------------CCCCCCC----CCCCCCCcEEEEcCCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETD------------VGDEEPG----PQRSVEGWILFVTGVHEEA   70 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~~------------~~~~~~~----~~~~~~~~~l~V~nLp~~~   70 (192)
                      .++|.+..++..+.|+|||+||+|..+..+++....+-            ..|.+|.    ......-..|||+||+.++
T Consensus       192 VvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~t  271 (506)
T KOG0117|consen  192 VVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMEST  271 (506)
T ss_pred             eeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhh
Confidence            46888999999998999999999987887777665332            1333332    2223334789999999999


Q ss_pred             cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCCCCC
Q psy15152         71 QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVA  144 (192)
Q Consensus        71 t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~~~~  144 (192)
                      |++.|+++|.+||.|.+|+.++|        ||||.|.++++|.+|++.+||..|+|..|.|.+|+|...++..
T Consensus       272 TeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  272 TEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             hHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhccc
Confidence            99999999999999999988766        9999999999999999999999999999999999987654443

>KOG0131|consensus

Probab=99.81  E-value=2.4e-20  Score=135.82  Aligned_cols=135  Identities=23%  Similarity=0.364  Sum_probs=109.8

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhHHHhhhcc--cC---CC-----CCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNEIREYESM--ET---DV-----GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHE   77 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~--~~---~~-----~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~   77 (192)
                      .++.+.+|+.+. +++||||++|..++.++|+-.  ++   .+     ++..........+.++||+||.+.+++..|.+
T Consensus        37 v~i~iPkDrv~~-~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~d  115 (203)
T KOG0131|consen   37 VNLHIPKDRVTQ-KHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYD  115 (203)
T ss_pred             eeeecchhhhcc-cccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccccccccccccccccccCcchhHHHHHH
Confidence            578999999999 599999999955555555432  21   11     12222222334468899999999999999999


Q ss_pred             hhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCCCC
Q psy15152         78 KFSEYGEIKN-LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKV  143 (192)
Q Consensus        78 ~F~~~G~i~~-~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~~~  143 (192)
                      .|+.||.+.. -++++++.||.++|||||.|.+.+.+.+|+..|+|..+.++++.|.++..+..+..
T Consensus       116 tFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg~  182 (203)
T KOG0131|consen  116 TFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKGE  182 (203)
T ss_pred             HHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCcc
Confidence            9999999865 48899999999999999999999999999999999999999999999987766553

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

Probab=99.81  E-value=2.3e-19  Score=156.61  Aligned_cols=130  Identities=23%  Similarity=0.384  Sum_probs=101.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH--HhhhcccC---C----CCCC-----CCCC-----------------CCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI--REYESMET---D----VGDE-----EPGP-----------------QRS   55 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~--~~~~~~~~---~----~~~~-----~~~~-----------------~~~   55 (192)
                      +.++.+++|. ++ ++||||||+|...+.  .+...++.   .    +...     ....                 ...
T Consensus       205 i~~~~i~~~~-~g-~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~  282 (562)
T TIGR01628       205 ITSAAVMKDG-SG-RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK  282 (562)
T ss_pred             EEEEEEEECC-CC-CcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcc
Confidence            5678888885 46 499999999943332  23332221   1    1000     0000                 012


Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..+.+|||+||+.++++++|+++|+.||.|.+++++.| .+|.++|||||+|.+.++|.+|+..|||..+.|++|.|.+|
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            34578999999999999999999999999999999999 58999999999999999999999999999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            8653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.80  E-value=1.1e-18  Score=150.49  Aligned_cols=113  Identities=23%  Similarity=0.339  Sum_probs=87.2

Q ss_pred             CCCCccCCCCChhHHHhhhc--cc-----CCC-----CCCCCC----CCCCCCCcEEEEcCCCCCCcHHHHHHhhccC--
Q psy15152         21 KGRGFGTETSTRNEIREYES--ME-----TDV-----GDEEPG----PQRSVEGWILFVTGVHEEAQEDDMHEKFSEY--   82 (192)
Q Consensus        21 k~rG~gfv~f~~~~~~~~~~--~~-----~~~-----~~~~~~----~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~--   82 (192)
                      ++|||+||+|..++.+..+.  +.     ..+     .+..+.    +......++|||+||++++++++|+++|+.|  
T Consensus       180 KnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~  259 (578)
T TIGR01648       180 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKP  259 (578)
T ss_pred             ccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCC
Confidence            69999999995544433322  21     111     111221    1122345789999999999999999999999  


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCC
Q psy15152         83 GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK  141 (192)
Q Consensus        83 G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~  141 (192)
                      |.|.+|.++        ++||||+|.+.++|++|++.||+..|.|+.|+|.||.+....
T Consensus       260 G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       260 GKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             CceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcc
Confidence            999999765        459999999999999999999999999999999999886543

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=99.80  E-value=4.4e-19  Score=154.83  Aligned_cols=130  Identities=20%  Similarity=0.341  Sum_probs=104.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCCh--hHHHhhhcccCC---CC-----CCCCCC-CCCCCCcEEEEcCCCCCCcHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTR--NEIREYESMETD---VG-----DEEPGP-QRSVEGWILFVTGVHEEAQEDDM   75 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~--~~~~~~~~~~~~---~~-----~~~~~~-~~~~~~~~l~V~nLp~~~t~~~L   75 (192)
                      +.+|.+++|+.|++ ++|||||+|..  ++..+++.++..   +.     +....+ .+.....+|||+|||.++++++|
T Consensus        27 v~~v~v~~d~~t~~-s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L  105 (562)
T TIGR01628        27 VLSVRVCRDSVTRR-SLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKAL  105 (562)
T ss_pred             EEEEEEEecCCCCC-cceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccccccccCCCceEEcCCCccCCHHHH
Confidence            57899999999995 99999999933  444444444333   11     111111 11223457999999999999999


Q ss_pred             HHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         76 HEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        76 ~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      +++|+.||.|..+++..+. +|+++|||||+|.+.++|++|++.|+|..+.|+.|.|.....+
T Consensus       106 ~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628       106 FDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             HHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            9999999999999999985 8999999999999999999999999999999999999766544

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=3.6e-18  Score=140.23  Aligned_cols=86  Identities=23%  Similarity=0.381  Sum_probs=80.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ......++|||+|||+++++++|+++|+.||.|.+|+|+.|+.+++++|||||+|.+.++|++|++.|++..+.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecccC
Q psy15152        133 DWCFVK  138 (192)
Q Consensus       133 ~~a~~~  138 (192)
                      .|+.+.
T Consensus       182 ~~a~p~  187 (346)
T TIGR01659       182 SYARPG  187 (346)
T ss_pred             eccccc
Confidence            998754

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).

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.77  E-value=3e-18  Score=147.87  Aligned_cols=82  Identities=27%  Similarity=0.383  Sum_probs=78.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..+|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|+|..|.|+.|.|.++..
T Consensus       295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            47899999999999999999999999999999999998999999999999999999999999999999999999999975


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      ..
T Consensus       375 ~~  376 (509)
T TIGR01642       375 GA  376 (509)
T ss_pred             CC
Confidence            43

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0117|consensus

Probab=99.77  E-value=2.5e-18  Score=140.19  Aligned_cols=134  Identities=21%  Similarity=0.316  Sum_probs=104.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHhhhcccCCCCCCCCCC----CCCCCCcEEEEcCCCCCCcHHHHHHhhccC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGP----QRSVEGWILFVTGVHEEAQEDDMHEKFSEY   82 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~   82 (192)
                      |-++++|+|+.++. +|||+||+|...+.+..+....++....++.    ..+...++|||||+|...++++|.+.+++.
T Consensus       110 I~elRLMmD~~sG~-nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kV  188 (506)
T KOG0117|consen  110 IYELRLMMDPFSGD-NRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKV  188 (506)
T ss_pred             eeeEEEeecccCCC-CcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhh
Confidence            45789999999995 9999999994444333333333333344442    346778999999999999999999999998


Q ss_pred             CC-eeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHHhCCC--eeCCeEEEEEecccCCCC
Q psy15152         83 GE-IKNLHLNLDRR-TGFLKGYALVEYDSYKEASAARDALNGT--TILGQTVTVDWCFVKGPK  141 (192)
Q Consensus        83 G~-i~~~~i~~~~~-tg~~~g~afV~f~~~~~a~~al~~l~~~--~~~g~~l~v~~a~~~~~~  141 (192)
                      ++ |.+|.+..++. ..++||||||+|.++..|..|-++|-..  .+.|..+.|+||.+....
T Consensus       189 teGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~  251 (506)
T KOG0117|consen  189 TEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEP  251 (506)
T ss_pred             CCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCC
Confidence            75 66776655553 6789999999999999999999887443  478999999999987543

>KOG0122|consensus

Probab=99.76  E-value=2.6e-18  Score=130.48  Aligned_cols=83  Identities=31%  Similarity=0.499  Sum_probs=80.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|-|.||+.++++++|+++|.+||.|.++.+.+|+.||.++|||||.|.++++|.+||..|||.-++.-.|+|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      .|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            875

>PF00076 RRM_1: RNA recognition motif

Probab=99.76  E-value=9.1e-18  Score=106.63  Aligned_cols=70  Identities=31%  Similarity=0.638  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++..+|+|||+|.+.++|++|++.|+|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 5899999999999999999999999999999999885

(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 ....

>KOG0127|consensus

Probab=99.76  E-value=7e-18  Score=140.52  Aligned_cols=130  Identities=25%  Similarity=0.448  Sum_probs=101.1

Q ss_pred             eeEEeeccCcCCCCCCccCCCC--ChhHHHhhhcccC---CC-------------CC-CCC---------CCC-----C-
Q psy15152          9 GIARLKEKARKKKGRGFGTETS--TRNEIREYESMET---DV-------------GD-EEP---------GPQ-----R-   54 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f--~~~~~~~~~~~~~---~~-------------~~-~~~---------~~~-----~-   54 (192)
                      ...+..++.+++ +||||||+|  ..+...++...+.   .+             +. ..+         ..+     . 
T Consensus        34 ~~~vVt~~gs~~-~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~  112 (678)
T KOG0127|consen   34 HAVVVTNKGSSE-KRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAK  112 (678)
T ss_pred             eeEEecCCCccc-ccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccccchhhhcccccCCcchhh
Confidence            456778889987 999999999  3333333333322   11             00 000         001     0 


Q ss_pred             -CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         55 -SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        55 -~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                       ..+.++|.|+||||.+.+.+|+.+|+.||.|..|.|++.+ .|+-+|||||+|....+|..|++.+|+..|+|++|.|+
T Consensus       113 v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVD  191 (678)
T KOG0127|consen  113 VDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVD  191 (678)
T ss_pred             ccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEe
Confidence             1236899999999999999999999999999999999886 56666999999999999999999999999999999999


Q ss_pred             ecccCCC
Q psy15152        134 WCFVKGP  140 (192)
Q Consensus       134 ~a~~~~~  140 (192)
                      ||.++..
T Consensus       192 WAV~Kd~  198 (678)
T KOG0127|consen  192 WAVDKDT  198 (678)
T ss_pred             eeccccc
Confidence            9987754

>KOG0149|consensus

Probab=99.75  E-value=8e-18  Score=127.30  Aligned_cols=82  Identities=24%  Similarity=0.386  Sum_probs=75.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .-++||||+|+|.+..++|+++|++||+|.+..++.|+.||++||||||+|.+.++|.+|++- .+-.|+||+..+.+|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            347899999999999999999999999999999999999999999999999999999999985 6678999999999987


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      -..
T Consensus        90 lg~   92 (247)
T KOG0149|consen   90 LGG   92 (247)
T ss_pred             hcC
Confidence            633

>KOG0124|consensus

Probab=99.75  E-value=6.1e-18  Score=135.14  Aligned_cols=133  Identities=24%  Similarity=0.318  Sum_probs=107.9

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHH--hhhcccCC---CCCCCCCCCCCC---------------CCcEEEEcCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIR--EYESMETD---VGDEEPGPQRSV---------------EGWILFVTGV   66 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~--~~~~~~~~---~~~~~~~~~~~~---------------~~~~l~V~nL   66 (192)
                      |++|++.+|+.|+ |++||+||+|+.++.+  +.+.+++.   |.....+.....               .-++|||..+
T Consensus       140 IKSInMSWDp~T~-kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSv  218 (544)
T KOG0124|consen  140 IKSINMSWDPATG-KHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASV  218 (544)
T ss_pred             cceeecccccccc-cccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeec
Confidence            5799999999999 6999999999655543  33444332   222222211111               1268999999


Q ss_pred             CCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCC
Q psy15152         67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP  140 (192)
Q Consensus        67 p~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~  140 (192)
                      +++.+++||+.+|..||+|..|.+.+++.++.++||||++|.+..+...|+..||-..++|+.|+|..+...+.
T Consensus       219 HpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~  292 (544)
T KOG0124|consen  219 HPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD  292 (544)
T ss_pred             CCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCc
Confidence            99999999999999999999999999998899999999999999999999999999999999999987765543

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.73  E-value=3e-17  Score=141.65  Aligned_cols=129  Identities=23%  Similarity=0.380  Sum_probs=96.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCCCCCCCC----CCCCCCCCcEEEEcCCCCCCcHHHHHHhhc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETDVGDEEP----GPQRSVEGWILFVTGVHEEAQEDDMHEKFS   80 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~~~~~~~----~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~   80 (192)
                      +.++++++| .+++ +|||+||+|...+  ..++..++...  ..+    ....+...++|||+|||.++++++|.+.|+
T Consensus        85 I~~vrl~~D-~sG~-sRGfaFV~F~~~e~A~~Ai~~lng~~--i~~Gr~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFs  160 (578)
T TIGR01648        85 IYELRLMMD-FSGQ-NRGYAFVTFCGKEEAKEAVKLLNNYE--IRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFS  160 (578)
T ss_pred             EEEEEEEEC-CCCC-ccceEEEEeCCHHHHHHHHHHcCCCe--ecCCccccccccccCceeEeecCCcchhhHHHHHHhh
Confidence            568899999 7885 9999999994443  33444443221  111    122344578999999999999999999999


Q ss_pred             cCCC-eeEEEE-eecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEEecccCC
Q psy15152         81 EYGE-IKNLHL-NLDRRTGFLKGYALVEYDSYKEASAARDALNG--TTILGQTVTVDWCFVKG  139 (192)
Q Consensus        81 ~~G~-i~~~~i-~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~--~~~~g~~l~v~~a~~~~  139 (192)
                      +++. +.++.+ .....+++++|||||+|.++++|..|++.|+.  ..+.|+.|.|+|+.+..
T Consensus       161 kv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       161 KVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             cccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccc
Confidence            9864 444433 23334678899999999999999999998864  35889999999998764

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.

>KOG0121|consensus

Probab=99.73  E-value=9.6e-18  Score=115.76  Aligned_cols=83  Identities=25%  Similarity=0.402  Sum_probs=78.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..+++||||||.+.++|++|.++|+..|+|..|.+-.|+.+..+.|||||+|.+.++|+.|++.++|..++.++|+++|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ..-
T Consensus       114 ~GF  116 (153)
T KOG0121|consen  114 AGF  116 (153)
T ss_pred             ccc
Confidence            543

>KOG0147|consensus

Probab=99.73  E-value=7.7e-18  Score=140.39  Aligned_cols=129  Identities=18%  Similarity=0.309  Sum_probs=105.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCC-ChhHHHhhhcccCCC----------------------CCCCCCCCCCCCCcEEE
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETS-TRNEIREYESMETDV----------------------GDEEPGPQRSVEGWILF   62 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f-~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~l~   62 (192)
                      ++.+|.++.|+.+++ ++|.+||+| +.+......++.+..                      .+..++ .-..+...||
T Consensus       205 kVrdVriI~Dr~s~r-skgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k-~~~~p~~rl~  282 (549)
T KOG0147|consen  205 KVRDVRIIGDRNSRR-SKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEKNRAANASPALQGK-GFTGPMRRLY  282 (549)
T ss_pred             CcceeEeeccccchh-hcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHHHHHHhcccccccc-ccccchhhhh
Confidence            567999999999998 999999999 655555444544331                      001101 1112233499


Q ss_pred             EcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         63 VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        63 V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ||||++.+++++|+.+|.+||.|..|.+.+|..||.++|||||+|.+.++|.+|++.|||..|.|+.|+|..-.
T Consensus       283 vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  283 VGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            99999999999999999999999999999998899999999999999999999999999999999999997554

>KOG0145|consensus

Probab=99.72  E-value=4.5e-17  Score=124.99  Aligned_cols=82  Identities=28%  Similarity=0.482  Sum_probs=78.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+++|||-||.++.+|.-|+++|.+||.|..+++++|..|.+.+|||||...+.++|..|+..|||..++++.|.|.|..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            36899999999999999999999999999999999999899999999999999999999999999999999999999876


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      .+
T Consensus       357 nk  358 (360)
T KOG0145|consen  357 NK  358 (360)
T ss_pred             CC
Confidence            54

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.71  E-value=1.6e-16  Score=101.26  Aligned_cols=70  Identities=27%  Similarity=0.579  Sum_probs=65.1

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      |||+|||+++++++|.++|+.||.|..+.+..++. |..+|+|||+|.+.++|++|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999976 99999999999999999999999999999999885

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 ....

>KOG4205|consensus

Probab=99.68  E-value=1.4e-16  Score=127.94  Aligned_cols=137  Identities=20%  Similarity=0.320  Sum_probs=110.8

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH-H---hhhcccCCCCCCCCCCCCC----------CCCcEEEEcCCCCCCc
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI-R---EYESMETDVGDEEPGPQRS----------VEGWILFVTGVHEEAQ   71 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~-~---~~~~~~~~~~~~~~~~~~~----------~~~~~l~V~nLp~~~t   71 (192)
                      .+.+..+++|+.++| +|||+||+|+.+.. .   ....+.+++...++.++.+          ....++||++||.+++
T Consensus        32 ev~d~~vm~d~~t~r-srgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~  110 (311)
T KOG4205|consen   32 EVTDCVVMRDPSTGR-SRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTT  110 (311)
T ss_pred             ceeeEEEeccCCCCC-cccccceecCCCcchheeecccccccCCccccceeccCcccccccccccceeEEEecCcCCCCc
Confidence            356789999999997 99999999964432 2   2223345554444443222          1245899999999999


Q ss_pred             HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCCCCC
Q psy15152         72 EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVA  144 (192)
Q Consensus        72 ~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~~~~  144 (192)
                      +++++++|.+||.|..+.+++|..+.+++||+||.|.+.+++.+++. ..-+.|.|+.+.|..|.|+......
T Consensus       111 e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  111 EEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             hHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhcccc
Confidence            99999999999999999999999999999999999999999999887 4788899999999999988765544

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.68  E-value=1.7e-16  Score=137.42  Aligned_cols=80  Identities=29%  Similarity=0.466  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|++||.|.++.++.|+.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999998654

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

Probab=99.68  E-value=1.1e-16  Score=123.35  Aligned_cols=82  Identities=26%  Similarity=0.490  Sum_probs=79.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..-+||+.|...++.++|++.|.+||+|.++++++|..|+++||||||.|.+.++|+.||..|||..|++|.|+..||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            76

>KOG0107|consensus

Probab=99.67  E-value=2.7e-16  Score=114.12  Aligned_cols=78  Identities=22%  Similarity=0.451  Sum_probs=72.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++||||||+..+++.+|+..|..||.+..+.|...+     .|||||+|+++.+|+.|+..|+|..|.|..|+|+++..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            5789999999999999999999999999999998765     79999999999999999999999999999999999876


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      ...
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            543

>KOG0113|consensus

Probab=99.67  E-value=7.9e-16  Score=120.04  Aligned_cols=89  Identities=30%  Similarity=0.431  Sum_probs=82.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+-+||||+-|+.+++|..|+..|+.||.|..|+|+.|+.||+++|||||+|....+...|.+..+|..|+|+.|.|+
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            34667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCCCC
Q psy15152        134 WCFVKGPKK  142 (192)
Q Consensus       134 ~a~~~~~~~  142 (192)
                      +....-.+.
T Consensus       177 vERgRTvkg  185 (335)
T KOG0113|consen  177 VERGRTVKG  185 (335)
T ss_pred             ecccccccc
Confidence            886554443

>KOG0111|consensus

Probab=99.66  E-value=9.5e-17  Score=120.47  Aligned_cols=89  Identities=27%  Similarity=0.516  Sum_probs=83.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++||||+|..++++.-|...|-+||.|.+|.++.|..++++||||||+|...|+|.+||..||+..|.|+.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCC
Q psy15152        136 FVKGPKKVA  144 (192)
Q Consensus       136 ~~~~~~~~~  144 (192)
                      .|..-+...
T Consensus        88 kP~kikegs   96 (298)
T KOG0111|consen   88 KPEKIKEGS   96 (298)
T ss_pred             CCccccCCC
Confidence            987655444

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.66  E-value=9.6e-16  Score=119.32  Aligned_cols=77  Identities=27%  Similarity=0.272  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+.+++++|+++|+.||.|.++.|+.++.   .+|||||+|.+.++|+.|+. |+|..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            56899999999999999999999999999999998863   47899999999999999996 999999999999999864


Q ss_pred             C
Q psy15152        138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      -
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>KOG0125|consensus

Probab=99.65  E-value=6.9e-16  Score=121.75  Aligned_cols=81  Identities=20%  Similarity=0.363  Sum_probs=75.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|+|+...+.||+.+|.+||.|.+|.|+.+.  ..+||||||+|++.++|++|-++|||..+.||+|.|..|..
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            3789999999999999999999999999999999883  55799999999999999999999999999999999999987


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      +-.
T Consensus       174 rV~  176 (376)
T KOG0125|consen  174 RVH  176 (376)
T ss_pred             hhc
Confidence            643

>KOG4207|consensus

Probab=99.64  E-value=3.4e-16  Score=116.42  Aligned_cols=89  Identities=25%  Similarity=0.407  Sum_probs=81.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      |........|-|-||.+.++.++|+.+|++||.|-+|.|+.|+.|+.++|||||-|....+|+.|+++|+|.+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            33344457899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecccCCC
Q psy15152        132 VDWCFVKGP  140 (192)
Q Consensus       132 v~~a~~~~~  140 (192)
                      |.+|.-...
T Consensus        87 Vq~arygr~   95 (256)
T KOG4207|consen   87 VQMARYGRP   95 (256)
T ss_pred             ehhhhcCCC
Confidence            998875443

>PLN03213 repressor of silencing 3; Provisional

Probab=99.64  E-value=9.2e-16  Score=126.93  Aligned_cols=78  Identities=21%  Similarity=0.370  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCH--HHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY--KEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~--~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      .+.+||||||++.+++++|..+|+.||.|.++.|+  +.+|  ||||||+|.+.  .++.+||..|||..++|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            34689999999999999999999999999999999  4577  99999999987  789999999999999999999998


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8653

>KOG0123|consensus

Probab=99.64  E-value=1.7e-15  Score=125.24  Aligned_cols=126  Identities=23%  Similarity=0.381  Sum_probs=102.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCC--ChhHHHhhhcccCCCCCCCCC---CCCCCCCcEEEEcCCCCCCcHHHHHHhhcc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETS--TRNEIREYESMETDVGDEEPG---PQRSVEGWILFVTGVHEEAQEDDMHEKFSE   81 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f--~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~   81 (192)
                      ..+|++.+|. |   +-|||||.|  -.++..+++.++...-...+-   .... +...+||.||+++++..+|.++|+.
T Consensus        25 v~s~rvc~d~-t---slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r-d~~~~~i~nl~~~~~~~~~~d~f~~   99 (369)
T KOG0123|consen   25 VLSIRVCRDA-T---SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR-DPSLVFIKNLDESIDNKSLYDTFSE   99 (369)
T ss_pred             ceeEEEeecC-C---ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc-CCceeeecCCCcccCcHHHHHHHHh
Confidence            4689999999 7   899999999  445566667776654222221   1111 1223999999999999999999999


Q ss_pred             CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCC
Q psy15152         82 YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP  140 (192)
Q Consensus        82 ~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~  140 (192)
                      ||.|.+|++..+. .| ++|| ||+|++.++|++|++.|||..+.|+.|.|.....+..
T Consensus       100 ~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen  100 FGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             hcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            9999999999996 66 9999 9999999999999999999999999999988776543

>KOG0126|consensus

Probab=99.64  E-value=5.4e-17  Score=118.42  Aligned_cols=85  Identities=34%  Similarity=0.525  Sum_probs=78.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      -.++.-|||||||++.||.||.-+|++||+|.+|.+++|+.||+++||||+.|++..+.--|+..|||..|.|+.|+|+.
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            34566799999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      ...-.
T Consensus       112 v~~Yk  116 (219)
T KOG0126|consen  112 VSNYK  116 (219)
T ss_pred             ccccc
Confidence            65443

>smart00362 RRM_2 RNA recognition motif

Probab=99.61  E-value=5.5e-15  Score=93.23  Aligned_cols=72  Identities=38%  Similarity=0.666  Sum_probs=67.5

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      +|||+|||..+++++|+++|.+||.+..+.+..++  +.++|+|||+|.+.++|++|++.+++..+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999998875  7789999999999999999999999999999998873

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.61  E-value=7.7e-15  Score=125.98  Aligned_cols=80  Identities=21%  Similarity=0.306  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCC--eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE-----
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGE--IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT-----  129 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~--i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~-----  129 (192)
                      ++.+|||+|||.++++++|+++|+.||.  |..+++.... ++ .+|+|||+|.+.++|.+|+..||+..|.|+.     
T Consensus       393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~  470 (481)
T TIGR01649       393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPY  470 (481)
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccc
Confidence            4578999999999999999999999998  7888876543 33 5799999999999999999999999999985     


Q ss_pred             -EEEEecccC
Q psy15152        130 -VTVDWCFVK  138 (192)
Q Consensus       130 -l~v~~a~~~  138 (192)
                       |+|.|+.++
T Consensus       471 ~lkv~fs~~~  480 (481)
T TIGR01649       471 HLKVSFSTSR  480 (481)
T ss_pred             eEEEEeccCC
Confidence             999988653

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).

>KOG0114|consensus

Probab=99.61  E-value=8.6e-15  Score=97.65  Aligned_cols=83  Identities=22%  Similarity=0.387  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      .......|||.|||+.+|.++..++|.+||.|..|++-..+.|   +|-|||.|++..+|.+|++.|+|..+.++.|.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            3344678999999999999999999999999999999776655   8999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy15152        134 WCFVKG  139 (192)
Q Consensus       134 ~a~~~~  139 (192)
                      +-.+..
T Consensus        91 yyq~~~   96 (124)
T KOG0114|consen   91 YYQPED   96 (124)
T ss_pred             ecCHHH
Confidence            877653

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.60  E-value=6.6e-15  Score=125.59  Aligned_cols=83  Identities=27%  Similarity=0.380  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+..+|||+|||..+++++|+++|+.||.|..|.++.|+.+|+++|||||+|.+.++|++||. |+|..+.|+.|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3456799999999999999999999999999999999999999999999999999999999996 899999999999988


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      +...
T Consensus       165 ~~~~  168 (457)
T TIGR01622       165 SQAE  168 (457)
T ss_pred             cchh
Confidence            7543

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.

>KOG0110|consensus

Probab=99.60  E-value=1.5e-15  Score=130.03  Aligned_cols=130  Identities=21%  Similarity=0.381  Sum_probs=100.3

Q ss_pred             eEEeeccCcCCCCCCccCCCCC--hhHHHhhhcccCC---CC-------C------CCCCCCCCCCCcEEEEcCCCCCCc
Q psy15152         10 IARLKEKARKKKGRGFGTETST--RNEIREYESMETD---VG-------D------EEPGPQRSVEGWILFVTGVHEEAQ   71 (192)
Q Consensus        10 v~~~~d~~~~~k~rG~gfv~f~--~~~~~~~~~~~~~---~~-------~------~~~~~~~~~~~~~l~V~nLp~~~t   71 (192)
                      |...+|+..+-.|.|||||+|.  ..+..++..+.+.   |.       .      .+.........++|+|.|||+..+
T Consensus       547 I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt  626 (725)
T KOG0110|consen  547 ISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEAT  626 (725)
T ss_pred             EeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHH
Confidence            3444555545557799999993  3345555555422   21       0      111112223357899999999999


Q ss_pred             HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCC
Q psy15152         72 EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        72 ~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~  139 (192)
                      ..+++.+|..||.+..++|+.....+.++|||||+|-++.+|.+|+.+|..+.+.|++|.++||....
T Consensus       627 ~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  627 KREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             HHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            99999999999999999998886678889999999999999999999999999999999999997654

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.60  E-value=1.1e-14  Score=125.80  Aligned_cols=130  Identities=16%  Similarity=0.217  Sum_probs=94.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCC---CCC-----------------CC---C-----C-----
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETD---VGD-----------------EE---P-----G-----   51 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~---~~~-----------------~~---~-----~-----   51 (192)
                      +..+.+++|+.++. ++|||||+|....  ..++..++..   +..                 ..   +     .     
T Consensus       322 i~~~~~~~~~~~g~-~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (509)
T TIGR01642       322 LKAFNLIKDIATGL-SKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQS  400 (509)
T ss_pred             eeEEEEEecCCCCC-cCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhh
Confidence            45788999999995 9999999994333  3333333221   100                 00   0     0     


Q ss_pred             --CCCCCCCcEEEEcCCCCCC----------cHHHHHHhhccCCCeeEEEEeecC---CCCCcceEEEEEecCHHHHHHH
Q psy15152         52 --PQRSVEGWILFVTGVHEEA----------QEDDMHEKFSEYGEIKNLHLNLDR---RTGFLKGYALVEYDSYKEASAA  116 (192)
Q Consensus        52 --~~~~~~~~~l~V~nLp~~~----------t~~~L~~~F~~~G~i~~~~i~~~~---~tg~~~g~afV~f~~~~~a~~a  116 (192)
                        .....+..+|++.|+...-          ..++|+++|++||.|..|.|+.+.   .++...|++||+|.+.++|++|
T Consensus       401 ~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A  480 (509)
T TIGR01642       401 ILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKA  480 (509)
T ss_pred             hccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHH
Confidence              0011245789999996421          135789999999999999998752   3466789999999999999999


Q ss_pred             HHHhCCCeeCCeEEEEEeccc
Q psy15152        117 RDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus       117 l~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +..|||..+.|+.|.|.|...
T Consensus       481 ~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       481 MEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHcCCCEECCeEEEEEEeCH
Confidence            999999999999999998753

Members of this subfamily are found in plants, metazoa and fungi.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.59  E-value=1e-14  Score=111.98  Aligned_cols=77  Identities=25%  Similarity=0.258  Sum_probs=70.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..+++|||+||++.+|+++|+++|+.||+|.+|.|+.|.   ..+|||||+|.++++|+.|+. |+|..|.+++|.|...
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            356899999999999999999999999999999999884   345899999999999999995 8999999999999865


Q ss_pred             c
Q psy15152        136 F  136 (192)
Q Consensus       136 ~  136 (192)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            4

>KOG0108|consensus

Probab=99.59  E-value=5.4e-15  Score=123.58  Aligned_cols=82  Identities=27%  Similarity=0.425  Sum_probs=79.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ..+||||+|+++++++|..+|+..|.|.+++++.|+.||+++||||++|.+.++|+.|++.|||..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            77999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             CC
Q psy15152        139 GP  140 (192)
Q Consensus       139 ~~  140 (192)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>smart00360 RRM RNA recognition motif

Probab=99.58  E-value=1e-14  Score=91.61  Aligned_cols=71  Identities=35%  Similarity=0.630  Sum_probs=67.1

Q ss_pred             EcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         63 VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        63 V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|..|++.|++..+.|+.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999988789999999999999999999999999999999998873

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.57  E-value=1.4e-14  Score=113.86  Aligned_cols=80  Identities=33%  Similarity=0.537  Sum_probs=77.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||..+++++|.++|..||.|..+.+..++.+|.++|||||+|.+.++|..|++.+++..+.|++|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58999999999999999999999999999999999988999999999999999999999999999999999999999753

>KOG0131|consensus

Probab=99.56  E-value=5.5e-15  Score=107.97  Aligned_cols=80  Identities=28%  Similarity=0.412  Sum_probs=77.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ...+|||+||+..++++.|.++|-+.|+|.++.++.|+.+...+||||++|.++|+|+-|++.||...|.|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999887

>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=99.54  E-value=9e-14  Score=88.07  Aligned_cols=74  Identities=31%  Similarity=0.620  Sum_probs=68.8

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++. +.++|+|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999999998864 37789999999999999999999999999999999874

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).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.54  E-value=6.3e-14  Score=120.39  Aligned_cols=78  Identities=26%  Similarity=0.412  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      .++++|||+|||+ .+++++|+++|+.||.|.+++++.++     +|||||+|.+.++|+.|+..|||..|.|+.|+|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3568999999998 69999999999999999999998874     68999999999999999999999999999999999


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      +...
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8654

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).

>KOG0146|consensus

Probab=99.53  E-value=1.1e-14  Score=112.24  Aligned_cols=88  Identities=26%  Similarity=0.343  Sum_probs=82.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ..+++|+|||-.||.+..+.+|.+.|-+||.|.+.++..|+.|..+|+||||.|+++.+|++||.+|||..|+-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      ..+|+...
T Consensus       361 LKRPkdan  368 (371)
T KOG0146|consen  361 LKRPKDAN  368 (371)
T ss_pred             hcCccccC
Confidence            88777543

>KOG0144|consensus

Probab=99.52  E-value=3.1e-14  Score=116.05  Aligned_cols=86  Identities=30%  Similarity=0.435  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe-eC--CeEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT-IL--GQTVTV  132 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~-~~--g~~l~v  132 (192)
                      .+.-++|||.+|..++|.||+++|++||.|.+|.|++|+.||.++|||||.|.+.++|.+|+.+||+.. |-  ..+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            345679999999999999999999999999999999999999999999999999999999999998876 44  468999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      ++|.....+
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            999876543

>KOG0415|consensus

Probab=99.50  E-value=4.3e-14  Score=112.82  Aligned_cols=92  Identities=22%  Similarity=0.353  Sum_probs=85.2

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy15152         48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG  127 (192)
Q Consensus        48 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g  127 (192)
                      +.|.....++.+.|||..|.+-++.++|.-+|+.||.|..|.+++|+.||.+..||||+|++.+++++|.-+|++..|++
T Consensus       229 DlpdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD  308 (479)
T KOG0415|consen  229 DLPDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD  308 (479)
T ss_pred             CCcccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeecc
Confidence            45665666778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEecccCC
Q psy15152        128 QTVTVDWCFVKG  139 (192)
Q Consensus       128 ~~l~v~~a~~~~  139 (192)
                      ++|.|.|+.+-.
T Consensus       309 rRIHVDFSQSVs  320 (479)
T KOG0415|consen  309 RRIHVDFSQSVS  320 (479)
T ss_pred             ceEEeehhhhhh
Confidence            999999987543

>KOG0105|consensus

Probab=99.48  E-value=2.3e-13  Score=99.91  Aligned_cols=80  Identities=19%  Similarity=0.314  Sum_probs=71.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+++|||+|||.++.+.+|+++|.+||.|..|.+..-+   ..-.||||+|++..+|+.||..-+|..++|.+|+|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            45789999999999999999999999999999875432   235699999999999999999999999999999999998


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ...
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            654

>KOG0124|consensus

Probab=99.47  E-value=3.9e-14  Score=113.55  Aligned_cols=75  Identities=31%  Similarity=0.557  Sum_probs=73.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ++||||.+.+...|+.|+..|.+||.|+++.+..|+.|++++|||||+|+-+|.|+-|++.|||..++||.|+|.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999996

>PF13893 RRM_5: RNA recognition motif

Probab=99.47  E-value=3.9e-13  Score=81.92  Aligned_cols=56  Identities=30%  Similarity=0.642  Sum_probs=50.8

Q ss_pred             HHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         75 MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        75 L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      |.++|++||.|.++.+..+.     +++|||+|.+.++|+.|++.|||..+.|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999987663     589999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.46  E-value=3.8e-13  Score=85.79  Aligned_cols=61  Identities=25%  Similarity=0.495  Sum_probs=55.6

Q ss_pred             HHHHHHhhc----cCCCeeEEE-EeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         72 EDDMHEKFS----EYGEIKNLH-LNLDRRT--GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        72 ~~~L~~~F~----~~G~i~~~~-i~~~~~t--g~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      +++|+++|+    .||.|.++. +..++.+  +.++|||||+|.+.++|++|++.|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578889998    999999995 7777666  899999999999999999999999999999999986

>KOG0123|consensus

Probab=99.45  E-value=3.7e-13  Score=111.38  Aligned_cols=133  Identities=26%  Similarity=0.398  Sum_probs=105.0

Q ss_pred             ccceeeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCCCCC-------------------------CCCCCCCC
Q psy15152          3 ARFRLKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETDVGD-------------------------EEPGPQRS   55 (192)
Q Consensus         3 ~~~~~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~~~~-------------------------~~~~~~~~   55 (192)
                      +...+.++.++.|...+  ++|||||.|...+  ......++.....                         ....+...
T Consensus       190 ~~g~i~s~~v~~~~~g~--~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~  267 (369)
T KOG0123|consen  190 AYGSITSVAVMRDSIGK--SKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVS  267 (369)
T ss_pred             ccCcceEEEEeecCCCC--CCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhcccc
Confidence            34567788888887766  8999999994433  3333333222100                         11112234


Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .....|||.||+..++.+.|.++|+.||.|..++++.+. .|+++||+||.|.+.++|..|+..+|+..+.++.|.|.++
T Consensus       268 ~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~-~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~  346 (369)
T KOG0123|consen  268 LQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDE-NGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVA  346 (369)
T ss_pred             ccccccccccCccccchhHHHHHHhcccceeeEEEEecc-CCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHH
Confidence            556789999999999999999999999999999999995 8999999999999999999999999999999999999988


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ...
T Consensus       347 qr~  349 (369)
T KOG0123|consen  347 QRK  349 (369)
T ss_pred             hhh
Confidence            743

>KOG0127|consensus

Probab=99.44  E-value=1.3e-13  Score=115.42  Aligned_cols=85  Identities=19%  Similarity=0.281  Sum_probs=80.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +.||||++||++++.++|.++|+.+|+|..+.++.++.++.++|||||.|...+++++|+....+..+.|+.|+|..|..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCCC
Q psy15152        138 KGPKK  142 (192)
Q Consensus       138 ~~~~~  142 (192)
                      +....
T Consensus        85 R~r~e   89 (678)
T KOG0127|consen   85 RARSE   89 (678)
T ss_pred             cccch
Confidence            65443

>KOG0109|consensus

Probab=99.41  E-value=1.8e-13  Score=106.69  Aligned_cols=80  Identities=23%  Similarity=0.395  Sum_probs=73.1

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        51 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ...++..+++|+|||+.+.++.++|+..|.+||.|.++.|+.|        |+||.|+-.++|..|++.|++.++.|+++
T Consensus        71 SksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m  142 (346)
T KOG0109|consen   71 SKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRM  142 (346)
T ss_pred             ccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhccccccccccee
Confidence            3445557789999999999999999999999999999999855        99999999999999999999999999999


Q ss_pred             EEEecccC
Q psy15152        131 TVDWCFVK  138 (192)
Q Consensus       131 ~v~~a~~~  138 (192)
                      +|..+.++
T Consensus       143 ~vq~stsr  150 (346)
T KOG0109|consen  143 HVQLSTSR  150 (346)
T ss_pred             eeeeeccc
Confidence            99988754

>KOG4208|consensus

Probab=99.37  E-value=2.8e-12  Score=95.65  Aligned_cols=84  Identities=21%  Similarity=0.369  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEY-GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~-G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ......+||..+|..+.+.++..+|.+| |.+..+++.+++.||.++|||||+|++.+.|+-|-+.||+..+.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445569999999999999999999998 778888998999999999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy15152        134 WCFVK  138 (192)
Q Consensus       134 ~a~~~  138 (192)
                      +-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            88766

>KOG0109|consensus

Probab=99.32  E-value=3e-12  Score=99.92  Aligned_cols=72  Identities=25%  Similarity=0.421  Sum_probs=68.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      .+|||||||..+++.+|+.+|++||+|.+|.|+.+        ||||..++...|+.||..|||..|+|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            36999999999999999999999999999999866        9999999999999999999999999999999988766

>KOG4212|consensus

Probab=99.31  E-value=8.2e-12  Score=102.33  Aligned_cols=78  Identities=23%  Similarity=0.356  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSE-YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~-~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..+||.|+|+++.+++|+++|.+ .|+|+.|.++.|. +|+++|+|.|+|+++|.+++|++.||.+.+.|+.|.|+....
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            44999999999999999999985 8999999999995 999999999999999999999999999999999999986544

>KOG4206|consensus

Probab=99.28  E-value=1.6e-11  Score=92.87  Aligned_cols=80  Identities=24%  Similarity=0.456  Sum_probs=72.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHH----hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHE----KFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~----~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ..||||.||+.-+..++|+.    +|++||.|.+|...   .|.+.+|-|||.|.+.+.|-.|+..|+|..+.|+.+++.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            34899999999999988877    99999999998764   367889999999999999999999999999999999999


Q ss_pred             ecccCCC
Q psy15152        134 WCFVKGP  140 (192)
Q Consensus       134 ~a~~~~~  140 (192)
                      ||..+..
T Consensus        86 yA~s~sd   92 (221)
T KOG4206|consen   86 YAKSDSD   92 (221)
T ss_pred             cccCccc
Confidence            9987654

>KOG0146|consensus

Probab=99.26  E-value=8.1e-12  Score=96.65  Aligned_cols=85  Identities=27%  Similarity=0.414  Sum_probs=76.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee-C--CeEEEEE
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI-L--GQTVTVD  133 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~-~--g~~l~v~  133 (192)
                      +.++||||-|...-.|+|++.+|..||.|.+|.+++.+ .|.+||+|||.|.+..+|+.||..|||... -  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            56789999999999999999999999999999999997 899999999999999999999999999873 3  4689999


Q ss_pred             ecccCCCCC
Q psy15152        134 WCFVKGPKK  142 (192)
Q Consensus       134 ~a~~~~~~~  142 (192)
                      |+.....+.
T Consensus        97 ~ADTdkER~  105 (371)
T KOG0146|consen   97 FADTDKERT  105 (371)
T ss_pred             eccchHHHH
Confidence            998765443

>KOG0153|consensus

Probab=99.25  E-value=7.1e-11  Score=94.28  Aligned_cols=79  Identities=27%  Similarity=0.490  Sum_probs=69.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCeEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL-NGTTILGQTVTV  132 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l-~~~~~~g~~l~v  132 (192)
                      ......+|||++|...+++.+|+++|.+||+|..+.+...      +++|||+|.++++|+.|.+.+ +...|+|++|.|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            3344589999999999999999999999999999998766      469999999999999988755 555689999999


Q ss_pred             EecccC
Q psy15152        133 DWCFVK  138 (192)
Q Consensus       133 ~~a~~~  138 (192)
                      .|+.+.
T Consensus       298 ~Wg~~~  303 (377)
T KOG0153|consen  298 KWGRPK  303 (377)
T ss_pred             EeCCCc
Confidence            999983

>KOG0132|consensus

Probab=99.22  E-value=2.9e-11  Score=104.93  Aligned_cols=81  Identities=28%  Similarity=0.535  Sum_probs=75.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .-++|||||+|+..+++.+|..+|+.||+|.+|.++..      +|+|||......+|++|+.+|.+..+.++.|+|.||
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            34689999999999999999999999999999988766      689999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy15152        136 FVKGPKK  142 (192)
Q Consensus       136 ~~~~~~~  142 (192)
                      ..++.+.
T Consensus       493 ~g~G~ks  499 (894)
T KOG0132|consen  493 VGKGPKS  499 (894)
T ss_pred             ccCCcch
Confidence            9887665

>KOG4205|consensus

Probab=99.22  E-value=1.2e-11  Score=99.56  Aligned_cols=85  Identities=24%  Similarity=0.406  Sum_probs=77.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +.+++||++|+++++++.|++.|..||+|.++.+++|+.++.++||+||+|++.+...+++.. ..+.|+|+.|.+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            567899999999999999999999999999999999999999999999999999999988864 6778999999999988


Q ss_pred             cCCCCC
Q psy15152        137 VKGPKK  142 (192)
Q Consensus       137 ~~~~~~  142 (192)
                      ++....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            776443

>KOG4661|consensus

Probab=99.14  E-value=1.9e-10  Score=97.18  Aligned_cols=87  Identities=22%  Similarity=0.357  Sum_probs=79.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .-+..|||.+|...+...+|+.+|++||.|...+++.+..+...++|+||++.+.++|.+||+.||.+.|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34578999999999999999999999999999999999888888999999999999999999999999999999999998


Q ss_pred             ccCCCCC
Q psy15152        136 FVKGPKK  142 (192)
Q Consensus       136 ~~~~~~~  142 (192)
                      +..+...
T Consensus       483 KNEp~Gk  489 (940)
T KOG4661|consen  483 KNEPGGK  489 (940)
T ss_pred             ccCcccc
Confidence            7655433

>KOG4212|consensus

Probab=99.13  E-value=2.2e-10  Score=94.04  Aligned_cols=78  Identities=19%  Similarity=0.314  Sum_probs=70.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ......++|||+|||+++|++.|++-|..||.|....|+   ..|+++|  .|.|.++++|++|+..|++..++|+.|.|
T Consensus       531 gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V  605 (608)
T KOG4212|consen  531 GAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKV  605 (608)
T ss_pred             cccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeee
Confidence            344567899999999999999999999999999988883   3588887  89999999999999999999999999999


Q ss_pred             Eec
Q psy15152        133 DWC  135 (192)
Q Consensus       133 ~~a  135 (192)
                      .|.
T Consensus       606 ~y~  608 (608)
T KOG4212|consen  606 TYF  608 (608)
T ss_pred             eeC
Confidence            873

>KOG0533|consensus

Probab=99.12  E-value=2.4e-10  Score=88.82  Aligned_cols=81  Identities=23%  Similarity=0.368  Sum_probs=75.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|+|.|||..+++++|+++|..||.+..+.+.+++ +|.+.|.|-|.|...++|.+|++.+++..++|+.+++....+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            4789999999999999999999999999999999997 899999999999999999999999999999999999987765


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            43

>KOG0110|consensus

Probab=99.11  E-value=2.2e-10  Score=98.73  Aligned_cols=78  Identities=23%  Similarity=0.409  Sum_probs=70.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTG---FLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg---~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ++|||.||+++++.++|..+|...|.|..+.|...+...   .+.|||||+|.+.++|++|++.|+|+.|+|+.|.|+++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            349999999999999999999999999999887665221   24599999999999999999999999999999999999


Q ss_pred             c
Q psy15152        136 F  136 (192)
Q Consensus       136 ~  136 (192)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>KOG0116|consensus

Probab=99.10  E-value=7.5e-10  Score=92.47  Aligned_cols=82  Identities=21%  Similarity=0.289  Sum_probs=69.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..+|||+|||++++..+|+++|..||.|+...|..-...++..+||||+|.+.++++.|+++ +-..|++++|.|+...+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            34599999999999999999999999999887765432355559999999999999999997 67789999999998776


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      ...
T Consensus       367 ~~~  369 (419)
T KOG0116|consen  367 GFR  369 (419)
T ss_pred             ccc
Confidence            443

>KOG4209|consensus

Probab=99.07  E-value=7.1e-10  Score=86.22  Aligned_cols=88  Identities=26%  Similarity=0.386  Sum_probs=80.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      +...+...+||+|+.+.++.+++..+|+.+|.|..+.++.|+.+|.++||+||+|.+.+.++.|+. |++..|.|+.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            455667889999999999999999999999999999999999999999999999999999999998 9999999999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .+.....+.
T Consensus       175 t~~r~~~pg  183 (231)
T KOG4209|consen  175 TLKRTNVPG  183 (231)
T ss_pred             eeeeeecCC
Confidence            988766433

>KOG0226|consensus

Probab=99.03  E-value=3.9e-10  Score=86.71  Aligned_cols=83  Identities=19%  Similarity=0.348  Sum_probs=77.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ...+||+|.|.-+++++.|...|.+|-.-...++++|..||+++||+||.|.+..++.+|+..|+|..++.++|+++-+.
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            35789999999999999999999999888888999999999999999999999999999999999999999999998766


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      .+.
T Consensus       269 wke  271 (290)
T KOG0226|consen  269 WKE  271 (290)
T ss_pred             HHh
Confidence            554

>KOG1457|consensus

Probab=99.00  E-value=5.6e-09  Score=79.10  Aligned_cols=84  Identities=21%  Similarity=0.302  Sum_probs=68.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC---CeEEEEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLD-RRTGFLKGYALVEYDSYKEASAARDALNGTTIL---GQTVTVD  133 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~-~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~---g~~l~v~  133 (192)
                      -+||||.+||.++...+|..+|..|-.-+.+.+.+. +.....+-+||+.|.+.++|++|+..|||..++   +..|+++
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            578999999999999999999999876665554332 211223469999999999999999999999986   8899999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      +|+.....
T Consensus       114 lAKSNtK~  121 (284)
T KOG1457|consen  114 LAKSNTKR  121 (284)
T ss_pred             ehhcCccc
Confidence            99876543

>KOG4211|consensus

Probab=98.92  E-value=9.9e-09  Score=85.53  Aligned_cols=79  Identities=20%  Similarity=0.252  Sum_probs=66.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN-LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~-~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      .....|-+++||+.|+++||.+||+..--+.. +.++.++ .+++.|-|||.|++.+.|+.|+.. |...|..+.|.|..
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            34567999999999999999999998744444 5566775 788999999999999999999986 88889999999976


Q ss_pred             cc
Q psy15152        135 CF  136 (192)
Q Consensus       135 a~  136 (192)
                      +.
T Consensus       179 Ss  180 (510)
T KOG4211|consen  179 SS  180 (510)
T ss_pred             hH
Confidence            53

>KOG0106|consensus

Probab=98.89  E-value=3.1e-09  Score=81.07  Aligned_cols=72  Identities=24%  Similarity=0.493  Sum_probs=66.1

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCC
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~  139 (192)
                      .+|||+||+.+.+.+|+++|..||.+.++.+.        .||+||+|.+..+|..|+..||+..|.|..+.|+|+....
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            59999999999999999999999999988763        4689999999999999999999999999999999998643

>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=2.6e-08  Score=67.01  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=70.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhcc--CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC----CeEEEE
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSE--YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL----GQTVTV  132 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~--~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~----g~~l~v  132 (192)
                      +||.|+|+|...|.++|.+++..  .|...-+-++.|..++.+.|||||.|.+++.|.+..+.++|..+.    .+...|
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            68999999999999999888765  466777889999989999999999999999999999999999875    567888


Q ss_pred             EecccC
Q psy15152        133 DWCFVK  138 (192)
Q Consensus       133 ~~a~~~  138 (192)
                      .||.-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            888644

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0151|consensus

Probab=98.78  E-value=3.4e-08  Score=85.58  Aligned_cols=82  Identities=15%  Similarity=0.298  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR---TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~---tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ..+.+||+||++.++++.|...|..||+|..++++..+.   ....+-+|||.|-+..+|++|++.|+|..+.+..+++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            347899999999999999999999999999999987762   33456799999999999999999999999999999999


Q ss_pred             ecccC
Q psy15152        134 WCFVK  138 (192)
Q Consensus       134 ~a~~~  138 (192)
                      |+.+-
T Consensus       253 Wgk~V  257 (877)
T KOG0151|consen  253 WGKAV  257 (877)
T ss_pred             ccccc
Confidence            99543

>KOG4660|consensus

Probab=98.74  E-value=8.3e-09  Score=87.09  Aligned_cols=72  Identities=25%  Similarity=0.401  Sum_probs=65.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .....+|+|-|||.++++++|.++|+.||+|..++.-.     -.+|..||+|.+..+|++|+++|++..+.|++|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            34457899999999999999999999999999977544     4489999999999999999999999999999988

>KOG1548|consensus

Probab=98.68  E-value=7.8e-08  Score=77.11  Aligned_cols=80  Identities=25%  Similarity=0.336  Sum_probs=71.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--------~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      .+.|||.|||.++|.+++.++|+++|-|.        .|++-++. .|..+|=|++.|-..++..-|++.|++..+.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            35699999999999999999999999875        36777774 6999999999999999999999999999999999


Q ss_pred             EEEEecccC
Q psy15152        130 VTVDWCFVK  138 (192)
Q Consensus       130 l~v~~a~~~  138 (192)
                      |+|..|.-.
T Consensus       213 ~rVerAkfq  221 (382)
T KOG1548|consen  213 LRVERAKFQ  221 (382)
T ss_pred             EEEehhhhh
Confidence            999988643

>KOG4211|consensus

Probab=98.67  E-value=8.7e-08  Score=80.02  Aligned_cols=79  Identities=23%  Similarity=0.253  Sum_probs=67.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..-|-+++|||++|+++|.+||+.. .|.++.+.  +.+|+..|-|||+|.+.+++++|++. +...+..+.|.|--+..
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNC-GIENLEIP--RRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGG   85 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcC-ceeEEEEe--ccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCC
Confidence            4557789999999999999999988 67775544  44899999999999999999999985 88889999999988766


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      ...
T Consensus        86 ~e~   88 (510)
T KOG4211|consen   86 AEA   88 (510)
T ss_pred             ccc
Confidence            554

>KOG1190|consensus

Probab=98.67  E-value=3.4e-07  Score=75.03  Aligned_cols=77  Identities=22%  Similarity=0.425  Sum_probs=70.0

Q ss_pred             CcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         58 GWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        58 ~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ...|.|.||... +|.+.|..+|+.||.|.+|+|+.++     +--|+|.|.+...|+-|++.|+|..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            478889999875 9999999999999999999999986     3579999999999999999999999999999999987


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      -..
T Consensus       372 H~~  374 (492)
T KOG1190|consen  372 HTN  374 (492)
T ss_pred             Ccc
Confidence            543

>KOG4454|consensus

Probab=98.61  E-value=1.8e-08  Score=76.16  Aligned_cols=78  Identities=15%  Similarity=0.144  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ...+|||+|+...++++-|.++|-.-|.|..+.|..++ .+..+ ||||.|.++.+..-|++-|||..+.++.+.+.+-.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            45789999999999999999999999999999998886 67777 99999999999999999999999998888876543

>KOG0120|consensus

Probab=98.55  E-value=5.6e-08  Score=82.49  Aligned_cols=83  Identities=28%  Similarity=0.383  Sum_probs=78.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..+.+||++||...++.++.++...||.+....+..|..+|.++||||.+|.+......|+..|||..++++.|.|..|.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ...
T Consensus       368 ~g~  370 (500)
T KOG0120|consen  368 VGA  370 (500)
T ss_pred             ccc
Confidence            654

>KOG0106|consensus

Probab=98.50  E-value=1.5e-07  Score=71.96  Aligned_cols=74  Identities=22%  Similarity=0.390  Sum_probs=64.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ....+.+.|.+++..+.+.+|.++|.++|.+.....        ..+++||+|.+.++|..|+..|++..+.++.|.+..
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            344678999999999999999999999999954433        256999999999999999999999999999999954


Q ss_pred             cc
Q psy15152        135 CF  136 (192)
Q Consensus       135 a~  136 (192)
                      ..
T Consensus       168 ~~  169 (216)
T KOG0106|consen  168 NS  169 (216)
T ss_pred             cC
Confidence            43

>KOG1456|consensus

Probab=98.42  E-value=4e-06  Score=68.19  Aligned_cols=123  Identities=17%  Similarity=0.155  Sum_probs=89.1

Q ss_pred             CCCCCCcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         53 QRSVEGWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ....+++.+.|-+|... ++.+.|..+|-.||.|.+|++++.+     .|-|.|+..+..+.++|+..||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            44566789999999986 7778899999999999999998876     57899999999999999999999999999999


Q ss_pred             EEecccCCCCCCCC--CCCCCCCCCccccCCccccccccCCccccccCccc
Q psy15152        132 VDWCFVKGPKKVAG--EQKVGPEGGVKVLFPVIMYSTETSMSTTLYNAPWI  180 (192)
Q Consensus       132 v~~a~~~~~~~~~~--~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~p~~  180 (192)
                      |..++..--....+  -...++.-.-.+.+.+..+++..+.+...+++|..
T Consensus       357 v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~  407 (494)
T KOG1456|consen  357 VCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSN  407 (494)
T ss_pred             EeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcc
Confidence            98886544332222  11122222223334444455555555555555543

>KOG4206|consensus

Probab=98.42  E-value=2.6e-06  Score=64.84  Aligned_cols=77  Identities=30%  Similarity=0.460  Sum_probs=68.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL-GQTVTVD  133 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~-g~~l~v~  133 (192)
                      ..+...+|+.|||..++.+.|..+|.+|..-..++++...     .+.|||+|.+...|..|...+++..|- ...+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            4566789999999999999999999999999999988765     689999999999999999999999876 7888887


Q ss_pred             ecc
Q psy15152        134 WCF  136 (192)
Q Consensus       134 ~a~  136 (192)
                      ++.
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            764

>KOG0147|consensus

Probab=98.35  E-value=1.8e-07  Score=79.11  Aligned_cols=81  Identities=26%  Similarity=0.365  Sum_probs=74.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +..++|+..|+...++.+|.++|+.+|.|.+|+++.|+.++.++|.|||+|.+.++...|| .|.|..+.|.+|.|....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccH
Confidence            3478999999999999999999999999999999999999999999999999999999999 589999999999998765


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      ..
T Consensus       257 ae  258 (549)
T KOG0147|consen  257 AE  258 (549)
T ss_pred             HH
Confidence            43

>KOG0105|consensus

Probab=98.35  E-value=5.4e-06  Score=61.46  Aligned_cols=66  Identities=18%  Similarity=0.290  Sum_probs=58.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      .......|.|.+||.+-++++|+++..+-|.|....+.+|       |++.|+|...|+.+-|+..|....+.
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            3345678999999999999999999999999999888777       48999999999999999999887654

>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=98.32  E-value=3.4e-06  Score=54.59  Aligned_cols=68  Identities=15%  Similarity=0.382  Sum_probs=47.3

Q ss_pred             cEEEEcCCCCCCcHHH----HHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         59 WILFVTGVHEEAQEDD----MHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~----L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ..|||.|||.+.+...    |++++..+| .|..+.          .+-|+|.|.+.+.|.+|.+.|+|..+.|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4699999999988765    556666665 566652          3579999999999999999999999999999999


Q ss_pred             ecc
Q psy15152        134 WCF  136 (192)
Q Consensus       134 ~a~  136 (192)
                      |..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            874

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4210|consensus

Probab=98.30  E-value=4.3e-07  Score=72.94  Aligned_cols=83  Identities=23%  Similarity=0.328  Sum_probs=75.5

Q ss_pred             CcEEE-EcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         58 GWILF-VTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        58 ~~~l~-V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++| |++|++.+++++|+.+|..+|.|..++++.++.+|..+|||||.|.+...+..++.. +...+.++++.+.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            34566 999999999999999999999999999999999999999999999999999999987 8888999999999887


Q ss_pred             cCCCC
Q psy15152        137 VKGPK  141 (192)
Q Consensus       137 ~~~~~  141 (192)
                      +.+..
T Consensus       263 ~~~~~  267 (285)
T KOG4210|consen  263 PRPKS  267 (285)
T ss_pred             CCccc
Confidence            76543

>KOG1995|consensus

Probab=98.30  E-value=7.8e-07  Score=71.85  Aligned_cols=86  Identities=28%  Similarity=0.375  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--------~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      .....+|||.+||..+++++|.++|.++|.|.        .|.+-+|+.|+..||-|.|.|.+...|+.|+.-+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44457899999999999999999999999874        3667788889999999999999999999999999999999


Q ss_pred             CeEEEEEecccCCC
Q psy15152        127 GQTVTVDWCFVKGP  140 (192)
Q Consensus       127 g~~l~v~~a~~~~~  140 (192)
                      |..|+|.+|..+..
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999998876653

>KOG0128|consensus

Probab=98.23  E-value=3.6e-07  Score=80.79  Aligned_cols=113  Identities=17%  Similarity=0.128  Sum_probs=87.3

Q ss_pred             ccCcCCCCCCccCCCCChh--HHHhhhcccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEee
Q psy15152         15 EKARKKKGRGFGTETSTRN--EIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNL   92 (192)
Q Consensus        15 d~~~~~k~rG~gfv~f~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~   92 (192)
                      -..+++ -||+++++|..+  +.++..-....-          -....++|.|+|+..|.++|+.+++.+|.+.+++++.
T Consensus       702 h~n~~~-~rG~~Y~~F~~~~~~~aaV~f~d~~~----------~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt  770 (881)
T KOG0128|consen  702 HKNEKR-FRGKAYVEFLKPEHAGAAVAFRDSCF----------FGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVT  770 (881)
T ss_pred             Hhhccc-cccceeeEeecCCchhhhhhhhhhhh----------hhhhhhheeCCCCCCchHHHHhhccccCCccccchhh
Confidence            455675 899999999322  222221111110          0145699999999999999999999999999999888


Q ss_pred             cCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCC
Q psy15152         93 DRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        93 ~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~  139 (192)
                      .+ .|+++|.|||.|.+..++.+++...+...+.-..+.|..+.|..
T Consensus       771 ~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~  816 (881)
T KOG0128|consen  771 VR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPER  816 (881)
T ss_pred             hh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCcc
Confidence            86 89999999999999999999998888888877777787766633

>KOG4849|consensus

Probab=98.18  E-value=1.5e-06  Score=70.07  Aligned_cols=75  Identities=24%  Similarity=0.349  Sum_probs=66.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ...+|||||-|++|++||.+.+...|  .+.++++..++.+|+++|||+|...+..+.++.++.|....|.|+.-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            35799999999999999999888766  5678889999999999999999999999999999999999998875444

>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=98.16  E-value=5.8e-06  Score=56.69  Aligned_cols=70  Identities=27%  Similarity=0.489  Sum_probs=43.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-----eeCCeEEEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT-----TILGQTVTV  132 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~-----~~~g~~l~v  132 (192)
                      ++.|++.+++..++.++|++.|+.||.|..|.+....      ..|||.|.+.++|+.|++.+...     .+.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            3578999999999999999999999999988875442      37999999999999999977544     455555544


Q ss_pred             E
Q psy15152        133 D  133 (192)
Q Consensus       133 ~  133 (192)
                      .
T Consensus        75 ~   75 (105)
T PF08777_consen   75 E   75 (105)
T ss_dssp             E
T ss_pred             E
Confidence            3

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1457|consensus

Probab=98.15  E-value=2.3e-06  Score=65.09  Aligned_cols=64  Identities=22%  Similarity=0.449  Sum_probs=53.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      .+|||.||...++|++|+.+|+.|-....++|. .+ .|.  ..||++|++.+.|..|+..|+|..|.
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~-~g~--~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIR-AR-GGM--PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cC-CCc--ceEeecHHHHHHHHHHHHHhhcceec
Confidence            589999999999999999999999776666553 21 333  48999999999999999999997753

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.98  E-value=2e-05  Score=63.50  Aligned_cols=82  Identities=18%  Similarity=0.413  Sum_probs=63.1

Q ss_pred             CCCcEEEEcCCCCCCcHHH----H--HHhhccCCCeeEEEEeecCCCCC-cce--EEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         56 VEGWILFVTGVHEEAQEDD----M--HEKFSEYGEIKNLHLNLDRRTGF-LKG--YALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~----L--~~~F~~~G~i~~~~i~~~~~tg~-~~g--~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      ....-+||-+||+.+..++    |  .++|.+||.|..|.+.+...+-. ..+  -.||+|.+.++|.+||...+|..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            4456799999999876665    3  48999999999887754421111 112  2399999999999999999999999


Q ss_pred             CeEEEEEeccc
Q psy15152        127 GQTVTVDWCFV  137 (192)
Q Consensus       127 g~~l~v~~a~~  137 (192)
                      |+.|+..|...
T Consensus       192 Gr~lkatYGTT  202 (480)
T COG5175         192 GRVLKATYGTT  202 (480)
T ss_pred             CceEeeecCch
Confidence            99999988753

>KOG2314|consensus

Probab=97.93  E-value=2.8e-05  Score=66.35  Aligned_cols=77  Identities=29%  Similarity=0.393  Sum_probs=63.0

Q ss_pred             CcEEEEcCCCCCCcH------HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC-CeEE
Q psy15152         58 GWILFVTGVHEEAQE------DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL-GQTV  130 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~------~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~-g~~l  130 (192)
                      ...|+|.|+|.--..      .-|..+|+++|++....++.+..+ ..+||.|++|.+..+|+.|++.|||..|+ ++.+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~g-gtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEG-GTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccC-CeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            456999999874222      235688999999999999988754 48999999999999999999999999975 6777


Q ss_pred             EEEec
Q psy15152        131 TVDWC  135 (192)
Q Consensus       131 ~v~~a  135 (192)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77543

>KOG1365|consensus

Probab=97.79  E-value=3.8e-05  Score=62.84  Aligned_cols=74  Identities=19%  Similarity=0.145  Sum_probs=58.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccC----CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEY----GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~----G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      -.|-.++||+++++.++.+||.+-    |....+-++..+ .|+..|-|||.|..+++|+.|+.+ |...|+-|.|.+-.
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            346668999999999999999742    344556555554 799999999999999999999986 77777777766643

>KOG4307|consensus

Probab=97.79  E-value=0.00011  Score=64.38  Aligned_cols=75  Identities=21%  Similarity=0.342  Sum_probs=65.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCee-EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIK-NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~-~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      +.|-+.|+|++++-+||.+||..|-.+- +|.+-++ +.|+..|-|.|.|++.++|.+|...|++..|..+.+.+..
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3788899999999999999999997654 4455444 6899999999999999999999999999999999998864

>KOG0112|consensus

Probab=97.77  E-value=0.00013  Score=65.34  Aligned_cols=83  Identities=23%  Similarity=0.367  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVT  131 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~  131 (192)
                      .....+.+|+++|..++....|...|..||.|..|.+-    .|.  -||+|.|.+...|+.|++.|-|..|+|  ++|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~----hgq--~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR----HGQ--PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc----cCC--cceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            56677889999999999999999999999999887652    333  399999999999999999999999986  7899


Q ss_pred             EEecccCCCCC
Q psy15152        132 VDWCFVKGPKK  142 (192)
Q Consensus       132 v~~a~~~~~~~  142 (192)
                      |.++.+.....
T Consensus       525 vdla~~~~~~P  535 (975)
T KOG0112|consen  525 VDLASPPGATP  535 (975)
T ss_pred             cccccCCCCCh
Confidence            99998765443

>KOG1190|consensus

Probab=97.74  E-value=8.5e-05  Score=61.26  Aligned_cols=78  Identities=18%  Similarity=0.128  Sum_probs=64.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCe-EEEEEe
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ-TVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~-~l~v~~  134 (192)
                      +++.+++..|+|.+++|++|++.|..-|........    -++.+-+|++.+.+.|+|-.|+-.++++.+++. .|+|.|
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            567789999999999999999999998766444322    233456999999999999999999999998865 899999


Q ss_pred             ccc
Q psy15152        135 CFV  137 (192)
Q Consensus       135 a~~  137 (192)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            864

>KOG3152|consensus

Probab=97.69  E-value=3.5e-05  Score=59.81  Aligned_cols=73  Identities=22%  Similarity=0.293  Sum_probs=61.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCC--------CCcce----EEEEEecCHHHHHHHHHHhCCCe
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT--------GFLKG----YALVEYDSYKEASAARDALNGTT  124 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~t--------g~~~g----~afV~f~~~~~a~~al~~l~~~~  124 (192)
                      ..-.||++++|+.++..-|+++|+.||.|-+|.+.....+        |.+.+    -|.|+|.+...|..+...||+..
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            4467999999999999999999999999999888665433        33332    46799999999999999999999


Q ss_pred             eCCeE
Q psy15152        125 ILGQT  129 (192)
Q Consensus       125 ~~g~~  129 (192)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG1365|consensus

Probab=97.69  E-value=6.1e-05  Score=61.69  Aligned_cols=78  Identities=19%  Similarity=0.278  Sum_probs=68.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCC-ee--EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGE-IK--NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~-i~--~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+|-+++||+..+.++|..||..|-. |.  .+.+..+. .|+..|-|||+|.+.++|.+|....+++..+.+.|.|-.
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            567999999999999999999998864 33  37778774 799999999999999999999999888888899999976


Q ss_pred             cc
Q psy15152        135 CF  136 (192)
Q Consensus       135 a~  136 (192)
                      +.
T Consensus       359 ~S  360 (508)
T KOG1365|consen  359 CS  360 (508)
T ss_pred             cc
Confidence            64

>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=97.66  E-value=0.00023  Score=48.25  Aligned_cols=78  Identities=22%  Similarity=0.219  Sum_probs=50.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEE-EeecC------CCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCe-E
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLH-LNLDR------RTGFLKGYALVEYDSYKEASAARDALNGTTILGQ-T  129 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~-i~~~~------~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~-~  129 (192)
                      .+-|.|-+.|+. ....+.+.|++||.|.+.. +..+.      .......+-.|.|+++.+|++||.. ||..+.|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEE
Confidence            344778899998 4466778899999997764 11100      0011245899999999999999985 99999886 5


Q ss_pred             EEEEeccc
Q psy15152        130 VTVDWCFV  137 (192)
Q Consensus       130 l~v~~a~~  137 (192)
                      +-|.+..+
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            55777643

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.

>KOG0129|consensus

Probab=97.65  E-value=0.00017  Score=61.03  Aligned_cols=67  Identities=16%  Similarity=0.242  Sum_probs=61.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFS-EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA  119 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~  119 (192)
                      +.-.+..|||||+||.-++.++|..+|. .||.|..+.|-.|++-+.++|-|=|.|.+..+-.+||.+
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3445678999999999999999999999 599999999999988899999999999999999999985

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.61  E-value=0.00016  Score=43.22  Aligned_cols=52  Identities=25%  Similarity=0.433  Sum_probs=41.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHH
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR  117 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al  117 (192)
                      +.|-|.+.+.+..+ .+..+|..||+|..+.+...      .-+.+|.|.+..+|++|+
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            35778888887654 45568889999999887522      348999999999999985

>KOG1456|consensus

Probab=97.60  E-value=0.00055  Score=56.07  Aligned_cols=84  Identities=23%  Similarity=0.317  Sum_probs=65.8

Q ss_pred             CCCCCCCCcEEEEc--CCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC-
Q psy15152         51 GPQRSVEGWILFVT--GVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG-  127 (192)
Q Consensus        51 ~~~~~~~~~~l~V~--nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g-  127 (192)
                      +.....+.+.|.+.  |--+.+|-+-|..+..+.|+|.+|.|...  +|.   .|.|+|++.+.|++|...|||..|.. 
T Consensus       113 g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsG  187 (494)
T KOG1456|consen  113 GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSG  187 (494)
T ss_pred             CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhccccccccc
Confidence            33334445555555  44446888999999999999999988765  443   69999999999999999999999763 


Q ss_pred             -eEEEEEecccCC
Q psy15152        128 -QTVTVDWCFVKG  139 (192)
Q Consensus       128 -~~l~v~~a~~~~  139 (192)
                       -.|+|+||+|.+
T Consensus       188 CCTLKIeyAkP~r  200 (494)
T KOG1456|consen  188 CCTLKIEYAKPTR  200 (494)
T ss_pred             ceeEEEEecCcce
Confidence             489999998764

>KOG0120|consensus

Probab=97.51  E-value=0.00037  Score=59.67  Aligned_cols=64  Identities=16%  Similarity=0.307  Sum_probs=52.8

Q ss_pred             HHHHhhccCCCeeEEEEeec-C--CCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         74 DMHEKFSEYGEIKNLHLNLD-R--RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        74 ~L~~~F~~~G~i~~~~i~~~-~--~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +++.-+++||.|..|.++++ .  .-.-..|--||+|.+.+++++|.++|+|..+.|+.+...|...
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            34556778999999999877 2  1233457789999999999999999999999999999988754

>KOG2416|consensus

Probab=97.41  E-value=0.00021  Score=61.55  Aligned_cols=84  Identities=21%  Similarity=0.360  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee--
Q psy15152         49 EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSE-YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI--  125 (192)
Q Consensus        49 ~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~--  125 (192)
                      .+.|.+...++.|||.||-.-.|..+|++++.. .|.|...  ++|+    -+..|||.|.+.++|-+...+|||..+  
T Consensus       435 vpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  435 VPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             CCCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCC
Confidence            455667788899999999999999999999995 5566665  3343    256899999999999999999999985  


Q ss_pred             -CCeEEEEEecccC
Q psy15152        126 -LGQTVTVDWCFVK  138 (192)
Q Consensus       126 -~g~~l~v~~a~~~  138 (192)
                       .++.|.+.|....
T Consensus       509 sNPK~L~adf~~~d  522 (718)
T KOG2416|consen  509 SNPKHLIADFVRAD  522 (718)
T ss_pred             CCCceeEeeecchh
Confidence             5788999988643

>KOG1855|consensus

Probab=97.41  E-value=0.00021  Score=59.35  Aligned_cols=70  Identities=24%  Similarity=0.397  Sum_probs=57.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeec---CCC--CCc--------ceEEEEEecCHHHHHHHHHHhC
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLD---RRT--GFL--------KGYALVEYDSYKEASAARDALN  121 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~---~~t--g~~--------~g~afV~f~~~~~a~~al~~l~  121 (192)
                      ..++.+|.+-|||.+-.-+.|.++|+.+|.|..|+|...   +.+  |..        +-+|+|+|+..+.|.+|.+.|+
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            356899999999999888999999999999999998665   222  222        4579999999999999999875


Q ss_pred             CCe
Q psy15152        122 GTT  124 (192)
Q Consensus       122 ~~~  124 (192)
                      ...
T Consensus       308 ~e~  310 (484)
T KOG1855|consen  308 PEQ  310 (484)
T ss_pred             hhh
Confidence            543

>KOG4307|consensus

Probab=97.29  E-value=0.00031  Score=61.58  Aligned_cols=79  Identities=16%  Similarity=0.074  Sum_probs=66.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKN-LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~-~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+..|||..||..+++.++.++|..--.|++ |.|.+.+ +++.++.|||.|..++++..|...-+.+.++.+.|+|+-.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            3578999999999999999999998777776 6776665 8888999999999999988888766777788889999754


Q ss_pred             c
Q psy15152        136 F  136 (192)
Q Consensus       136 ~  136 (192)
                      .
T Consensus       512 ~  512 (944)
T KOG4307|consen  512 A  512 (944)
T ss_pred             h
Confidence            3

>KOG0129|consensus

Probab=97.26  E-value=0.00079  Score=57.16  Aligned_cols=64  Identities=16%  Similarity=0.334  Sum_probs=49.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCC---CCCcce---EEEEEecCHHHHHHHHHHhCC
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR---TGFLKG---YALVEYDSYKEASAARDALNG  122 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~---tg~~~g---~afV~f~~~~~a~~al~~l~~  122 (192)
                      +++||||+||++++|+.|...|..||.+ .+.++....   ---++|   |+|+.|+++.+.+..+.+...
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~  328 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE  328 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh
Confidence            5789999999999999999999999987 344542111   112456   999999999988887776543

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.20  E-value=0.0034  Score=45.21  Aligned_cols=78  Identities=22%  Similarity=0.266  Sum_probs=52.3

Q ss_pred             CCCCcEEEEcCCC------CCCcH---HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         55 SVEGWILFVTGVH------EEAQE---DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        55 ~~~~~~l~V~nLp------~~~t~---~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      .++..||.|.=+.      ....+   .+|.+.|..||.+.=+++.-+        .-+|+|.+-++|.+|+. |+|..+
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            3445567776554      12222   367788999999988877654        47899999999999997 799999


Q ss_pred             CCeEEEEEecccCCCC
Q psy15152        126 LGQTVTVDWCFVKGPK  141 (192)
Q Consensus       126 ~g~~l~v~~a~~~~~~  141 (192)
                      .|+.|+|+...+....
T Consensus        95 ~g~~l~i~LKtpdW~~  110 (146)
T PF08952_consen   95 NGRTLKIRLKTPDWLK  110 (146)
T ss_dssp             TTEEEEEEE-------
T ss_pred             CCEEEEEEeCCccHHH
Confidence            9999999988776543

; PDB: 1UFW_A 2DNR_A.

>KOG2193|consensus

Probab=97.20  E-value=0.00037  Score=57.87  Aligned_cols=76  Identities=18%  Similarity=0.276  Sum_probs=59.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe-eCCeEEEEEeccc
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT-ILGQTVTVDWCFV  137 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~-~~g~~l~v~~a~~  137 (192)
                      ..+|++||.+.++..+|+.+|..----..-.++.      ..||+||.+.+...|.+|++.++|.. +.|+++.|.++-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            3599999999999999999987541111112222      24799999999999999999999985 8999999998877


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      +..
T Consensus        76 kkq   78 (584)
T KOG2193|consen   76 KKQ   78 (584)
T ss_pred             HHH
Confidence            643

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.16  E-value=0.0034  Score=40.74  Aligned_cols=55  Identities=22%  Similarity=0.332  Sum_probs=43.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG  122 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~  122 (192)
                      +..||. .|..+...||.++|++||.| .|.++.|.       -|||...+.+.|..++..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            556775 99999999999999999998 66777773       699999999999999988764

; 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.

>KOG1548|consensus

Probab=97.15  E-value=0.0019  Score=52.41  Aligned_cols=82  Identities=17%  Similarity=0.362  Sum_probs=62.4

Q ss_pred             CCCCCCCcEEEEcCCCC----CCc-------HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy15152         52 PQRSVEGWILFVTGVHE----EAQ-------EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL  120 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~----~~t-------~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l  120 (192)
                      +.+....++|.+.|+=-    ..+       .++|.+-..+||.|.+|.|- ++   -+.|.+-|.|.+.++|..|++.|
T Consensus       259 ~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d~---hPdGvvtV~f~n~eeA~~ciq~m  334 (382)
T KOG1548|consen  259 PSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-DR---HPDGVVTVSFRNNEEADQCIQTM  334 (382)
T ss_pred             cccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-cc---CCCceeEEEeCChHHHHHHHHHh
Confidence            34444567888888732    223       24566667889999998663 22   24689999999999999999999


Q ss_pred             CCCeeCCeEEEEEeccc
Q psy15152        121 NGTTILGQTVTVDWCFV  137 (192)
Q Consensus       121 ~~~~~~g~~l~v~~a~~  137 (192)
                      +|..++||.|.-.....
T Consensus       335 ~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  335 DGRWFDGRQLTASIWDG  351 (382)
T ss_pred             cCeeecceEEEEEEeCC
Confidence            99999999999876543

>KOG0149|consensus

Probab=96.98  E-value=0.00048  Score=53.00  Aligned_cols=29  Identities=14%  Similarity=0.282  Sum_probs=24.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCC-ChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETS-TRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f-~~~~~   35 (192)
                      .|...+++.|+.|+| |||||||+| +.++.
T Consensus        38 eI~eavvitd~~t~r-skGyGfVTf~d~~aa   67 (247)
T KOG0149|consen   38 EIVEAVVITDKNTGR-SKGYGFVTFRDAEAA   67 (247)
T ss_pred             ceEEEEEEeccCCcc-ccceeeEEeecHHHH
Confidence            356889999999997 999999999 54443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.94  E-value=0.0052  Score=37.75  Aligned_cols=54  Identities=28%  Similarity=0.277  Sum_probs=44.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccC---CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEY---GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL  120 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~---G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l  120 (192)
                      ..|+|.|+.. ++.++++.+|..|   .....+.|+-|.       -|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4699999966 6778899999988   235588998884       5889999999999999864

>KOG0128|consensus

Probab=96.78  E-value=6.9e-05  Score=66.76  Aligned_cols=69  Identities=23%  Similarity=0.319  Sum_probs=59.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      ..++||+||+..+.+++|...|..+|.+..+++.-...+++.+|+||++|...+.+.+|+....+..++
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            367999999999999999999999999887776655568999999999999999999999865555544

>KOG2202|consensus

Probab=96.72  E-value=0.00071  Score=52.72  Aligned_cols=63  Identities=27%  Similarity=0.406  Sum_probs=49.7

Q ss_pred             HHHHhhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         74 DMHEKFS-EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        74 ~L~~~F~-~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +|...|+ +||+|..+.+-.+. .---.|=+||.|...++|++|++.||+..+.|++|...+..-
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            4444444 79999988665443 223467899999999999999999999999999999987743

>KOG0115|consensus

Probab=96.60  E-value=0.0029  Score=49.40  Aligned_cols=77  Identities=22%  Similarity=0.251  Sum_probs=62.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC----eeCCeEEEEEe
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT----TILGQTVTVDW  134 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~----~~~g~~l~v~~  134 (192)
                      ..|||.||...++.+.|.+.|+.||.|....+..| ..++..+-++|.|...-.|.+|+..+...    ...+++.-|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            67999999999999999999999999987666666 36888999999999999999999887332    24456666654


Q ss_pred             cc
Q psy15152        135 CF  136 (192)
Q Consensus       135 a~  136 (192)
                      ..
T Consensus       111 ~e  112 (275)
T KOG0115|consen  111 ME  112 (275)
T ss_pred             hh
Confidence            44

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=96.55  E-value=0.0067  Score=47.13  Aligned_cols=110  Identities=17%  Similarity=0.257  Sum_probs=68.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCC---C-----CC----CCC-------------------CCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETD---V-----GD----EEP-------------------GPQ   53 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~---~-----~~----~~~-------------------~~~   53 (192)
                      +..+.+..|+.++. +||||||+|....  ..+...++..   +     ..    ..+                   ...
T Consensus       142 ~~~~~~~~d~~~~~-~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (306)
T COG0724         142 VKRVRLVRDRETGK-SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKAL  220 (306)
T ss_pred             eeEEEeeeccccCc-cCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhccccccccc
Confidence            35788899999995 9999999993333  3333333211   1     00    000                   011


Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHH
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR  117 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al  117 (192)
                      .......+++++++..++..++...|..+|.+....+...........+.++.+.....+....
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         221 LLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             cccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhh
Confidence            2234578999999999999999999999999977766655433334444444444444433333

>KOG2068|consensus

Probab=96.33  E-value=0.0016  Score=52.65  Aligned_cols=79  Identities=19%  Similarity=0.349  Sum_probs=60.9

Q ss_pred             CcEEEEcCCCCCCcHHHH-H--HhhccCCCeeEEEEeecCC----CCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         58 GWILFVTGVHEEAQEDDM-H--EKFSEYGEIKNLHLNLDRR----TGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L-~--~~F~~~G~i~~~~i~~~~~----tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ..-+||-+|+.....+.+ +  +.|.+||.|..+.+..++.    .+.. .-++|+|...++|..||...+|..++|+.|
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            456889899988665544 3  6799999999998877651    1222 238999999999999999999999999887


Q ss_pred             EEEeccc
Q psy15152        131 TVDWCFV  137 (192)
Q Consensus       131 ~v~~a~~  137 (192)
                      +..+..+
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            7666543

>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=96.25  E-value=0.012  Score=44.18  Aligned_cols=82  Identities=12%  Similarity=0.201  Sum_probs=52.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhcc-CCCe---eEEEEeecCC-C-CCcceEEEEEecCHHHHHHHHHHhCCCeeCC---
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSE-YGEI---KNLHLNLDRR-T-GFLKGYALVEYDSYKEASAARDALNGTTILG---  127 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~-~G~i---~~~~i~~~~~-t-g~~~g~afV~f~~~~~a~~al~~l~~~~~~g---  127 (192)
                      ...+|.|++||+.+|++++.+.+++ ++.-   ..+.-..... . -..-.-|||.|.+.+++......++|+.+.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999998887 6655   2333112211 1 1123569999999999999999999987632   


Q ss_pred             --eEEEEEecccC
Q psy15152        128 --QTVTVDWCFVK  138 (192)
Q Consensus       128 --~~l~v~~a~~~  138 (192)
                        .+..|++|--.
T Consensus        86 ~~~~~~VE~Apyq   98 (176)
T PF03467_consen   86 NEYPAVVEFAPYQ   98 (176)
T ss_dssp             -EEEEEEEE-SS-
T ss_pred             CCcceeEEEcchh
Confidence              35677777653

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.

>KOG4208|consensus

Probab=96.22  E-value=0.0024  Score=48.27  Aligned_cols=62  Identities=10%  Similarity=0.064  Sum_probs=40.4

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhHHHhhhcccCCCCCCCCCCCCCCCCcEEEEcCCCCC-CcHHHHHHh
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEE-AQEDDMHEK   78 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~t~~~L~~~   78 (192)
                      ..+++.+.+.||. |+|||||+|+.++.+.+.+-.+++. .--       ++.|.+.-+|+. .-+..+...
T Consensus        78 ~r~rlsRnkrTGN-SKgYAFVEFEs~eVA~IaAETMNNY-Ll~-------e~lL~c~vmppe~~v~~~~~k~  140 (214)
T KOG4208|consen   78 TRFRLSRNKRTGN-SKGYAFVEFESEEVAKIAAETMNNY-LLM-------EHLLECHVMPPEQKVEKNLKKV  140 (214)
T ss_pred             EEEEeecccccCC-cCceEEEEeccHHHHHHHHHHhhhh-hhh-------hheeeeEEeCchhhhhhhhhhh
Confidence            3566779999995 9999999998888877766555541 111       134666667776 333333333

>KOG0122|consensus

Probab=96.17  E-value=0.0029  Score=49.10  Aligned_cols=38  Identities=13%  Similarity=0.171  Sum_probs=29.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCC--ChhHHHhhhcccCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETS--TRNEIREYESMETDV   45 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f--~~~~~~~~~~~~~~~   45 (192)
                      +..|.+.+|+.|+. +|||+||+|  ..++..++..+++.+
T Consensus       216 i~rvylardK~TG~-~kGFAFVtF~sRddA~rAI~~LnG~g  255 (270)
T KOG0122|consen  216 ITRVYLARDKETGL-SKGFAFVTFESRDDAARAIADLNGYG  255 (270)
T ss_pred             cceeEEEEccccCc-ccceEEEEEecHHHHHHHHHHccCcc
Confidence            45688999999996 999999999  455566666666655

>KOG0111|consensus

Probab=96.17  E-value=0.0015  Score=49.90  Aligned_cols=35  Identities=23%  Similarity=0.331  Sum_probs=27.9

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCC--ChhHHHhhhccc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETS--TRNEIREYESME   42 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f--~~~~~~~~~~~~   42 (192)
                      +.+|+++.|-.++ |+||||||+|  .+++.++++.++
T Consensus        37 I~dIqiPlDyesq-kHRgFgFVefe~aEDAaaAiDNMn   73 (298)
T KOG0111|consen   37 IKDIQIPLDYESQ-KHRGFGFVEFEEAEDAAAAIDNMN   73 (298)
T ss_pred             hhhcccccchhcc-cccceeEEEeeccchhHHHhhcCc
Confidence            5689999999999 5999999999  555566666553

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.03  E-value=0.036  Score=39.74  Aligned_cols=74  Identities=19%  Similarity=0.314  Sum_probs=55.5

Q ss_pred             CCCCcEEEEcCCCCCCcH-H---HHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         55 SVEGWILFVTGVHEEAQE-D---DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~-~---~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      .++-.+|.|+=|..++.. +   .+...++.||+|.++.+     .|  +.-|.|.|.+..+|-.|+.+++. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-----cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-----CG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-----cC--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            455678888766665443 3   45566788999999865     33  34799999999999999999766 6677888


Q ss_pred             EEEecc
Q psy15152        131 TVDWCF  136 (192)
Q Consensus       131 ~v~~a~  136 (192)
                      .+.|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            888754

>KOG2193|consensus

Probab=95.88  E-value=0.0014  Score=54.63  Aligned_cols=109  Identities=17%  Similarity=0.262  Sum_probs=76.7

Q ss_pred             CccCCCCChhHH--HhhhcccCC----CCCC--CCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEE-eecC
Q psy15152         24 GFGTETSTRNEI--REYESMETD----VGDE--EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHL-NLDR   94 (192)
Q Consensus        24 G~gfv~f~~~~~--~~~~~~~~~----~~~~--~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i-~~~~   94 (192)
                      ||+||.......  .+.+.++..    |...  ....+....++++-+.|+|+...++.|..++..||.+..+.. ..+.
T Consensus        38 gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~  117 (584)
T KOG2193|consen   38 GYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDS  117 (584)
T ss_pred             ceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccch
Confidence            899998843333  223333222    2111  111223334567999999999999999999999999988754 4443


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         95 RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        95 ~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+    -.--|+|.+.+.+..|+..|+|..+....++|.|-.
T Consensus       118 et----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen  118 ET----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             HH----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            32    123468899999999999999999999999998864

>KOG1996|consensus

Probab=95.85  E-value=0.033  Score=44.50  Aligned_cols=64  Identities=22%  Similarity=0.235  Sum_probs=50.3

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcc-eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         73 DDMHEKFSEYGEIKNLHLNLDRRTGFLK-GYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        73 ~~L~~~F~~~G~i~~~~i~~~~~tg~~~-g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +++++-..+||.|..|.|...+..-... ---||+|...++|.+|+--|||..++|+.+..-|..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            4566778899999999887775322222 246999999999999999999999999998776543

>KOG4676|consensus

Probab=95.85  E-value=0.045  Score=45.42  Aligned_cols=75  Identities=19%  Similarity=0.313  Sum_probs=60.4

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCC---CCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT---GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~t---g~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .|.|.||.++++.+++..+|.-.|.|..+.|......   ....-.|||.|.+...+..|.. |.++++-++.|.|..+
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            6999999999999999999999999999988654321   2234589999999999888875 7788877777666543

>KOG2135|consensus

Probab=95.81  E-value=0.0052  Score=51.85  Aligned_cols=77  Identities=18%  Similarity=0.267  Sum_probs=61.7

Q ss_pred             CCcEEEEcCCCCCC-cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         57 EGWILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~-t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +.+.|-+.-.|+.. +-++|..+|.+||.|..|.+-+..      --|.|+|.+..+|-.|.. .++..|+++.|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhc-cccceecCceeEEEEe
Confidence            34556666667764 458999999999999999875552      369999999999977776 4899999999999999


Q ss_pred             ccCCC
Q psy15152        136 FVKGP  140 (192)
Q Consensus       136 ~~~~~  140 (192)
                      .+.+.
T Consensus       444 nps~~  448 (526)
T KOG2135|consen  444 NPSPV  448 (526)
T ss_pred             cCCcc
Confidence            87653

>KOG0113|consensus

Probab=95.70  E-value=0.0064  Score=48.55  Aligned_cols=33  Identities=18%  Similarity=0.337  Sum_probs=25.9

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChh--HHHhhhc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRN--EIREYES   40 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~--~~~~~~~   40 (192)
                      |+.|.+++|+.|+ |++||+||+|..+  ...+|..
T Consensus       128 IkrirlV~d~vTg-kskGYAFIeye~erdm~~AYK~  162 (335)
T KOG0113|consen  128 IKRIRLVRDKVTG-KSKGYAFIEYEHERDMKAAYKD  162 (335)
T ss_pred             ceeEEEeeecccC-CccceEEEEeccHHHHHHHHHh
Confidence            6789999999999 6999999999433  3444443

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.60  E-value=0.036  Score=41.79  Aligned_cols=63  Identities=22%  Similarity=0.224  Sum_probs=46.5

Q ss_pred             cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC--CCeeCCeEEEEEecccCC
Q psy15152         71 QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN--GTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        71 t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~--~~~~~g~~l~v~~a~~~~  139 (192)
                      ..+.|+++|..|+.+.....+...      +-..|.|.+.++|.+|...|+  +..+.|..+++.|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            347899999999998888776553      358899999999999999999  999999999999996544

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.

>KOG4207|consensus

Probab=95.56  E-value=0.0056  Score=46.48  Aligned_cols=36  Identities=14%  Similarity=0.304  Sum_probs=27.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCC--ChhHHHhhhcccC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETS--TRNEIREYESMET   43 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f--~~~~~~~~~~~~~   43 (192)
                      +-+|-|.+|+.|+. +|||+||.|  ..++..+++++++
T Consensus        40 vgDVyIPrdr~Tr~-sRgFaFVrf~~k~daedA~damDG   77 (256)
T KOG4207|consen   40 VGDVYIPRDRYTRQ-SRGFAFVRFHDKRDAEDALDAMDG   77 (256)
T ss_pred             ccceeccccccccc-ccceeEEEeeecchHHHHHHhhcc
Confidence            34899999999996 999999999  4555555555543

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

Probab=95.50  E-value=0.0091  Score=43.26  Aligned_cols=28  Identities=14%  Similarity=0.279  Sum_probs=23.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|+.+++ +||||||+|...+.
T Consensus        61 I~~v~i~~d~~tg~-~kGfaFV~F~~~e~   88 (144)
T PLN03134         61 VVDAKVIVDRETGR-SRGFGFVNFNDEGA   88 (144)
T ss_pred             eEEEEEEecCCCCC-cceEEEEEECCHHH
Confidence            67899999999995 99999999954443

>KOG4454|consensus

Probab=95.49  E-value=0.0052  Score=47.05  Aligned_cols=112  Identities=17%  Similarity=0.224  Sum_probs=78.0

Q ss_pred             eEEeeccCcCCCCCCccCCCCChhHHHhhhcccCCCCCCCCCCCCCCCCcEEEEcC----CCCCCcHHHHHHhhccCCCe
Q psy15152         10 IARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTG----VHEEAQEDDMHEKFSEYGEI   85 (192)
Q Consensus        10 v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~t~~~L~~~F~~~G~i   85 (192)
                      |.+..++..+  .+ |+||.|..+....++-.-.++......    ....+++.|+    |...++++.+.+.|+.-|.+
T Consensus        39 v~ip~~~d~~--~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~----e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~  111 (267)
T KOG4454|consen   39 VGIPSGQDQE--QK-FAYVFFPNENSVQLAGQLENGDDLEED----EEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPI  111 (267)
T ss_pred             EeCCCCccCC--Cc-eeeeecccccchhhhhhhcccchhccc----hhhcccccCCCcchhhhhcchhhheeeecccCCC
Confidence            4444444444  34 999999555544444333333222222    2234688888    88899999999999999999


Q ss_pred             eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         86 KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        86 ~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      ..+++..+. .|+++.++|+.+.-..+.-.++....+..+--++
T Consensus       112 ~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen  112 EGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKK  154 (267)
T ss_pred             CCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCCCC
Confidence            999999996 5889999999998777777777776665544333

>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=95.30  E-value=0.1  Score=33.21  Aligned_cols=67  Identities=24%  Similarity=0.377  Sum_probs=38.8

Q ss_pred             EEEEc-CCCCCCcHHHHHHhhccCCCe-----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         60 ILFVT-GVHEEAQEDDMHEKFSEYGEI-----KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        60 ~l~V~-nLp~~~t~~~L~~~F~~~G~i-----~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ++||. +--..++..+|..++..-+.|     -.+.+..+        |+||+-.. +.|+.+++.|++..+.|++++|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            35552 223357888888888876544     45665433        89999885 58899999999999999999998


Q ss_pred             ec
Q psy15152        134 WC  135 (192)
Q Consensus       134 ~a  135 (192)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            65

; PDB: 2G0C_A 3MOJ_B.

>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=95.22  E-value=0.46  Score=32.73  Aligned_cols=65  Identities=11%  Similarity=0.085  Sum_probs=47.5

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      .+.+...|..++.++|..+.+.+- .|..+++++|.  ..++-.+++.|.+.++|......+||..+.
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            344444455555566766655553 56788888884  346778999999999999999999999864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0226|consensus

Probab=95.00  E-value=0.013  Score=45.92  Aligned_cols=37  Identities=14%  Similarity=0.105  Sum_probs=26.5

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhHHHhhhcccCCCC
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVG   46 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~~~~   46 (192)
                      ..++++|+.|+ |++|||||+|...+....+-.++++.
T Consensus       219 ~akviRdkRTg-KSkgygfVSf~~pad~~rAmrem~gk  255 (290)
T KOG0226|consen  219 KAKVIRDKRTG-KSKGYGFVSFRDPADYVRAMREMNGK  255 (290)
T ss_pred             hcccccccccc-ccccceeeeecCHHHHHHHHHhhccc
Confidence            45688999999 69999999995555444444445543

>smart00361 RRM_1 RNA recognition motif

Probab=94.94  E-value=0.016  Score=36.32  Aligned_cols=27  Identities=22%  Similarity=0.067  Sum_probs=19.2

Q ss_pred             eeeE-EeeccCc--CCCCCCccCCCCChhHH
Q psy15152          8 KGIA-RLKEKAR--KKKGRGFGTETSTRNEI   35 (192)
Q Consensus         8 ~~v~-~~~d~~~--~~k~rG~gfv~f~~~~~   35 (192)
                      .+|. +..|+.+  ++ +|||+||+|...+.
T Consensus        20 ~~v~~v~~~~~~~~~~-~rG~~fV~f~~~~d   49 (70)
T smart00361       20 GKINKIYIDNVGYENH-KRGNVYITFERSED   49 (70)
T ss_pred             eEEEEEEeCCCCCCCC-CcEEEEEEECCHHH
Confidence            3553 6777776  75 99999999944443

>KOG0112|consensus

Probab=94.88  E-value=0.0057  Score=55.30  Aligned_cols=79  Identities=16%  Similarity=0.227  Sum_probs=65.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ...+||+|||+..+++.+|+..|..+|.|.+|.|-.-. -+.-.-||||.|.+...+..|...+.+..|..-.+++.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            45789999999999999999999999999998876553 23334599999999999999999999988776566665554

>KOG4660|consensus

Probab=94.81  E-value=0.066  Score=46.21  Aligned_cols=82  Identities=16%  Similarity=0.212  Sum_probs=60.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC----CeEEEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFS-EYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL----GQTVTV  132 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~----g~~l~v  132 (192)
                      .+++.|.|+|...|...|.+.-. ..|.-..+.++.|-.+....|||||.|.+.+++..+.++.||+.+.    .+...+
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            35566666666666555544422 2566667778888778888999999999999999999999998743    466777


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .||.-.+
T Consensus       468 tYArIQG  474 (549)
T KOG4660|consen  468 TYARIQG  474 (549)
T ss_pred             ehhhhhc
Confidence            7876554

>KOG4210|consensus

Probab=94.77  E-value=0.046  Score=44.15  Aligned_cols=83  Identities=18%  Similarity=0.089  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ...++|++++.+.+.+.+...++..+|......+........++|++++.|...+.+..|+.......+.+..+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            45789999999999999888899999988777776666688899999999999999999998644456777776666655


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ...
T Consensus       167 ~~~  169 (285)
T KOG4210|consen  167 RRG  169 (285)
T ss_pred             ccc
Confidence            444

>KOG0126|consensus

Probab=94.27  E-value=0.023  Score=42.45  Aligned_cols=28  Identities=18%  Similarity=0.317  Sum_probs=23.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+++|++++|+.|| ||+||+|.-|+...
T Consensus        61 e~vdinLiRDk~TG-KSKGFaFLcYEDQR   88 (219)
T KOG0126|consen   61 EIVDINLIRDKKTG-KSKGFAFLCYEDQR   88 (219)
T ss_pred             ceEEEEEEecCCCC-cccceEEEEecCcc
Confidence            46799999999999 69999999884333

>KOG2253|consensus

Probab=94.18  E-value=0.036  Score=48.75  Aligned_cols=79  Identities=13%  Similarity=0.043  Sum_probs=66.0

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy15152         48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG  127 (192)
Q Consensus        48 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g  127 (192)
                      ..|..+...+..++||+|+...+..+-+..+...+|.|..+....         |||.+|..+..+.+|+..++...++|
T Consensus        30 ~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~  100 (668)
T KOG2253|consen   30 IQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDD  100 (668)
T ss_pred             CcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCc
Confidence            344455566778999999999999999999999999887654321         99999999999999999999999999


Q ss_pred             eEEEEEec
Q psy15152        128 QTVTVDWC  135 (192)
Q Consensus       128 ~~l~v~~a  135 (192)
                      ..+.+..-
T Consensus       101 ~kl~~~~d  108 (668)
T KOG2253|consen  101 QKLIENVD  108 (668)
T ss_pred             chhhccch
Confidence            98887653

>KOG4285|consensus

Probab=93.96  E-value=0.26  Score=39.65  Aligned_cols=68  Identities=25%  Similarity=0.267  Sum_probs=50.4

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE-EEEEecc
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT-VTVDWCF  136 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~-l~v~~a~  136 (192)
                      |-|-+.|+.-. .-|..+|++||.|.+....      ..-.+-+|.|.++.+|++||.. +|..|+|.. |-|+...
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            55557777533 4567889999999876433      2235899999999999999986 999998764 5555543

>KOG4574|consensus

Probab=93.20  E-value=0.057  Score=48.90  Aligned_cols=74  Identities=22%  Similarity=0.236  Sum_probs=62.9

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee--CCeEEEEEeccc
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI--LGQTVTVDWCFV  137 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~--~g~~l~v~~a~~  137 (192)
                      +.++.|.+-..+...|..+++.||.+.+.+.+++-      ..|.|+|.+.+.|-.|+.+|+|..+  -|-+.+|.+|+.
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 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            45566667777888899999999999999888774      4899999999999999999999984  588899999976


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      -+
T Consensus       374 ~~  375 (1007)
T KOG4574|consen  374 LP  375 (1007)
T ss_pred             cc
Confidence            54

>KOG0125|consensus

Probab=92.64  E-value=0.074  Score=43.20  Aligned_cols=35  Identities=14%  Similarity=0.208  Sum_probs=23.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHhhhcccCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIREYESMETD   44 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~~   44 (192)
                      +.+|.++.+.   |.|||||||+|+..+.++.++.++.
T Consensus       123 VldVEIIfNE---RGSKGFGFVTmen~~dadRARa~LH  157 (376)
T KOG0125|consen  123 VLDVEIIFNE---RGSKGFGFVTMENPADADRARAELH  157 (376)
T ss_pred             eeeEEEEecc---CCCCccceEEecChhhHHHHHHHhh
Confidence            4577777643   3699999999966665555554444

>KOG2591|consensus

Probab=91.86  E-value=0.56  Score=40.89  Aligned_cols=69  Identities=13%  Similarity=0.211  Sum_probs=53.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhcc--CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC--eeCCeEEEE
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSE--YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT--TILGQTVTV  132 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~--~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~--~~~g~~l~v  132 (192)
                      ..+.+.++-+|..+-.|+++.+|+.  +-.+.+|.+..+-       -=||+|++..+|+.|.+.|...  .|.|++|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            3467888999999999999999986  5577788776653       2489999999999999877543  366665544

>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=90.43  E-value=2.1  Score=26.60  Aligned_cols=55  Identities=22%  Similarity=0.329  Sum_probs=42.7

Q ss_pred             CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         69 EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        69 ~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      .++-++++..+..|+-   .+|..|+ |    | =||.|.+..+|+++....+|..+.+.+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~---~~I~~d~-t----G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW---DRIRDDR-T----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEecC-C----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3577899999999853   2445554 3    2 389999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804|consensus

Probab=88.59  E-value=1.7  Score=36.99  Aligned_cols=67  Identities=13%  Similarity=0.199  Sum_probs=57.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      +..|+|=.+|-.++.-||..|...+- .|.++++++|. . -.+=..+|.|.+.++|....+.+||..+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~-~-pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG-M-PNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC-C-CceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            78899999999999999999988754 57899999974 2 23457889999999999999999999865

>smart00360 RRM RNA recognition motif

Probab=87.51  E-value=0.54  Score=27.96  Aligned_cols=27  Identities=19%  Similarity=0.385  Sum_probs=21.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +..+.+..++.++. ++||+||+|...+
T Consensus        23 v~~~~i~~~~~~~~-~~~~a~v~f~~~~   49 (71)
T smart00360       23 IESVRLVRDKDTGK-SKGFAFVEFESEE   49 (71)
T ss_pred             EeEEEEEeCCCCCC-CCceEEEEeCCHH
Confidence            45778888888784 9999999994433

>KOG2318|consensus

Probab=86.82  E-value=4.6  Score=35.58  Aligned_cols=84  Identities=21%  Similarity=0.283  Sum_probs=62.2

Q ss_pred             CCCCCCCcEEEEcCCCCC-CcHHHHHHhhccC----CCeeEEEEeecC----------CCCC------------------
Q psy15152         52 PQRSVEGWILFVTGVHEE-AQEDDMHEKFSEY----GEIKNLHLNLDR----------RTGF------------------   98 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~-~t~~~L~~~F~~~----G~i~~~~i~~~~----------~tg~------------------   98 (192)
                      +.....+++|-|-|+.|+ +..++|.-+|..|    |.|.+|.|-...          ..|.                  
T Consensus       168 ~~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~  247 (650)
T KOG2318|consen  168 PVLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDD  247 (650)
T ss_pred             cccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccch
Confidence            455677889999999997 8889999888764    578888763221          1121                  


Q ss_pred             -------------------cceEEEEEecCHHHHHHHHHHhCCCeeCCe--EEEEEec
Q psy15152         99 -------------------LKGYALVEYDSYKEASAARDALNGTTILGQ--TVTVDWC  135 (192)
Q Consensus        99 -------------------~~g~afV~f~~~~~a~~al~~l~~~~~~g~--~l~v~~a  135 (192)
                                         ..=||.|+|.+.+.|.+..+.++|..+...  .|-++|.
T Consensus       248 ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  248 EEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                               123899999999999999999999998754  5555544

>KOG0108|consensus

Probab=86.18  E-value=0.54  Score=40.22  Aligned_cols=35  Identities=17%  Similarity=0.264  Sum_probs=25.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCCh--hHHHhhhccc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTR--NEIREYESME   42 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~--~~~~~~~~~~   42 (192)
                      +.++++.-|+.||+ .|||||++|..  ....+...++
T Consensus        45 v~s~~~v~D~~tG~-~~G~~f~~~~~~~~~~~a~~~lN   81 (435)
T KOG0108|consen   45 VLSFRLVYDRETGK-PKGFGFCEFTDEETAERAIRNLN   81 (435)
T ss_pred             cceeeecccccCCC-cCceeeEecCchhhHHHHHHhcC
Confidence            45788999999995 99999999943  3344444443

>PF00076 RRM_1: RNA recognition motif

Probab=83.63  E-value=0.37  Score=29.28  Aligned_cols=27  Identities=15%  Similarity=0.299  Sum_probs=19.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +..+.+..+ .++ +++|||||+|...+.
T Consensus        25 i~~~~~~~~-~~~-~~~~~a~V~F~~~~~   51 (70)
T PF00076_consen   25 IESIKVMRN-SSG-KSKGYAFVEFESEED   51 (70)
T ss_dssp             EEEEEEEEE-TTS-SEEEEEEEEESSHHH
T ss_pred             ccccccccc-ccc-cccceEEEEEcCHHH
Confidence            356777777 556 499999999954443

(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 ....

>KOG4483|consensus

Probab=82.67  E-value=3.1  Score=35.01  Aligned_cols=55  Identities=20%  Similarity=0.236  Sum_probs=47.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCC-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA  119 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~-i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~  119 (192)
                      -+.|-|.++|.....+||...|..|+. --+|.|+-|.       .||..|.+...|..||-.
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            478889999999989999999999875 4578888774       899999999999999964

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	192
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		4e-54
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		8e-43
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		6e-42
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		4e-40
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		4e-40
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		1e-38
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-38
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		7e-37
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		4e-08
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-08
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		7e-08
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		8e-08
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		9e-08
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		1e-07
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		3e-07
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		7e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-07
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		4e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		5e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		5e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		6e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		7e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		3e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-05
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		5e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		7e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		8e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		8e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		2e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		4e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		4e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		4e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		4e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		4e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		4e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-04
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		5e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		5e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		6e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		6e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		6e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		6e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		7e-04
2la6_A	99	Solution Nmr Structure Of Rrm Domain Of Rna-Binding		7e-04
2lcw_A	116	Solution Structure Of FusTLS RRM DOMAIN Length = 11		8e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		9e-04

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score =  207 bits (526), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 95/142 (66%), Positives = 119/142 (83%), Gaps = 1/142 (0%)
Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDE-EPGPQRSVEGWILFVTGV 66
           +GI RLKEKA+ +KGRGFG++++TR  I  YE +  +  DE EPGPQRSVEGWILFVT +
Sbjct: 21  QGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI 80
Query: 67  HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
           HEEAQED++ EKF +YGEIKN+HLNLDRRTGF KGYALVEY+++K+A AA++ALNG  I+
Sbjct: 81  HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM 140
Query: 127 GQTVTVDWCFVKGPKKVAGEQK 148
           GQT+ VDWCFVKGPK+V   +K
Sbjct: 141 GQTIQVDWCFVKGPKRVKKSEK 162

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score =  169 bits (429), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 77/109 (70%), Positives = 93/109 (85%), Gaps = 1/109 (0%)
Query: 35  IREYESMETDVGDE-EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLD 93
           I  YE +  +  DE EPGPQRSVEGWILFVT +HEEAQED++ EKF +YGEIKN+HLNLD
Sbjct: 2   IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61
Query: 94  RRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           RRTGF KGYALVEY+++K+A AA++ALNG  I+GQT+ VDWCFVKGPK+
Sbjct: 62  RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score =  166 bits (421), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 76/104 (73%), Positives = 93/104 (89%), Gaps = 2/104 (1%)
Query: 37  EYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT 96
           +Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRT
Sbjct: 4   DYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 97  GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           G+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV+GP
Sbjct: 62  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score =  160 bits (405), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 74/101 (73%), Positives = 90/101 (89%), Gaps = 2/101 (1%)
Query: 37  EYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT 96
           +Y+S+E D GDE PGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRT
Sbjct: 3   DYDSVEQD-GDE-PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 97  GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV 137
           G+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV
Sbjct: 61  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score =  160 bits (405), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 83/91 (91%)
Query: 50  PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           PGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++
Sbjct: 1   PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 110 YKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           YKEA AA + LNG  ++GQ ++VDWCFV+GP
Sbjct: 61  YKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 91

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score =  155 bits (392), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 67/89 (75%), Positives = 81/89 (91%)
Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           PQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YK
Sbjct: 1   PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 112 EASAARDALNGTTILGQTVTVDWCFVKGP 140
           EA AA + LNG  ++GQ ++VDWCFV+GP
Sbjct: 61  EAQAAMEGLNGQDLMGQPISVDWCFVRGP 89

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score =  155 bits (392), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 67/89 (75%), Positives = 81/89 (91%)
Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           PQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YK
Sbjct: 1   PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 112 EASAARDALNGTTILGQTVTVDWCFVKGP 140
           EA AA + LNG  ++GQ ++VDWCFV+GP
Sbjct: 61  EAQAAMEGLNGQDLMGQPISVDWCFVRGP 89

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score =  149 bits (377), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 65/86 (75%), Positives = 78/86 (90%)
Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           PQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRTG+LKGY LVEY++YK
Sbjct: 1   PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 112 EASAARDALNGTTILGQTVTVDWCFV 137
           EA AA + LNG  ++GQ ++VDWCFV
Sbjct: 61  EAQAAMEGLNGQDLMGQPISVDWCFV 86

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 47/76 (61%)
Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D 
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 120 LNGTTILGQTVTVDWC 135
           +N + + G+T+ V+  
Sbjct: 74  MNESELFGRTIRVNLA 89

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 53.9 bits (128), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 48/86 (55%), Gaps = 4/86 (4%)
Query: 51  GPQ-RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           GP  RS     LFV G+ E+  E+ + E F   G ++   +  DR TG  KG+  V+++S
Sbjct: 7   GPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNS 63
Query: 110 YKEASAARDALNGTTILGQTVTVDWC 135
            ++A AA++A+    I G  VT+DW 
Sbjct: 64  EEDAKAAKEAMEDGEIDGNKVTLDWA 89

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 53.5 bits (127), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 47/76 (61%)
Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D 
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 120 LNGTTILGQTVTVDWC 135
           +N + + G+T+ V+  
Sbjct: 69  MNESELFGRTIRVNLA 84

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 47/76 (61%)
Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 120 LNGTTILGQTVTVDWC 135
           +N + + G+T+ V+  
Sbjct: 67  MNESELFGRTIRVNLA 82

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 53.1 bits (126), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 47/76 (61%)
Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D 
Sbjct: 4   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 120 LNGTTILGQTVTVDWC 135
           +N + + G+T+ V+  
Sbjct: 64  MNESELFGRTIRVNLA 79

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 47/74 (63%)
Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D 
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 120 LNGTTILGQTVTVD 133
           +N + + G+T+ V+
Sbjct: 125 MNESELFGRTIRVN 138

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  V+ +  E  +  +F  YG IK +H+   +R+G  +GYA +EY+  ++  +A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 121 NGTTILGQTVTVD 133
           +G  I G+ V VD
Sbjct: 165 DGKKIDGRRVLVD 177

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  V+ +  E  +  +F  YG IK +H+   +R+G  +GYA +EY+  ++  +A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 121 NGTTILGQTVTVD 133
           +G  I G+ V VD
Sbjct: 165 DGKKIDGRRVLVD 177

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 50  PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           P   RS+    +FV  +  EA E+ + + FSE G + +  L  DR TG  KGY   EY  
Sbjct: 2   PAVDRSLRS--VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 110 YKEASAARDALNGTTILGQTVTVD 133
            + A +A   LNG    G+ + VD
Sbjct: 60  QETALSAMRNLNGREFSGRALRVD 83

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 40/82 (48%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + +M + FS+YG I    + LD+ TG  +G   + +D   EA  A   L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG   LG    +   F   P +
Sbjct: 64  NGQKPLGAAEPITVKFANNPSQ 85

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 42/88 (47%)
Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           S+    L+V+G+ +   + +M + FS+YG I    + LD+ TG  +G   + +D   EA 
Sbjct: 87  SIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAE 146
Query: 115 AARDALNGTTILGQTVTVDWCFVKGPKK 142
            A   LNG   LG    +   F   P +
Sbjct: 147 EAIKGLNGQKPLGAAEPITVKFANNPSQ 174

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  VH++  +DD+   F  +G+IK+  L  D  TG  KGY  +EY+  + +  A  ++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 121 NGTTILGQTVTV 132
           N   + GQ + V
Sbjct: 173 NLFDLGGQYLRV 184

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  VH++  +DD+   F  +G+IK+  L  D  TG  KGY  +EY+  + +  A  ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 121 NGTTILGQTVTV 132
           N   + GQ + V
Sbjct: 188 NLFDLGGQYLRV 199

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 42/75 (56%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV G+  +  E  + + FS+YG+I  + +  DR T   +G+  V +++  +A  A  A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 121 NGTTILGQTVTVDWC 135
           NG ++ G+ + VD  
Sbjct: 75  NGKSVDGRQIRVDQA 89

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 45/82 (54%)
Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
             L V G+     E D+ E FS+YG I ++ +  D+++   +G+A V +++  +A  A++
Sbjct: 13  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 72
Query: 119 ALNGTTILGQTVTVDWCFVKGP 140
             NG  + G+ + VD+   K P
Sbjct: 73  RANGMELDGRRIRVDFSITKRP 94

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEI-KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +F+  +  E  E  +++ FS +G I +   +  D  TG  KGYA + + S+  + AA +A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 120 LNGTTILGQTVTVDWCFVKGPK 141
           +NG  +  + +TV + F K  K
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSK 89

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 45/82 (54%)
Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
             L V G+     E D+ E FS+YG I ++ +  D+++   +G+A V +++  +A  A++
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 119 ALNGTTILGQTVTVDWCFVKGP 140
             NG  + G+ + VD+   K P
Sbjct: 76  RANGMELDGRRIRVDFSITKRP 97

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 45/82 (54%)
Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
             L V G+     E D+ E FS+YG I ++ +  D+++   +G+A V +++  +A  A++
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 119 ALNGTTILGQTVTVDWCFVKGP 140
             NG  + G+ + VD+   K P
Sbjct: 107 RANGMELDGRRIRVDFSITKRP 128

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  VH++  +DD+   F  +G+IK+  L  D  TG  KGY  +EY+  + +  A  + 
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 121 NGTTILGQTVTV 132
           N   + GQ + V
Sbjct: 172 NLFDLGGQYLRV 183

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 10/110 (9%)
Query: 45  VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL 104
            G ++ GP    EG  LF+  + +E  + D+ + F  +G + +  + +D++T   K +  
Sbjct: 16  AGSQKEGP----EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 71
Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
           V YD+   A AA  ++NG  I  + + V        K+   + K GP  G
Sbjct: 72  VSYDNPVSAQAAIQSMNGFQIGMKRLKVQL------KRSKNDSKSGPSSG 115

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 1/86 (1%)
Query: 51  GPQRSVE-GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           GP R  +    + VT + E+ +E D+ E F  +G I  ++L  D+ TG  KG+A + +  
Sbjct: 7   GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66
Query: 110 YKEASAARDALNGTTILGQTVTVDWC 135
            ++A+ A   ++G       + V+W 
Sbjct: 67  REDAARAIAGVSGFGYDHLILNVEWA 92

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFL-KGYALVEYDSYKEASAARDALNGTTILGQTV 130
           +D + E FS YG+IK + + ++R    L KGYA VE+++  EA  A   ++G  I GQ +
Sbjct: 18  KDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
Query: 131 TVDWCFVKGPK 141
           T        P+
Sbjct: 78  TATAVLAPWPR 88

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           GP R      L+V  +H    ED +   F  +G I+++ L +D  TG  KGY  + +   
Sbjct: 25  GPMR------LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDS 78
Query: 111 KEASAARDALNGTTILGQTVTV 132
           + A  A + LNG  + G+ + V
Sbjct: 79  ECAKKALEQLNGFELAGRPMKV 100

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+++G+     + D+ + FS +G I N  + +D+ TG  +G A + +D   EA  A  + 
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 121 NGTTILGQTVTVDWCF 136
           NG    G +  +   F
Sbjct: 151 NGHKPPGSSEPITVXF 166

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+++G+     + D+ + FS +G I N  + +D+ TG  +G A + +D   EA  A  + 
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 121 NGTTILGQT--VTVDWC 135
           NG    G +  +TV + 
Sbjct: 151 NGHKPPGSSEPITVKFA 167

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 40/79 (50%)
Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           +G  L V  + +   +D++   FS  GE+++  L  D+  G   GY  V Y + K+A  A
Sbjct: 18  QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 117 RDALNGTTILGQTVTVDWC 135
            + LNG  +  +T+ V + 
Sbjct: 78  INTLNGLRLQSKTIKVSYA 96

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 44/89 (49%)
Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           GD E   +   +   L+V  +     E+ ++E FS+ G+IK + + LD+      G+  V
Sbjct: 27  GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
           EY S  +A  A   +NGT +  + +  DW
Sbjct: 87  EYYSRADAENAMRYINGTRLDDRIIRTDW 115

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 4/85 (4%)
Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           GP R+     L V  + +   +D++   FS  GE+++  L  D+  G   GY  V Y + 
Sbjct: 1   GPGRTN----LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTA 56
Query: 111 KEASAARDALNGTTILGQTVTVDWC 135
           K+A  A + LNG  +  +T+ V + 
Sbjct: 57  KDAERAINTLNGLRLQSKTIKVSYA 81

>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 = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 37/74 (50%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H +  E  ++EKFS  G I ++ +  D  T    GYA V +    +A  A D +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 121 NGTTILGQTVTVDW 134
           N   I G+ V + W
Sbjct: 78  NFDVIKGKPVRIMW 91

>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 = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 37/74 (50%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H +  E  ++EKFS  G I ++ +  D  T    GYA V +    +A  A D +
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 121 NGTTILGQTVTVDW 134
           N   I G+ V + W
Sbjct: 73  NFDVIKGKPVRIMW 86

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           S+    L+V+G+ +   + ++ + FS+YG I    + +D+ TG  +G   + +D   EA 
Sbjct: 85  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144
Query: 115 AARDALNGTTILGQT--VTVDWC 135
            A   LNG    G T  +TV + 
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V  + +   ED + + F   G I N+ + +D+    +  YA VEY    +A+ A   
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN-YAFVEYHQSHDANIALQT 60
Query: 120 LNGTTILGQTVTVDWCF 136
           LNG  I    V ++W F
Sbjct: 61  LNGKQIENNIVKINWAF 77

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 1/89 (1%)
Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           GD E   +   +   L+V  +     E+ ++E FS+ G+IK + + LD+      G+  V
Sbjct: 6   GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFV 64
Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
           EY S  +A  A   +NGT +  + +  DW
Sbjct: 65  EYYSRADAENAMRYINGTRLDDRIIRTDW 93

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++++  EDD+   F  +G I+   + L    G  KG A V+Y S+ EA AA +AL
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 121 NGTTIL 126
           +G+  +
Sbjct: 77  HGSQTM 82

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           + PG   +V+   +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +
Sbjct: 96  QRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 108 DSY 110
           D +
Sbjct: 154 DDH 156

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
           Q S +   ++  G+     +  M + FS +G+I  + +  +      KGY+ V + +++ 
Sbjct: 20  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHES 73
Query: 113 ASAARDALNGTTILGQTVTVDW 134
           A+ A  ++NGTTI G  V   W
Sbjct: 74  AAHAIVSVNGTTIEGHVVKCYW 95

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           + PG   +V+   +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +
Sbjct: 89  QRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Query: 108 DSY 110
           D +
Sbjct: 147 DDH 149

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           + PG   +V+   +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +
Sbjct: 97  QRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Query: 108 DSY 110
           D +
Sbjct: 155 DDH 157

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           + PG   +V+   +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +
Sbjct: 95  QRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Query: 108 DSY 110
           D +
Sbjct: 153 DDH 155

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           + PG   +V+   +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +
Sbjct: 96  QRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 108 DSY 110
           D +
Sbjct: 154 DDH 156

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 52  PQRSVEGWI-LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           P   VEG   L V  +      D +   F +YG + ++++  DR T   +G+A V +   
Sbjct: 40  PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 111 KEASAARDALNGTTILGQTVTVDWC 135
           ++A  A DA++G  + G+ + V   
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQMA 124

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 43/97 (44%), Gaps = 14/97 (14%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV---EYDSYKEASAAR 117
           L V G+  +  E D+ E FS +GE+  + +  D +TG  KG+  V   EY++  +  + R
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 118 DALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
             ++G           WC  K P      Q  GP  G
Sbjct: 78  HMIDGR----------WCDCKLPNSKQ-SQDSGPSSG 103

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           + PG   +V+   +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +
Sbjct: 94  QRPGAHLTVKK--IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Query: 108 DSY 110
           D +
Sbjct: 152 DDH 154

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 30/65 (46%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +D + E  + +G +K  +L  D  TG  KGYA  EY        A   L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 121 NGTTI 125
           NG  +
Sbjct: 177 NGMQL 181

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 40/73 (54%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V G+ E+  E  + E F + G + N H+  DR TG  +GY  VE+ S ++A  A   +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 121 NGTTILGQTVTVD 133
           +   + G+ + V+
Sbjct: 78  DMIKLYGKPIRVN 90

>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 = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           S+E   LF++G+     ++++ E    +G +K+L L +  R G  KG A VEY++  +AS
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRL-VTNRAGKPKGLAYVEYENESQAS 72
Query: 115 AARDALNGTTI 125
            A   ++G TI
Sbjct: 73  QAVMKMDGMTI 83

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 41/74 (55%)
Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
             L V G+     E D+ E FS+YG I ++ +  D+++   +G+A V +++  +A  A++
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 119 ALNGTTILGQTVTV 132
             NG  + G+ + V
Sbjct: 76  RANGMELDGRRIRV 89

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 30/65 (46%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +D + E  + +G +K  +L  D  TG  KGYA  EY        A   L
Sbjct: 99  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 121 NGTTI 125
           NG  +
Sbjct: 159 NGMQL 163

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 7/95 (7%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +     E  + + F  YG I+++ +  DR T   +GY  V++ S   A  A   L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGV 155
           NG  IL + + V           +G Q+ G  G V
Sbjct: 105 NGFNILNKRLKVALA-------ASGHQRPGIAGAV 132

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/75 (24%), Positives = 38/75 (50%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++    ++ +   F ++    + H+  D +TG  +GY  V + S  +A  A D++
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 121 NGTTILGQTVTVDWC 135
            G  + G+ + ++W 
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 8/97 (8%)
Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYA 103
           P    +   ++V G+++    DD+ + F + G +K         +H+ LD+ TG  KG A
Sbjct: 9   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68
Query: 104 LVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
            V Y+    A AA +  +G    G  + V     K P
Sbjct: 69  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 30/65 (46%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +D + E  + +G +K  +L  D  TG  KGYA  EY        A   L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 121 NGTTI 125
           NG  +
Sbjct: 157 NGMQL 161

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H    ED +   F  +G+I N+ L  D  TG  KGY  + +   + A  A + L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 68  NGFELAGRPMRV 79

>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding Protein Fus From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6430a Length = 99

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYALVEYDSYKE 112
           +FV G+ E    + + + F + G IK         ++L  DR TG LKG A V +D    
Sbjct: 16  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 113 ASAARDALNGTTILGQTVTVDWC 135
           A AA D  +G    G  + V + 
Sbjct: 76  AKAAIDWFDGKEFSGNPIKVSFA 98

>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN Length = 116

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 8/91 (8%)
Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYAL 104
           Q + +   +FV G+ E    + + + F + G IK         ++L  DR TG LKG A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWC 135
           V +D    A AA D  +G    G  + V + 
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 50  PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           PG + S++   L+VT +     +D +   F +YG I   ++  D+ TG  +G A V Y+ 
Sbjct: 82  PGGE-SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140
Query: 110 YKEASAARDALN 121
            +EA  A  ALN
Sbjct: 141 REEAQEAISALN 152

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 36/72 (50%)
Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +   + E+D+ + FS YG +  LH  +D  T   KG+A V +   + A  A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 121 NGTTILGQTVTV 132
           +G    G+ + V
Sbjct: 71  DGQVFQGRMLHV 82

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	192
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-53
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-49
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-48
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	8e-47
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-25
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-21
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-20
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-20
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-19
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-19
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-19
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-19
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	9e-19
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-18
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-18
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	9e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-12
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-17
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-16
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-16
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	6e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-15
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-15
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-15
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-14
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-14
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-14
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-14
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-13
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-13
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-13
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	9e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-12
2div_A	99	TRNA selenocysteine associated protein; structural	6e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-10
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-09
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	9e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-07
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-06
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	8e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	3e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	4e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	8e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-04

>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 =  166 bits (423), Expect = 2e-53
 Identities = 95/142 (66%), Positives = 119/142 (83%), Gaps = 1/142 (0%)

Query: 8   KGIARLKEKARKKKGRGFGTETSTRNEIREYESMETDVGDE-EPGPQRSVEGWILFVTGV 66
           +GI RLKEKA+ +KGRGFG++++TR  I  YE +  +  DE EPGPQRSVEGWILFVT +
Sbjct: 21  QGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI 80

Query: 67  HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL 126
           HEEAQED++ EKF +YGEIKN+HLNLDRRTGF KGYALVEY+++K+A AA++ALNG  I+
Sbjct: 81  HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM 140

Query: 127 GQTVTVDWCFVKGPKKVAGEQK 148
           GQT+ VDWCFVKGPK+V   +K
Sbjct: 141 GQTIQVDWCFVKGPKRVKKSEK 162

>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 =  154 bits (391), Expect = 4e-49
 Identities = 77/109 (70%), Positives = 93/109 (85%), Gaps = 1/109 (0%)

Query: 35  IREYESMETDVGDE-EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLD 93
           I  YE +  +  DE EPGPQRSVEGWILFVT +HEEAQED++ EKF +YGEIKN+HLNLD
Sbjct: 2   IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61

Query: 94  RRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           RRTGF KGYALVEY+++K+A AA++ALNG  I+GQT+ VDWCFVKGPK+
Sbjct: 62  RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  153 bits (388), Expect = 1e-48
 Identities = 74/105 (70%), Positives = 92/105 (87%), Gaps = 2/105 (1%)

Query: 36  REYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR 95
            +Y+S+E D   +EPGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRR
Sbjct: 3   EDYDSVEQD--GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60

Query: 96  TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP 140
           TG+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV+GP
Sbjct: 61  TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>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 =  149 bits (377), Expect = 8e-47
 Identities = 75/106 (70%), Positives = 93/106 (87%), Gaps = 2/106 (1%)

Query: 37  EYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT 96
           +Y+S+E D   +EPGPQRSVEGWILFVTGVHEEA E+D+H+KF+EYGEIKN+HLNLDRRT
Sbjct: 3   DYDSVEQD--GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60

Query: 97  GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           G+LKGY LVEY++YKEA AA + LNG  ++GQ ++VDWCFV+GP K
Sbjct: 61  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK 106

>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 = 93.1 bits (232), Expect = 3e-25
 Identities = 22/84 (26%), Positives = 44/84 (52%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
             +R+ +   + VT + E+ +E D+ E F  +G I  ++L  D+ TG  KG+A + +   
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 111 KEASAARDALNGTTILGQTVTVDW 134
           ++A+ A   ++G       + V+W
Sbjct: 68  EDAARAIAGVSGFGYDHLILNVEW 91

>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 = 84.9 bits (210), Expect = 2e-21
 Identities = 26/89 (29%), Positives = 44/89 (49%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           GD E   +   +   L+V  +     E+ ++E FS+ G+IK + + LD+      G+  V
Sbjct: 27  GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
           EY S  +A  A   +NGT +  + +  DW
Sbjct: 87  EYYSRADAENAMRYINGTRLDDRIIRTDW 115

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 82.5 bits (204), Expect = 1e-20
 Identities = 23/116 (19%), Positives = 43/116 (37%)

Query: 19  KKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEK 78
                G     S    +   + M          P        L V  +      D +   
Sbjct: 8   HHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRV 67

Query: 79  FSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           F +YG + ++++  DR T   +G+A V +   ++A  A DA++G  + G+ + V  
Sbjct: 68  FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

>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 = 81.7 bits (202), Expect = 1e-20
 Identities = 26/104 (25%), Positives = 43/104 (41%), Gaps = 8/104 (7%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGF 98
                P    +   ++V G+++    DD+ + F + G +K         +H+ LD+ TG 
Sbjct: 4   GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63

Query: 99  LKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
            KG A V Y+    A AA +  +G    G  + V     K P  
Sbjct: 64  PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>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 = 78.8 bits (195), Expect = 1e-19
 Identities = 22/74 (29%), Positives = 40/74 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V G+ E+  E  + E F + G + N H+  DR TG  +GY  VE+ S ++A  A   +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77

Query: 121 NGTTILGQTVTVDW 134
           +   + G+ + V+ 
Sbjct: 78  DMIKLYGKPIRVNK 91

>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 = 78.4 bits (194), Expect = 1e-19
 Identities = 19/88 (21%), Positives = 41/88 (46%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++  +  +  E+ + +  S  G + NL +  D +TG  KGYA +E+   + +++A   L
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
           NG  +  + +   +        V+ E  
Sbjct: 65  NGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>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 = 79.9 bits (197), Expect = 1e-19
 Identities = 24/120 (20%), Positives = 46/120 (38%)

Query: 15  EKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDD 74
           EK  K+     G +     +        T+                L V  +      D 
Sbjct: 27  EKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDT 86

Query: 75  MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           +   F +YG + ++++  DR T   +G+A V +   ++A  A DA++G  + G+ + V  
Sbjct: 87  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 78.6 bits (194), Expect = 2e-19
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 50  PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
             P + V         +++  +E  + +   +YGE++ + + L  RT    G A V + S
Sbjct: 3   QIPLKEV-----TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTS 57

Query: 110 YKEASAARDALNGTTILGQTVTVD 133
            + A      L+ T+++G  +   
Sbjct: 58  TRGAKETVKNLHLTSVMGNIIHAQ 81

>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 = 77.3 bits (191), Expect = 4e-19
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +  +  E  + + FS+ G  K+  +  +  +     Y  VE+  +++A+AA  A+
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 75

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG  ILG+ V V+W      +K
Sbjct: 76  NGRKILGKEVKVNWATTPSSQK 97

>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 = 76.5 bits (189), Expect = 8e-19
 Identities = 24/83 (28%), Positives = 38/83 (45%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           G   S     LFV  +   + E+D+ + FS YG +  LH  +D  T   KG+A V +   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 111 KEASAARDALNGTTILGQTVTVD 133
           + A  A   ++G    G+ + V 
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVL 83

>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 = 76.6 bits (189), Expect = 8e-19
 Identities = 20/85 (23%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSY 110
             +      + V  +  +A + ++ E FS +GE+K + L      TG  +G+  V++ + 
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 111 KEASAARDAL-NGTTILGQTVTVDW 134
           ++A  A +AL + T + G+ + ++W
Sbjct: 69  QDAKKAFNALCHSTHLYGRRLVLEW 93

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 77.5 bits (191), Expect = 9e-19
 Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 5/108 (4%)

Query: 27  TETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK 86
           T  +      +  S  +         +R      L+V G+ EE  +  +H  F  +G+I 
Sbjct: 37  TCVNCTERHVDGGSGGSGGSGGSATTKRV-----LYVGGLAEEVDDKVLHAAFIPFGDIT 91

Query: 87  NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           ++ + LD  T   +G+A VE++  ++A+AA D +N + + G+T+ V+ 
Sbjct: 92  DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139

>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 = 76.1 bits (188), Expect = 1e-18
 Identities = 16/74 (21%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +      D +   F +YG + ++++  +  T   +G+A V +   ++A  A  A+
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75

Query: 121 NGTTILGQTVTVDW 134
           +G  + G+ + V  
Sbjct: 76  DGAELDGRELRVQV 89

>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 = 75.8 bits (187), Expect = 2e-18
 Identities = 27/74 (36%), Positives = 38/74 (51%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  EA E+ + + FSE G + +  L  DR TG  KGY   EY   + A +A   L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 121 NGTTILGQTVTVDW 134
           NG    G+ + VD 
Sbjct: 71  NGREFSGRALRVDN 84

>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 = 76.3 bits (188), Expect = 2e-18
 Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 5/106 (4%)

Query: 29  TSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNL 88
            S     +             P P        L V G+     E D+ E FS+YG I ++
Sbjct: 22  ASMTGGQQMGRGSRHVGNRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADV 76

Query: 89  HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
            +  D+++   +G+A V +++  +A  A++  NG  + G+ + VD+
Sbjct: 77  SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>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 = 75.3 bits (186), Expect = 2e-18
 Identities = 24/74 (32%), Positives = 46/74 (62%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74

Query: 121 NGTTILGQTVTVDW 134
           N + + G+T+ V+ 
Sbjct: 75  NESELFGRTIRVNL 88

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 75.4 bits (186), Expect = 2e-18
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
               S+E   LF++G+     ++++ E    +G +K+L L  +R  G  KG A VEY++ 
Sbjct: 10  RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENE 68

Query: 111 KEASAARDALNGTTILGQTVTVD 133
            +AS A   ++G TI    + V 
Sbjct: 69  SQASQAVMKMDGMTIKENIIKVA 91

>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 = 74.5 bits (184), Expect = 3e-18
 Identities = 24/74 (32%), Positives = 46/74 (62%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69

Query: 121 NGTTILGQTVTVDW 134
           N + + G+T+ V+ 
Sbjct: 70  NESELFGRTIRVNL 83

>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 = 74.3 bits (183), Expect = 5e-18
 Identities = 29/97 (29%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 45  VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRT 96
           +G        S    I FV G+ E    + + + F + G IK         ++L  DR T
Sbjct: 1   MGHHHHHHSHSDNNTI-FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59

Query: 97  GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           G LKG A V +D    A AA D  +G    G  + V 
Sbjct: 60  GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 73.8 bits (182), Expect = 7e-18
 Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 5/95 (5%)

Query: 40  SMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL 99
           S  +      P P        L V G+     E D+ E FS+YG I ++ +  D+++   
Sbjct: 2   SSGSSGNRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 56

Query: 100 KGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           +G+A V +++  +A  A++  NG  + G+ + V  
Sbjct: 57  RGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG 91

>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 = 76.2 bits (188), Expect = 9e-18
 Identities = 23/79 (29%), Positives = 34/79 (43%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +D + E  + +G +K  +L  D  TG  KGYA  EY        A   L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176

Query: 121 NGTTILGQTVTVDWCFVKG 139
           NG  +  + + V    V  
Sbjct: 177 NGMQLGDKKLLVQRASVGA 195

>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 = 61.2 bits (149), Expect = 4e-12
 Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 6/100 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
           L+V  +     E+ M + F+    +  L        L  +    K +A +E+ S  E + 
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 116 ARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGV 155
           A  A +G    GQ++ +       P     E       GV
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGV 105

>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 = 73.9 bits (182), Expect = 1e-17
 Identities = 23/109 (21%), Positives = 46/109 (42%), Gaps = 8/109 (7%)

Query: 26  GTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEI 85
           G+  S+  EIR+            PG    V    L++  +     E D+   F+ + E 
Sbjct: 1   GSSGSSGEEIRKIPMF----SSYNPGEPNKV----LYLKNLSPRVTERDLVSLFARFQEK 52

Query: 86  KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           K   +     TG ++G A + + + + A  A   +NG  + G+ + +++
Sbjct: 53  KGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF 101

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 73.0 bits (180), Expect = 1e-17
 Identities = 23/73 (31%), Positives = 36/73 (49%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H    ED +   F  +G+I N+ L  D  TG  KGY  + +   + A  A + L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67

Query: 121 NGTTILGQTVTVD 133
           NG  + G+ + V 
Sbjct: 68  NGFELAGRPMRVG 80

>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 = 73.0 bits (180), Expect = 2e-17
 Identities = 15/73 (20%), Positives = 34/73 (46%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V+ +      +D++  FS+YG++  + +  D+ T   KG A + +     A     A+
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78

Query: 121 NGTTILGQTVTVD 133
           N   + G+ +   
Sbjct: 79  NNKQLFGRVIKAS 91

>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 = 74.1 bits (183), Expect = 3e-17
 Identities = 19/74 (25%), Positives = 37/74 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + ++  + +++  F   G I    +  D +TG+  GYA V++ S  ++  A   L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 121 NGTTILGQTVTVDW 134
           NG T+  + + V +
Sbjct: 66  NGITVRNKRLKVSY 79

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 61.8 bits (151), Expect = 1e-12
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+VT +     +D +   F +YG I   ++  D+ TG  +G A V Y+  +EA  A  AL
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 121 NGTTILGQT--VTVDW 134
           N     G +  ++V  
Sbjct: 152 NNVIPEGGSQPLSVRL 167

>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 = 73.8 bits (182), Expect = 5e-17
 Identities = 22/74 (29%), Positives = 33/74 (44%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +D + E  + +G +K  +L  D  TG  KGYA  EY        A   L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 121 NGTTILGQTVTVDW 134
           NG  +  + + V  
Sbjct: 157 NGMQLGDKKLLVQR 170

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
           L+V  +     E+ M + F+    +  L        L  +    K +A +E+ S  E + 
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 116 ARDALNGTTILGQTVTVDW 134
           A  A +G    GQ++ +  
Sbjct: 67  AM-AFDGIIFQGQSLKIRR 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 71.4 bits (176), Expect = 5e-17
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAARDA 119
           + +  +     +D + E FS YG+IK + + ++R      KGYA VE+++  EA  A   
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 120 LNGTTILGQTVTVD 133
           ++G  I GQ +T  
Sbjct: 67  MDGGQIDGQEITAT 80

>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 = 73.4 bits (181), Expect = 6e-17
 Identities = 22/74 (29%), Positives = 36/74 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + +   +++    F   GEI++  L  D+ TG   GY  V Y   K+A  A + L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 121 NGTTILGQTVTVDW 134
           NG  +  +T+ V +
Sbjct: 65  NGLRLQTKTIKVSY 78

>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 = 60.3 bits (147), Expect = 5e-12
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V+G+ +   + ++ + FS+YG I    + +D+ TG  +G   + +D   EA  A   L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 121 NGTTILGQT--VTVDW 134
           NG    G T  +TV +
Sbjct: 151 NGQKPSGATEPITVKF 166

>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 = 71.2 bits (175), Expect = 1e-16
 Identities = 22/74 (29%), Positives = 37/74 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H    ED +   F  +G I+++ L +D  TG  KGY  + +   + A  A + L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ + V  
Sbjct: 89  NGFELAGRPMKVGH 102

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.8 bits (174), Expect = 1e-16
 Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 6/96 (6%)

Query: 39  ESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGF 98
                 +  E+   Q S +   ++  G+     +  M + FS +G+I  + +  +     
Sbjct: 6   SGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----- 60

Query: 99  LKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
            KGY+ V + +++ A+ A  ++NGTTI G  V   W
Sbjct: 61  -KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 95

>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 = 70.0 bits (172), Expect = 3e-16
 Identities = 25/108 (23%), Positives = 40/108 (37%), Gaps = 5/108 (4%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G       +  +   LF+  +     E D+   F E+G+I  L +  DR TG  KG A +
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 106 EYDSYKEASAARDALNGTTIL---GQTVTVDWCFVKGPKKVAGEQKVG 150
            Y   + A  A+ AL+    L    + + V         +       G
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVK--PADSESRGGSGPSSG 106

>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 = 69.5 bits (171), Expect = 3e-16
 Identities = 20/72 (27%), Positives = 33/72 (45%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++ G+     + D+ +    YG+I +    LD+ T   KGY  V++DS   A  A  AL
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 121 NGTTILGQTVTV 132
             + +  Q    
Sbjct: 68  KASGVQAQMAKQ 79

>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 = 70.9 bits (174), Expect = 3e-16
 Identities = 22/74 (29%), Positives = 34/74 (45%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +     E  + + F  YG I+++ +  DR T   +GY  V++ S   A  A   L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 121 NGTTILGQTVTVDW 134
           NG  IL + + V  
Sbjct: 105 NGFNILNKRLKVAL 118

>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 = 73.5 bits (181), Expect = 3e-16
 Identities = 21/82 (25%), Positives = 32/82 (39%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
           Q      +L V  +     +    E    +G ++   L    RTG  KGY   EY     
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 113 ASAARDALNGTTILGQTVTVDW 134
           A+ A+  L G  +  +T+ V W
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHW 171

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 67.7 bits (166), Expect = 5e-14
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 61  LFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           L V  +       D +    S         L   +  G LKG+A++EY++ + A  A+  
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQ 245

Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
            +G ++ G  + V +C    P +
Sbjct: 246 ADGLSLGGSHLRVSFCAPGPPGR 268

>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 = 58.1 bits (141), Expect = 1e-10
 Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           + + G+  +    ++H+  S+Y  +K   ++        KG A V   + ++A AA +A 
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY------KGTAFVTLLNGEQAEAAINAF 77

Query: 121 NGTTILGQTVTVDW 134
           + + +  + ++V  
Sbjct: 78  HQSRLRERELSVQL 91

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 70.1 bits (172), Expect = 4e-16
 Identities = 29/106 (27%), Positives = 44/106 (41%), Gaps = 8/106 (7%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYAL 104
           Q + +   +FV G+ E    + + + F + G IK         ++L  DR TG LKG A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVG 150
           V +D    A AA D  +G    G  + V +   +      G    G
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRG 107

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 69.3 bits (170), Expect = 4e-16
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
            ++  +   A E D+   F  +G I +     +      KG   ++YD++++A+    AL
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVAL 83

Query: 121 NGTTILGQTVTVDW 134
                 G+ +   W
Sbjct: 84  ANFPFQGRNLRTGW 97

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 68.9 bits (169), Expect = 6e-16
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 6/91 (6%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYD 108
           G         + +  +      D +    S Y    + N+ L  D++T   +G+A V+  
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 109 SYKEASAARDALNGT----TILGQTVTVDWC 135
           S  +AS     L        I G+T+ VD+ 
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 69.2 bits (170), Expect = 6e-16
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV G+  +  E  + + FS+YG+I  + +  DR T   +G+  V +++  +A  A  A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74

Query: 121 NGTTILGQTVTVDW 134
           NG ++ G+ + VD 
Sbjct: 75  NGKSVDGRQIRVDQ 88

>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 = 70.7 bits (174), Expect = 8e-16
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 45  VGDEEPGPQRSVEGWI-LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYA 103
           +   +    + V     L    +     ED++ E F +  EI+     L  + G  KG A
Sbjct: 85  LEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIA 139

Query: 104 LVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG 139
            +E+ S  +A    +   G  I G++V++ +   KG
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 19/97 (19%), Positives = 43/97 (44%), Gaps = 2/97 (2%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
             S   + LF+  ++      ++    SE     +L + +D RTG  + +  V+++S ++
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAED 66

Query: 113 ASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKV 149
              A + L G  + G  + ++    +  KKV   + +
Sbjct: 67  LEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTL 102

>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 = 68.5 bits (168), Expect = 9e-16
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
                G  ++     L ++ +   A E+ + E F +   IK        + G  KGYA +
Sbjct: 8   NSTWSGESKT-----LVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFI 58

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
           E+ S+++A  A ++ N   I G+ + ++ 
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRLEL 87

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 71.2 bits (175), Expect = 1e-15
 Identities = 23/80 (28%), Positives = 40/80 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  VH++  +DD+   F  +G+IK+  L  D  TG  KGY  +EY+  + +  A  ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 121 NGTTILGQTVTVDWCFVKGP 140
           N   + GQ + V        
Sbjct: 188 NLFDLGGQYLRVGKAVTPPM 207

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 70.4 bits (173), Expect = 2e-15
 Identities = 23/99 (23%), Positives = 47/99 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  ++ E  ED + + F+ +G IK++ ++ D  T   KG+A VEY+  + A  A + +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLF 159
           N   + G+ + V      G  +   +Q          ++
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY 129

>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 = 71.3 bits (174), Expect = 1e-15
 Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 2/96 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           L++  +     ++D+ E     G  +I  +    +R  G  KG+ALV   S   +    D
Sbjct: 71  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130

Query: 119 ALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
            L    + GQ   V     +   +   + +   + G
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSG 166

>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 = 68.6 bits (168), Expect = 1e-15
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
            IL++  +  +   ++M++ F +YG I+ + +     T   +G A V Y+   +A  A D
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVD 65

Query: 119 ALNGTTILGQTVTVDW 134
            L+G  +  + + V +
Sbjct: 66  HLSGFNVSNRYLVVLY 81

>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 = 68.1 bits (167), Expect = 1e-15
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 5/91 (5%)

Query: 43  TDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGY 102
           + + ++    ++      L    +     ED++ E F +  EI+     L  + G  KG 
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGI 55

Query: 103 ALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           A +E+ S  +A    +   G  I G++V++ 
Sbjct: 56  AYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 86

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 67.4 bits (165), Expect = 4e-15
 Identities = 19/78 (24%), Positives = 38/78 (48%)

Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           EG  LF+  + +E  + D+   F  +G + +  + +D++T   K +  V +D+   A  A
Sbjct: 39  EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98

Query: 117 RDALNGTTILGQTVTVDW 134
             A+NG  +  + + V  
Sbjct: 99  IKAMNGFQVGTKRLKVQL 116

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 67.4 bits (165), Expect = 4e-15
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G++ E  E  +   F ++G I  + L  DR T   +G+A + +++  +A  A   +
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68

Query: 121 NGTTILGQTVTVDW 134
           NG ++ G+ + V+ 
Sbjct: 69  NGKSLHGKAIKVEQ 82

>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 = 66.9 bits (164), Expect = 5e-15
 Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V+ +    ++ D+ + F ++G+I ++ +  + R    KG+  V +++  +A  AR+ L
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 75

Query: 121 NGTTILGQTVTVDW 134
           +GT + G+ + V+ 
Sbjct: 76  HGTVVEGRKIEVNN 89

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 67.0 bits (164), Expect = 5e-15
 Identities = 21/76 (27%), Positives = 40/76 (52%)

Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           EG  LF+  + +E  + D+ + F  +G + +  + +D++T   K +  V YD+   A AA
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83

Query: 117 RDALNGTTILGQTVTV 132
             ++NG  I  + + V
Sbjct: 84  IQSMNGFQIGMKRLKV 99

>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 = 66.5 bits (163), Expect = 5e-15
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 50  PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
            G +   +   LFV  +  +  E++M + F +YG+   + ++ D      KG+  +  ++
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLET 60

Query: 110 YKEASAARDALNGTTILGQTVTVDW 134
              A  A+  L+   + G+ + V +
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRF 85

>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 = 69.2 bits (170), Expect = 5e-15
 Identities = 24/74 (32%), Positives = 37/74 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H +  E  ++EKFS  G I ++ +  D  T    GYA V +    +A  A D +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 121 NGTTILGQTVTVDW 134
           N   I G+ V + W
Sbjct: 78  NFDVIKGKPVRIMW 91

>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 = 65.4 bits (160), Expect = 1e-13
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+  + +      +++ FS +G I +  +  D      KGY  V +++ + A  A + +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
           NG  +  + V V     +  ++     +
Sbjct: 164 NGMLLNDRKVFVGRFKSRKEREAELGAR 191

>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 = 66.1 bits (162), Expect = 6e-15
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 12/98 (12%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G              L++  +      DD+ + F +          L  +     GYA V
Sbjct: 1   GSSGSSGMNK-----LYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFV 49

Query: 106 EYDSYKEASAARDALNGTTIL-GQTVTVDWCFVKGPKK 142
           +Y     A  A + L+G   L G+ + VD+   K  + 
Sbjct: 50  DYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRS 87

>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 = 66.6 bits (163), Expect = 6e-15
 Identities = 19/74 (25%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  E   +D+   F+ +G I +  +  D  TG  KGY  V + +  +A  A   +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 121 NGTTILGQTVTVDW 134
            G  + G+ +  +W
Sbjct: 78  GGQWLGGRQIRTNW 91

>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 = 66.1 bits (162), Expect = 7e-15
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +    +E+ ++E F + G +  + +  DR  G  K +  V +   +  S A   L
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALL 77

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ + V  
Sbjct: 78  NGIRLYGRPINVSG 91

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 66.2 bits (162), Expect = 8e-15
 Identities = 18/86 (20%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                +   +   L V+ +    ++ D+ + F ++G+I ++ +  + R    KG+  V +
Sbjct: 19  SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTF 76

Query: 108 DSYKEASAARDALNGTTILGQTVTVD 133
           ++  +A  AR+ L+GT + G+ + V+
Sbjct: 77  ENSADADRAREKLHGTVVEGRKIEVN 102

>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 = 66.7 bits (163), Expect = 9e-15
 Identities = 23/104 (22%), Positives = 45/104 (43%), Gaps = 1/104 (0%)

Query: 30  STRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLH 89
           +T +++      E          ++ ++   ++V  V   +   D+   FS  G I  + 
Sbjct: 8   TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67

Query: 90  LNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           +  D+ +G  KGYA +E+       AA  A++ T   G+T+ V 
Sbjct: 68  ILCDKFSGHPKGYAYIEFAERNSVDAA-VAMDETVFRGRTIKVL 110

>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 = 65.3 bits (160), Expect = 1e-14
 Identities = 18/74 (24%), Positives = 33/74 (44%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  E     +   F+ +G I +  +  D  TG  KGY  V + +  +A  A   +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 121 NGTTILGQTVTVDW 134
            G  + G+ +  +W
Sbjct: 69  GGQWLGGRQIRTNW 82

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 64.8 bits (159), Expect = 1e-14
 Identities = 18/74 (24%), Positives = 38/74 (51%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++    ++ +   F ++    + H+  D +TG  +GY  V + S  +A  A D++
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 121 NGTTILGQTVTVDW 134
            G  + G+ + ++W
Sbjct: 64  QGQDLNGRPLRINW 77

>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 = 65.4 bits (160), Expect = 2e-14
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +  + +  D+ + F +YG I+++ L   R       +A VE++  ++A  A    
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAVYGR 81

Query: 121 NGTTILGQTVTVDW 134
           +G    G  + V++
Sbjct: 82  DGYDYDGYRLRVEF 95

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 64.9 bits (159), Expect = 2e-14
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +   A  + + E FS++G++ N+ L  DR T   KG+  VE    +  S A   L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62

Query: 121 NGTTILGQTVTVD 133
           + T  +G+T+ V 
Sbjct: 63  DNTDFMGRTIRVT 75

>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 = 65.4 bits (160), Expect = 2e-14
 Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 6/89 (6%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           P    EG  +F+  +  +++E+ + E   ++G++K + + L   T   KG A  ++ + +
Sbjct: 9   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68

Query: 112 EASAARDALN------GTTILGQTVTVDW 134
            A     A +      G  + G+ + VD 
Sbjct: 69  AAQKCLAAASLEAEGGGLKLDGRQLKVDL 97

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 65.0 bits (159), Expect = 2e-14
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 8/88 (9%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
                 +   +G  L+V G  E+     +   FS +G I +L ++        +  A V 
Sbjct: 4   GSSGERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVT 55

Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW 134
           Y+  + A  A   LNGT +    + V+ 
Sbjct: 56  YEKMESADQAVAELNGTQVESVQLKVNI 83

>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 = 64.6 bits (158), Expect = 3e-14
 Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 3/87 (3%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                 RS     LFV G+ E+  E+ + E F      +   +  DR TG  KG+  V++
Sbjct: 5   SSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---IVTDRETGSSKGFGFVDF 61

Query: 108 DSYKEASAARDALNGTTILGQTVTVDW 134
           +S ++A AA++A+    I G  VT+DW
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDW 88

>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 = 64.2 bits (157), Expect = 4e-14
 Identities = 21/107 (19%), Positives = 37/107 (34%), Gaps = 12/107 (11%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                       IL+V  +     E+ + ++F+              R   ++ YA V +
Sbjct: 5   SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHF 58

Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
            + ++A  A  ALNG  + G  + V         K   +   GP  G
Sbjct: 59  SNREDAVEAMKALNGKVLDGSPIEVTL------AKPVDKDSSGPSSG 99

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 63.6 bits (155), Expect = 6e-14
 Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 4/89 (4%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G     P+R      L +  +    Q + +     +YG +++                 V
Sbjct: 4   GSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNV 59

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
            Y S  +A  A D LNG  +   T+ V +
Sbjct: 60  TYSSKDQARQALDKLNGFQLENFTLKVAY 88

>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 = 63.3 bits (155), Expect = 6e-14
 Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  V   A  +++   F   G +  + +  D+ +G  KG+A +E+   +    +  AL
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67

Query: 121 NGTTILGQTVTVD 133
           + +   G+ + V 
Sbjct: 68  DESLFRGRQIKVI 80

>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 = 64.0 bits (156), Expect = 6e-14
 Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDRR-TGFLKGYALVEYD 108
           G   S     LF+ G+ +  + +++ E+ ++  E + ++ +          +G+A VEY+
Sbjct: 1   GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60

Query: 109 SYKEASAARDALN--GTTILGQTVTVDW 134
           S++ A+ AR  L      + G  + VDW
Sbjct: 61  SHRAAAMARRKLMPGRIQLWGHQIAVDW 88

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 66.9 bits (164), Expect = 9e-14
 Identities = 12/74 (16%), Positives = 28/74 (37%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++T       + ++ +   +   +         R    + +A ++  S ++A    + L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 121 NGTTILGQTVTVDW 134
           NG  I G T+    
Sbjct: 180 NGLKIEGYTLVTKV 193

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 17/137 (12%), Positives = 41/137 (29%), Gaps = 20/137 (14%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
                  R+ E   + V  + +   ++ +++ F   G I ++ +           +A +E
Sbjct: 30  KANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIE 87

Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW-----CFVKG-PKKVAGEQ------KVGPEGG 154
           +  Y  A AA    +   +    + V        ++   P              +     
Sbjct: 88  FARYDGALAAITKTHK-VVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINV--- 143

Query: 155 VKVLFPVIMYSTETSMS 171
             V   + + S   + S
Sbjct: 144 --VALSIRLPSLRFNTS 158

>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 = 58.1 bits (141), Expect = 1e-10
 Identities = 14/89 (15%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALV 105
            +     ++EG  + +  +  E   E+ + E F  +G I+ +++   ++   F    A +
Sbjct: 200 SKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFM 259

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
            +++   A  A   +N + +  + ++V  
Sbjct: 260 VFENKDSAERAL-QMNRSLLGNREISVSL 287

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 63.1 bits (154), Expect = 1e-13
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV     + QE +++E F  +G +K + +        L G+A VE++  + A+ A + +
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85

Query: 121 NGTTILGQTVTVDW 134
           +G +   Q + V +
Sbjct: 86  HGKSFANQPLEVVY 99

>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 = 63.0 bits (154), Expect = 1e-13
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEI-KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +F+  +  E  E  +++ FS +G I +   +  D  TG  KGYA + + S+  + AA +A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 120 LNGTTILGQTVTVDWCFVKGPK 141
           +NG  +  + +TV + F K  K
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSK 89

>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 = 63.1 bits (154), Expect = 1e-13
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 1/87 (1%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
               G      G  L V+ +     + D+ E F+E+G +K   ++ DR +G   G A V 
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76

Query: 107 YDSYKEASAARDALNGTTILGQTVTVD 133
           ++   +A  A    NG  + G+ + + 
Sbjct: 77  FERKADALKAMKQYNGVPLDGRPMNIQ 103

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL--KGYALVEYDSYKEASAARD 118
           +FV  V     E D+ E F +YG +  +++  DR       KG   V + + K A  A++
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 119 ALNGTTILGQTVTVDW 134
           AL+   +L        
Sbjct: 66  ALHNMKVLPGMHHPIQ 81

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+  + ++  E+D+   FS +G+I+   +      G  +G A V + +   A  A  A+
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 121 NGTTIL---GQTVTVDW 134
           +    +      + V +
Sbjct: 157 HQAQTMEGCSSPMVVKF 173

>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 = 64.5 bits (158), Expect = 1e-13
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  + +   ED + + F   G I N+ + +D+       YA VEY    +A+ A   L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKV 149
           NG  I    V ++W F            +
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNL 90

>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 = 64.1 bits (157), Expect = 2e-13
 Identities = 18/74 (24%), Positives = 38/74 (51%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++    ++ +   F ++    + H+  D +TG  +GY  V + S  +A  A D++
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 121 NGTTILGQTVTVDW 134
            G  + G+ + ++W
Sbjct: 150 QGQDLNGRPLRINW 163

>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 = 65.1 bits (158), Expect = 1e-13
 Identities = 17/127 (13%), Positives = 36/127 (28%), Gaps = 4/127 (3%)

Query: 14  KEKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQED 73
           +      +  G    + +  +  E  +      ++    +      +L       E  E+
Sbjct: 79  QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEE 138

Query: 74  DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           +  E   E G  +   + +           L+E+DS  +A      LN   +        
Sbjct: 139 NFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

Query: 134 ----WCF 136
                CF
Sbjct: 199 YTLKLCF 205

>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 = 51.2 bits (122), Expect = 2e-08
 Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 8/96 (8%)

Query: 60  ILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           +L V G+ +     D +   F  YG ++ +     +      G A+VE         A  
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAIT 60

Query: 119 ALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
            LN   + GQ + V     K P  + G+     +G 
Sbjct: 61  HLNNNFMFGQKMNVCVS--KQPAIMPGQSYGLEDGS 94

>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 = 2e-13
 Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 2/99 (2%)

Query: 36  REYESMETDVGDEEPGPQRSVE-GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDR 94
           R+ +  + D+ D   G    VE G  L V+ +     + D+ E F+E+G +K   ++ DR
Sbjct: 12  RDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR 71

Query: 95  RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
            +G   G A V ++   +A  A     G  + G+ + + 
Sbjct: 72  -SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 109

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 64.2 bits (156), Expect = 2e-13
 Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 2/77 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           ++V        +  + +     G  ++  L    +R  G  KGYA V   S        +
Sbjct: 58  VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117

Query: 119 ALNGTTILGQTVTVDWC 135
            L G  + G+ V V   
Sbjct: 118 LLPGKVLNGEKVDVRPA 134

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 61.8 bits (151), Expect = 2e-13
 Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           L++  +     ++D+ E     G  +I  +    +R  G  KG+ALV   S   +    D
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 119 ALNGTTILGQTVTVD 133
            L    + GQ   V 
Sbjct: 64  LLPKRELHGQNPVVT 78

>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 = 65.5 bits (160), Expect = 2e-13
 Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 12/98 (12%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
            +PG +   +   LFV  +  +  E+D    F  YGE   + +N DR      G+  +  
Sbjct: 12  LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRL 65

Query: 108 DSYKEASAARDALNGTTILGQTVTVDW------CFVKG 139
           +S   A  A+  L+GT +  + + + +        VK 
Sbjct: 66  ESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKN 103

>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 = 52.4 bits (126), Expect = 1e-08
 Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 1/69 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +      + + + FS++G ++   + +D   G   G   VE+ +   A  A +  
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERC 157

Query: 121 NGTTILGQT 129
                L  T
Sbjct: 158 GDGAFLLTT 166

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 63.3 bits (154), Expect = 4e-13
 Identities = 23/120 (19%), Positives = 46/120 (38%), Gaps = 3/120 (2%)

Query: 16  KARKKKGRGFGTETSTRNEIREYESMETDVGDEEP--GPQRSVEGWILFVTGVHEEAQED 73
           + R    RG     +  +  +           +    G +    G  L V+ +     + 
Sbjct: 44  RNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDA 103

Query: 74  DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD 133
           D+ E F+E+G +K   ++ D R+G   G A V ++   +A  A     G  + G+ + + 
Sbjct: 104 DIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 162

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 61.5 bits (150), Expect = 4e-13
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  ++++  E+D+   F  +G I    +      G  KG A V++ S+ EA AA  AL
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76

Query: 121 NGTTIL---GQTVTVDW 134
           +G+  +     ++ V +
Sbjct: 77  HGSQTMPGASSSLVVKF 93

>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 = 61.9 bits (151), Expect = 5e-13
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+  + +      +++ FS +G I +  +  D      KGY  V +++ + A  A + +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEKM 65

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
           NG  +  + V V     +  ++     +
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGAR 93

>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 = 61.1 bits (149), Expect = 5e-13
 Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +     E+ + + FS++G+++ +          LK YA + +D    A  A + +
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAMEEM 65

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ + + +
Sbjct: 66  NGKDLEGENIEIVF 79

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 61.1 bits (149), Expect = 6e-13
 Identities = 19/106 (17%), Positives = 39/106 (36%), Gaps = 11/106 (10%)

Query: 49  EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYD 108
                 +   +  +V  +     + D+   F +   I+++ L  D+ T   KG+  VE+D
Sbjct: 6   SGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFD 64

Query: 109 SYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
                  A    +G  +  +++ VD         +A  +K    G 
Sbjct: 65  EVDSLKEAL-TYDGALLGDRSLRVD---------IAEGRKQDKSGP 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 = 60.7 bits (148), Expect = 6e-13
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA-SAARDA 119
           L+V G+ +   E D+   F ++GEI+ + +         +  A +++ + + A  AA  +
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 120 LNGTTILGQTVTVDW 134
            N   + G+ + V W
Sbjct: 69  FNKLIVNGRRLNVKW 83

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 60.7 bits (148), Expect = 6e-13
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 6/84 (7%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V G+        +  +F  +G I+ +    D   G    +A ++Y+S   A AA   +
Sbjct: 20  LWVGGLGPNTSLAALAREFDRFGSIRTI----DHVKG--DSFAYIQYESLDAAQAACAKM 73

Query: 121 NGTTILGQTVTVDWCFVKGPKKVA 144
            G  + G    +   F K      
Sbjct: 74  RGFPLGGPDRRLRVDFAKSGPSSG 97

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 60.7 bits (148), Expect = 7e-13
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  +  +     + +KF+E G +  L+ ++    G  KG  +V+++S + A  A   +
Sbjct: 11  IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 68

Query: 121 NGTTILGQTVTV 132
           NG  + G+ + V
Sbjct: 69  NGMKLSGREIDV 80

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.5 bits (147), Expect = 9e-13
 Identities = 14/69 (20%), Positives = 28/69 (40%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
              +        +  +   FS+ G++ N+   +D  TG  KG+  VE  S  +A     +
Sbjct: 14  APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73

Query: 120 LNGTTILGQ 128
            +G  +  +
Sbjct: 74  FHGKRLDLK 82

>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 = 60.8 bits (148), Expect = 9e-13
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
            E    R+V     F   +    +  D+ + FS  G+++++ +  DR +   KG A VE+
Sbjct: 20  PEERDARTV-----FCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74

Query: 108 DSYKEASAARDALNGTTILGQTVTVD 133
              +    A   L G  +LG  + V 
Sbjct: 75  CEIQSVPLAI-GLTGQRLLGVPIIVQ 99

>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 = 59.9 bits (146), Expect = 1e-12
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV  V       ++   F   G +    +        +K YA V  +   +A AA   L
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIAQL 63

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ + V+ 
Sbjct: 64  NGKEVKGKRINVEL 77

>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 = 64.5 bits (156), Expect = 1e-12
 Identities = 25/76 (32%), Positives = 41/76 (53%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  V+ +  E  +  +F  YG IK +H+   +R+G  +GYA +EY+  ++  +A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 121 NGTTILGQTVTVDWCF 136
           +G  I G+ V VD   
Sbjct: 165 DGKKIDGRRVLVDVER 180

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 60.0 bits (146), Expect = 2e-12
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +   A + ++   FS YG ++ + +  +       G+A VE++  ++A  A   L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGL 57

Query: 121 NGTTILGQTVTVDW 134
           +G  I G  V V+ 
Sbjct: 58  DGKVICGSRVRVEL 71

>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 = 58.8 bits (143), Expect = 4e-12
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  +       ++  KF EYG +    +        +K YA V  +  ++A  A   L
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDAVEAIRGL 64

Query: 121 NGTTILGQTVTVDW 134
           + T   G+ + V  
Sbjct: 65  DNTEFQGKRMHVQL 78

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.7 bits (143), Expect = 4e-12
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           G   S     LF+  +  EA E ++   F +YG++    +        +K Y  V  +  
Sbjct: 1   GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDK 52

Query: 111 KEASAARDALNGTTILGQTVTVDW 134
             A  A   L+   + G  + V+ 
Sbjct: 53  TAAEDAIRNLHHYKLHGVNINVEA 76

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 59.6 bits (144), Expect = 4e-12
 Identities = 19/108 (17%), Positives = 40/108 (37%), Gaps = 13/108 (12%)

Query: 36  REYESMETDVGDEE-PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDR 94
               ++    G E      +S+   +    G+      + +     + G +  L +  + 
Sbjct: 7   GAKHTLLRHEGIETVSYATQSL--VV-ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN- 62

Query: 95  RTGFLKGYALVEYDSYKEASAARDALNGTTIL---GQTVTVDWCFVKG 139
                K Y+   Y + +E+  A   LNG  ++   GQ +T+   FV+ 
Sbjct: 63  -----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 58.9 bits (143), Expect = 4e-12
 Identities = 31/130 (23%), Positives = 55/130 (42%), Gaps = 21/130 (16%)

Query: 26  GTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGV-HEEAQEDDMHEKFSEYGE 84
           G+  S+   ++   S  T+  D +    R      +F+  +     ++ D+   FS+YG 
Sbjct: 1   GSSGSSGMSLKLQASNVTNKNDPKSINSR------VFIGNLNTALVKKSDVETIFSKYGR 54

Query: 85  IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVA 144
           +    ++        KGYA V+Y + + A AA    NG  + GQT+ ++      PK   
Sbjct: 55  VAGCSVH--------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA--GEPKP-- 102

Query: 145 GEQKVGPEGG 154
              + GP  G
Sbjct: 103 --DRSGPSSG 110

>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 = 58.5 bits (142), Expect = 6e-12
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           L++  +     E+ +   F+  GE + ++ +  +R TG   GY  VE+     A      
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 120 LNGTTILGQTVT----VDWCFVKGPKK 142
           +NG  + G T      +++    GP  
Sbjct: 72  INGKPLPGATPAKRFKLNYATYSGPSS 98

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 61.2 bits (148), Expect = 7e-12
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 58  GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAAR 117
              L ++ +     E+D+   FS  G +        +     +  AL++  S +EA  A 
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQAL 206

Query: 118 DALNGTTIL-GQTVTVDW 134
             L+   +     + V +
Sbjct: 207 IDLHNHDLGENHHLRVSF 224

>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 = 59.6 bits (144), Expect = 2e-11
 Identities = 23/142 (16%), Positives = 49/142 (34%), Gaps = 8/142 (5%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL 104
           G             +L V+ ++ E      +   F  YG+++ + +  ++     K  AL
Sbjct: 22  GRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENAL 76

Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVIMY 164
           V+     +A  A   LNG  + G+ + +     +  +     Q+           P+  +
Sbjct: 77  VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRF 136

Query: 165 STETSMSTTLYNAPWIFKTMHI 186
               S +      P    T+H+
Sbjct: 137 KKPGSKNFQNIFPP--SATLHL 156

>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 = 58.3 bits (141), Expect = 9e-12
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 12/109 (11%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                 RS    ++    +       ++ E FS +G +  + L            A+VE+
Sbjct: 2   SSGSSGRS--KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEF 53

Query: 108 DSYKEASAARDALNGTTILGQTVTVDW----CFVKGPKKVAGEQKVGPE 152
               EA  A   L  +      + ++W     F   P+K   + +   E
Sbjct: 54  LEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102

>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 = 57.7 bits (140), Expect = 1e-11
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFL---KGYALVEYDSYKEASAAR 117
           LF+  ++    E+ +   FS+ G IK+  ++  +    +    G+  VEY   ++A  A 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67

Query: 118 DALNGTTILGQTVTVD 133
             L G T+ G  + V 
Sbjct: 68  KQLQGHTVDGHKLEVR 83

>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 = 59.9 bits (145), Expect = 1e-11
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
             L ++ +     E+D+   FS  G +        +     +  AL++  S +EA  A  
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALI 176

Query: 119 ALNGTTIL-GQTVTVDW 134
            L+   +     + V +
Sbjct: 177 DLHNHDLGENHHLRVSF 193

>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 = 54.1 bits (130), Expect = 2e-09
 Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 61  LFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           L V+ ++ E      +   F  YG+++ + +  ++     K  ALV+     +A  A   
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 120 LNGTTILGQTVTVDWCFVKGPKKVAGEQK 148
           LNG  + G+ + +     +  +     Q+
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQE 89

>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 = 58.1 bits (141), Expect = 1e-11
 Identities = 24/111 (21%), Positives = 38/111 (34%), Gaps = 5/111 (4%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                Q    G  +FV  +  +     + E FS  G +    +  D+  G  +G   V +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTF 63

Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGE----QKVGPEGG 154
           +   EA  A    NG  +  + + V       PK         Q+ GP  G
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>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 = 57.7 bits (140), Expect = 1e-11
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+  ++      ++    SE     +L + +D RTG  + +  V+++S ++   A + L
Sbjct: 20  LFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKALE-L 77

Query: 121 NGTTILGQTVTVDW 134
            G  + G  + ++ 
Sbjct: 78  TGLKVFGNEIKLEK 91

>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 = 57.2 bits (139), Expect = 2e-11
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  + +   ++ + + FS +G I +  + ++   G  KG+  V + S +EA+ A   +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 121 NGTTILGQTVTVDWCFVKGPKK 142
           NG  +  + + V     K  ++
Sbjct: 76  NGRIVATKPLYVALAQRKEERQ 97

>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 = 58.0 bits (140), Expect = 3e-11
 Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +     + ++   F  YG ++++ +  +       G+A VE++  ++A+ A   L
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVREL 130

Query: 121 NGTTILGQTVTVDW 134
           +G T+ G  V V+ 
Sbjct: 131 DGRTLCGCRVRVEL 144

>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 = 56.5 bits (137), Expect = 5e-11
 Identities = 11/72 (15%), Positives = 27/72 (37%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+++ +     E ++      +G++ +  +  D  +G  +G      +S ++  A     
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86

Query: 121 NGTTILGQTVTV 132
           NG  I       
Sbjct: 87  NGKFIKTPPGVS 98

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 56.1 bits (136), Expect = 5e-11
 Identities = 11/83 (13%), Positives = 33/83 (39%), Gaps = 11/83 (13%)

Query: 61  LFVTGVH-EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           LF+  +  +   ++D+   FS YG I  +++           +  +++D+ +    A + 
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEC 64

Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
            +     G+ + ++        +
Sbjct: 65  ESQEMNFGKKLILE--VSSSNAR 85

>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 = 59.1 bits (142), Expect = 6e-11
 Identities = 13/78 (16%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 61  LFVTGVHEEAQEDDM----HEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           +++  ++E+ ++D++    +  FS++G+I ++ +    R+  ++G A V +     A+ A
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68

Query: 117 RDALNGTTILGQTVTVDW 134
             ++ G     + + + +
Sbjct: 69  LRSMQGFPFYDKPMRIQY 86

>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 = 54.5 bits (130), Expect = 2e-09
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
            ILF+T + EE  E  +   F+++   K + L   R        A VE+D+  +A AARD
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262

Query: 119 ALNGTTIL-GQTVTVDW 134
           AL G  I     + + +
Sbjct: 263 ALQGFKITQNNAMKISF 279

>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 = 56.0 bits (135), Expect = 7e-11
 Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 8/91 (8%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ++ V G+ E   E D+ E   ++G I  + +         K  ALVE+++   A      
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF 70

Query: 120 L--NGTTILGQTVTVDWCFVKGPKKVAGEQK 148
                  I GQ    ++   K   +      
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 55.4 bits (134), Expect = 7e-11
 Identities = 18/76 (23%), Positives = 30/76 (39%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ++ V  +      D++ + F  Y  I           G   G A+V ++S  EA+AA   
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 120 LNGTTILGQTVTVDWC 135
           LN   I  + V +   
Sbjct: 77  LNDRPIGSRKVKLSGP 92

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 55.4 bits (134), Expect = 8e-11
 Identities = 11/83 (13%), Positives = 33/83 (39%), Gaps = 11/83 (13%)

Query: 61  LFVTGV-HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           LF+  +  +   ++D+   FS YG I  +++           +  +++D+ +    A + 
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76

Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
            +     G+ + ++        +
Sbjct: 77  ESQEMNFGKKLILE--VSSSNAR 97

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 54.9 bits (133), Expect = 1e-10
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+     E ++   F+ YG +K + +  D RTG  KGY  V + +  +     +  
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE-- 68

Query: 121 NGTTILGQTVTV 132
           +     G+ + +
Sbjct: 69  SQINFHGKKLKL 80

>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 = 54.9 bits (133), Expect = 1e-10
 Identities = 13/79 (16%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 60  ILFVTGVHEEAQEDDMHEK----FSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASA 115
            +++  ++E+ ++D++ +     FS +G+I ++ +    R+  ++G A V +     A+ 
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 66

Query: 116 ARDALNGTTILGQTVTVDW 134
           A  ++ G     + + + +
Sbjct: 67  ALRSMQGFPFYDKPMRIQY 85

>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 = 54.6 bits (132), Expect = 2e-10
 Identities = 19/76 (25%), Positives = 30/76 (39%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           I+ V  +      D++ + F  Y  I           G   G A+V ++S  EA+AA   
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 120 LNGTTILGQTVTVDWC 135
           LN   I  + V +   
Sbjct: 77  LNDRPIGSRKVKLVLG 92

>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 = 54.9 bits (132), Expect = 2e-10
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDM---HEKFSEYGEIKNLHLNLDRRTGFLK---GYALVE 106
            R V+  ++FV G+ +   + ++    E F ++G+I  + +N        +     A V 
Sbjct: 10  VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVT 69

Query: 107 YDSYKEASAARDALNGTTILGQTVTVDW-----CFVKGP 140
           Y   ++A  A   +N   + G+T+         C   GP
Sbjct: 70  YIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSGP 108

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 54.9 bits (132), Expect = 2e-10
 Identities = 15/112 (13%), Positives = 43/112 (38%), Gaps = 12/112 (10%)

Query: 27  TETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDM----HEKFSEY 82
              + + E +  +S +         P +     ++ +T ++ E  ++ +    +   S  
Sbjct: 3   ETAAAKFERQHMDSPDLGSTPPHTEPSQ-----VVLITNINPEVPKEKLQALLYALASSQ 57

Query: 83  GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW 134
           G+I ++ +     +    G A + + + + A A  +A  G    G  + + +
Sbjct: 58  GDILDIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 54.4 bits (131), Expect = 2e-10
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           P ++    ++ + G+ +   E D+ E   E+G I  + +         K  ALVE++   
Sbjct: 15  PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVL 68

Query: 112 EASAARDALNGT--TILGQTVTVDW 134
            A  A +        I G    V++
Sbjct: 69  GACNAVNYAADNQIYIAGHPAFVNY 93

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 54.0 bits (130), Expect = 3e-10
 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 7/92 (7%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
               GP        + V+G+       D+ +   E G++    +  D       G  +VE
Sbjct: 4   GSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVE 56

Query: 107 YDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
           +   ++ + A   L+ T          +  VK
Sbjct: 57  FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 88

>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 = 53.8 bits (129), Expect = 5e-10
 Identities = 10/77 (12%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD- 118
           ++ +  +  +  E ++      +G++ NL +         K  A +E ++ + A+   + 
Sbjct: 33  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 86

Query: 119 -ALNGTTILGQTVTVDW 134
                  + GQ + + +
Sbjct: 87  YTSVTPVLRGQPIYIQF 103

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 54.4 bits (131), Expect = 6e-10
 Identities = 26/122 (21%), Positives = 45/122 (36%), Gaps = 13/122 (10%)

Query: 32  RNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN 91
           R E+             EPG         ++V  + +  QE D+   F  Y +  +    
Sbjct: 27  REEMETLSVFR----SYEPGEPNCR----IYVKNLAKHVQEKDLKYIFGRYVDFSSETQR 78

Query: 92  L-----DRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGE 146
           +       + G +KG A +   + K A+ A    NG  + G+ + V +     PK+   E
Sbjct: 79  IMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKE 138

Query: 147 QK 148
            K
Sbjct: 139 GK 140

>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 = 53.0 bits (128), Expect = 7e-10
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT-GFLKGYALV 105
                P+     +  F+  +  +  E+ + E F     I  + L  +      LKG+   
Sbjct: 10  HRSRLPKSP--PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 66

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVD 133
           E++      +A  +LN  ++  + + VD
Sbjct: 67  EFEDLDSLLSAL-SLNEESLGNRRIRVD 93

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 53.2 bits (128), Expect = 7e-10
 Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 8/75 (10%)

Query: 60  ILFVTGV------HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
           ++ V  V        E  ++ +H+ FS++G+I N         G  KGY  +EY S   A
Sbjct: 17  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHA 74

Query: 114 SAARDALNGTTILGQ 128
             A    +G  +  Q
Sbjct: 75  VDAVKNADGYKLDKQ 89

>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 = 54.1 bits (131), Expect = 9e-10
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+  + +  +  E FS++G I +  L LD+ TG  +G+  V YDS           
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QN 148

Query: 121 NGTTILGQTVTVD 133
                  + + + 
Sbjct: 149 KFIDFKDRKIEIK 161

>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 = 42.9 bits (102), Expect = 1e-05
 Identities = 15/87 (17%), Positives = 37/87 (42%), Gaps = 6/87 (6%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+ G++ +  ED++ E F +YG + +L +  D  TG  +G+  + ++            
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 121 NGTTILGQTVTVDWCFVKG----PKKV 143
           +   + G+ +       +       K+
Sbjct: 66  H--ILDGKVIDPKRAIPRDEQDKTGKI 90

>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 = 51.7 bits (124), Expect = 2e-09
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
           L+V  +     E+ M + F+    +  L        L  +    K +A +E+ S  E + 
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 116 ARDALNGTTILGQTVTV 132
           A  A +G    GQ++ +
Sbjct: 69  AM-AFDGIIFQGQSLKI 84

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 8/72 (11%)

Query: 60  ILFVTGV------HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEA 113
           ++ V  V        E  ++ +H+ FS++G+I N         G  KGY  +EY S   A
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHA 60

Query: 114 SAARDALNGTTI 125
             A    +G  +
Sbjct: 61  VDAVKNADGYKL 72

>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 = 51.5 bits (124), Expect = 3e-09
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAAR 117
           +  F+  +  +  E+ + E F     I  + L  +      LKG+   E++      +A 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 118 DALNGTTILGQTVTVDW 134
            +LN  ++  + + VD 
Sbjct: 75  -SLNEESLGNKRIRVDV 90

>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 = 53.5 bits (129), Expect = 3e-09
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 47  DEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
           ++   P   +    +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V 
Sbjct: 93  EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152

Query: 107 YDSYKEASAARDALNGTTILGQTVTVD 133
           +D +             T+ G    V 
Sbjct: 153 FDDHDSVDKIV-IQKYHTVNGHNCEVR 178

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+  E  ++ +   F ++G + +  +  D  T   +G+  V Y + +E  AA +A 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74

Query: 121 NGTTILGQTVTVD 133
               + G+ V   
Sbjct: 75  RPHKVDGRVVEPK 87

>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 = 4e-09
 Identities = 10/77 (12%), Positives = 29/77 (37%), Gaps = 8/77 (10%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD- 118
           +L +  +  E  E ++      +G++ N+ +         K  A +E  + + A    + 
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNY 70

Query: 119 -ALNGTTILGQTVTVDW 134
            +     +  Q + + +
Sbjct: 71  YSAVTPHLRNQPIYIQY 87

>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 = 50.5 bits (121), Expect = 5e-09
 Identities = 13/94 (13%), Positives = 30/94 (31%), Gaps = 13/94 (13%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           + V  + +++   ++H+   +Y                 K  A V   + ++A  A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
           +  +  G+ + V        +        GP  G
Sbjct: 61  HQYSFRGKDLIVQL------QPTDALLCSGPSSG 88

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 50.6 bits (121), Expect = 6e-09
 Identities = 10/77 (12%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ++ +  +  +  E ++      +G++ NL +         K  A +E ++ + A+   + 
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 71

Query: 120 L--NGTTILGQTVTVDW 134
                  + GQ + + +
Sbjct: 72  YTSVTPVLRGQPIYIQF 88

>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 = 49.9 bits (120), Expect = 9e-09
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+     E ++ E F ++G +  + +  D      +G+  + ++  +    A   +
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71

Query: 121 NGTTILGQTVTVD 133
           +   I+G+ V V 
Sbjct: 72  HFHDIMGKKVEVK 84

>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 = 50.2 bits (120), Expect = 1e-08
 Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G   P  +RS     + V+G+       D+ +   E G++    +  D       G  +V
Sbjct: 6   GRYGPPSRRS--ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 56

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
           E+   ++ + A   L+ T          +  VK
Sbjct: 57  EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 89

>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 = 50.1 bits (120), Expect = 1e-08
 Identities = 23/109 (21%), Positives = 40/109 (36%), Gaps = 3/109 (2%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G        + +   + V G+   A E+D+ + F     +  +HL  D   G   G  LV
Sbjct: 4   GSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLV 61

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
           ++ S ++   A    N   ++ + V V     +      G    GP  G
Sbjct: 62  KFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 51.3 bits (122), Expect = 2e-08
 Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 15/88 (17%)

Query: 61  LFVTGVHE---------EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           L+V G+              E  +   FS  G+I  +           K    V++    
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQA 190

Query: 112 EASAARDALNGTTILGQTVTVDWCFVKG 139
            A  A++A++  T+L  +        +G
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREG 218

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++ G   +A  DD+ E   + G++ N+ +       F KG   V +DS + A       
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFV-ET 71

Query: 121 NGTTILGQTVTVDW 134
            G       + + +
Sbjct: 72  PGQKYKETDLLILF 85

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.5 bits (113), Expect = 6e-08
 Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 5/90 (5%)

Query: 45  VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL 104
            G   P  + +     ++V  +  +A+  D+     E G +      L       +  A 
Sbjct: 6   SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAF 60

Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDW 134
           + Y     A  A   L G  +   T+ V  
Sbjct: 61  LHYPDSAAAQQAVSCLQGLRLGTDTLRVAL 90

>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 = 47.2 bits (113), Expect = 9e-08
 Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 2/85 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V G+  +  E D+ E FS +GE+  + +  D +TG  KG+  V +  Y+         
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAG 145
           +   I G+         K  +    
Sbjct: 78  H--MIDGRWCDCKLPNSKQSQDSGP 100

>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 = 46.3 bits (111), Expect = 1e-07
 Identities = 12/73 (16%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+  +  E+ + E F  +GE++++ L +D +T   +G+  + +   +      +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 121 NGTTILGQTVTVD 133
               +      + 
Sbjct: 61  KYHNVGLSKCEIK 73

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 46.5 bits (111), Expect = 1e-07
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 9/93 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV+G         + E F  +G + ++   +D+  G    +A+VE        A   + 
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDKDKG---VFAIVEMGDVGAREAVL-SQ 64

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEG 153
           +  ++ G  + V     +  K+        P+G
Sbjct: 65  SQHSLGGHRLRVR---PREQKEFQSPASKSPKG 94

>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 = 48.2 bits (114), Expect = 1e-07
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 9/93 (9%)

Query: 44  DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYA 103
           D G    G         + V  +      D +H+ FS++G +  +              A
Sbjct: 35  DAGMAMAGQSPV---LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QA 87

Query: 104 LVEYDSYKEASAARDALNGTTIL--GQTVTVDW 134
           L++Y     A  A+ +L+G  I     T+ +D+
Sbjct: 88  LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 7/95 (7%)

Query: 44  DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYA 103
           D G    G    +    + V  +      D +H+ FS++G +  +              A
Sbjct: 17  DAGMAMAGQSPVL---RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QA 69

Query: 104 LVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
           L++Y     A  A+ +L+G  I     T+   F K
Sbjct: 70  LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 18/108 (16%), Positives = 42/108 (38%), Gaps = 7/108 (6%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN-LHLNLDRRTGFLKGYALVEYDSY 110
              +       +T +     + D+ +        +N +H+ +D   G   G ALV++ + 
Sbjct: 9   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNE 67

Query: 111 KEASAARDALNGTTILGQTVTVDWCFVKGPKKVA----GEQKVGPEGG 154
            +A  +   L+   + G+   V    ++  +++      + K GP  G
Sbjct: 68  DDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 45.5 bits (109), Expect = 2e-07
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+      +D+   F ++G++ +  L  D+ T   +G+  V ++S          +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 121 NGTTILGQTVTVD 133
           +   I  + V   
Sbjct: 61  HFHEINNKMVECK 73

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 20/115 (17%), Positives = 43/115 (37%), Gaps = 17/115 (14%)

Query: 26  GTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVT--GVHEEAQEDDMHEKFSEYG 83
           G+  S+   I    +      D+  G  +     +L ++          D ++   +  G
Sbjct: 1   GSSGSSGKRITRPGN-----TDDPSGGNK-----VLLLSIQNPLYPITVDVLYTVCNPVG 50

Query: 84  EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
           +++ + +            A+VE++S   A  A+ ALNG  I     T+   + +
Sbjct: 51  KVQRIVIFKRNGI-----QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR 100

>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 = 46.8 bits (111), Expect = 3e-07
 Identities = 25/133 (18%), Positives = 51/133 (38%), Gaps = 4/133 (3%)

Query: 22  GRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSE 81
             G     S    +   + M      +     +S  G  + + G+  +A E+D++  FS 
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGRG-SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSP 69

Query: 82  YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK 141
                 +H+ +    G + G A VE+ +++EA AA  + +   +  + + +      G  
Sbjct: 70  LN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS 126

Query: 142 KVAGEQKVGPEGG 154
             A   +V    G
Sbjct: 127 NGAYSSQVMQGMG 139

>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 = 45.4 bits (108), Expect = 6e-07
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 1/95 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+     +  + + F  +G+I+   +  DR+TG  +GY  V       A  A    
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGV 155
           N   I G+   V+  ++    +           G 
Sbjct: 80  NP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 15/101 (14%), Positives = 28/101 (27%), Gaps = 5/101 (4%)

Query: 32  RNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN 91
            +    + S     G            + + +  + E     D+ +   E          
Sbjct: 4   SHHHHHHSSGLVPRGSHMSKLPAK--RYRITMKNLPEGCSWQDLKDLARENSLE---TTF 58

Query: 92  LDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV 132
               T    G   +E+ S +    A + LN     G  +TV
Sbjct: 59  SSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>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 = 44.1 bits (105), Expect = 1e-06
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV     +  ED++ E FS+YG++ ++ +    R      +A V +    +  A     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFAD--DQIAQSLCG 60

Query: 121 NGTTILGQTVTVD 133
               I G +V + 
Sbjct: 61  EDLIIKGISVHIS 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 = 44.4 bits (105), Expect = 1e-06
 Identities = 17/111 (15%), Positives = 38/111 (34%), Gaps = 5/111 (4%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                     G+ +++ G+  EA+   + + F +   +++         G   G   VE+
Sbjct: 15  RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 74

Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAG----EQKVGPEGG 154
            +  +  AA    +   +  + + V     KG  +         + GP  G
Sbjct: 75  RNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 59  WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           W+L +  +  +     +     ++G + + H  L+      +G AL +Y + +EA+ A+ 
Sbjct: 9   WLL-LKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN------QGIALCKYTTREEANKAQM 61

Query: 119 ALNGTTILGQTVTVD 133
           ALN   +   T+  +
Sbjct: 62  ALNNCVLANTTIFAE 76

>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 = 42.6 bits (101), Expect = 3e-06
 Identities = 13/73 (17%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+  +  + D+ + F+++GE+ +  + +D  TG  +G+  + +          D  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 121 NGTTILGQTVTVD 133
               + G+ +   
Sbjct: 74  EH-RLDGRVIDPK 85

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 42.1 bits (100), Expect = 4e-06
 Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+ G+  +  ++ + E F ++GE+K   +  D  T   +G+  V +             
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 121 NGTTILGQTVTVD 133
           +   +  +T+   
Sbjct: 62  SRHELDSKTIDPK 74

>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 = 43.3 bits (102), Expect = 5e-06
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 1/87 (1%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
                    S     + + G+     ++++ + FS    + N         G + G A V
Sbjct: 30  MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89

Query: 106 EYDSYKEASAARDALNGTTILGQTVTV 132
           ++ S + A  A    +   I  + + V
Sbjct: 90  QFASQELAEKALG-KHKERIGHRYIEV 115

>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 = 42.5 bits (100), Expect = 6e-06
 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 68  EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG 127
           +E  E+   E   +YGE++ +++  D     L G   V++   ++A  A   LN     G
Sbjct: 37  DEFFEEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG 95

Query: 128 QTVTVDWC 135
           Q +  +  
Sbjct: 96  QPIHAELS 103

>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 = 41.8 bits (99), Expect = 8e-06
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV    E+   +++ + F +YGE+ ++ +    R      +A V +    +  A     
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFAD--DKVAQSLCG 66

Query: 121 NGTTILGQTVTVD 133
               I G +V + 
Sbjct: 67  EDLIIKGISVHIS 79

>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 = 41.8 bits (99), Expect = 8e-06
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 1/88 (1%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G        + E   LFV G+     ++ +   FS+YGE+ +  +  D+ T   +G+  V
Sbjct: 4   GSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVD 133
           ++           +    T+ G+ +   
Sbjct: 64  KFKDPNCVGTVLAS-RPHTLDGRNIDPK 90

>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 = 41.9 bits (99), Expect = 1e-05
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+  E  E+ +   + ++G++ +  +  D  +   +G+  V + S  E  AA  A 
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88

Query: 121 NGTTILGQTVTVD 133
              +I G+ V   
Sbjct: 89  RPHSIDGRVVEPK 101

>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 = 41.6 bits (98), Expect = 1e-05
 Identities = 24/107 (22%), Positives = 44/107 (41%), Gaps = 9/107 (8%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
                 +S  G  + + G+   A E+D++  FS       +H+ +    G + G A VE+
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEF 62

Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
            ++++A AA  A +   +  + V +           AG    GP  G
Sbjct: 63  ATHEDAVAAM-AKDKANMQHRYVELF------LNSTAGTSGSGPSSG 102

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           G      G  +F+ G+  +  ++ + E F ++GE+K   +  D  T   +G+  V +   
Sbjct: 18  GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77

Query: 111 KEASAARDALNGTTILGQTVTVD 133
                     +   +  +T+   
Sbjct: 78  AGVDKVLAQ-SRHELDSKTIDPK 99

>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 = 42.5 bits (99), Expect = 2e-05
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++ G   +A  DD+ E   + G++ N+ +       F KG   V +DS + A    +  
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVETP 170

Query: 121 NGT 123
              
Sbjct: 171 GQK 173

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 42.5 bits (99), Expect = 3e-05
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 61  LFV--TGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           L V   G+      + +     + G +  L +  +      K Y+   Y + +E+  A  
Sbjct: 21  LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYV 74

Query: 119 ALNGTTI---LGQTVTVDWCFVKGPKKVAGEQKVGPEG 153
            LNG  +   LGQ +T+   FV+  +      +  P G
Sbjct: 75  TLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPG 112

>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 = 3e-05
 Identities = 19/121 (15%), Positives = 36/121 (29%), Gaps = 8/121 (6%)

Query: 15  EKARKKKGRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDD 74
                    G     S    +   + M        P      EG+++ + G+      +D
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGG---EGFVVKLRGLPWSCSVED 60

Query: 75  MHEKFSEY---GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
           +    S+         +H    R  G   G A VE  S  +   A    +  ++  + + 
Sbjct: 61  VQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE 118

Query: 132 V 132
           V
Sbjct: 119 V 119

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 4/51 (7%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG 122
           +DD+ E+ +++G +  +H+ +D+ +   +G   V+  S   A AA +AL+G
Sbjct: 31  KDDVIEECNKHGGV--IHIYVDKNSA--QGNVYVKCPSIAAAIAAVNALHG 77

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 24/96 (25%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSE-YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           LFV  +  +  +  ++E F + Y   +   + LD+ TG  KGY  V++    E   A   
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70

Query: 120 LNGTTILGQ-TVTVDWCFVKGPKKVAGEQKVGPEGG 154
             G   LG   V +     K  +      + GP  G
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRV--KPVESGPSSG 104

>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 = 38.8 bits (91), Expect = 8e-05
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 3/78 (3%)

Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
                 + + G      E ++ E  +       + +  +   G   GY  V++ + +E  
Sbjct: 7   GTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVK 64

Query: 115 AARDALNGTTILGQTVTV 132
            A    N   + G+ + V
Sbjct: 65  QALK-CNREYMGGRYIEV 81

>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 = 38.6 bits (90), Expect = 1e-04
 Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 4/87 (4%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
               P          + + G+     ++++ + FS    + N         G   G A V
Sbjct: 6   SGNSPDTANDG---FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62

Query: 106 EYDSYKEASAARDALNGTTILGQTVTV 132
           ++ S + A  A    +   I  + + +
Sbjct: 63  QFASQEIAEKALK-KHKERIGHRYIEI 88

>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 = 2e-04
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEY---GEIKNLHLNLDRRTGFLKGYAL 104
              GP+   EG+++ + G+      +D+    S+      +  +H    R  G   G A 
Sbjct: 8   MMLGPE-GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAF 65

Query: 105 VEYDSYKEASAARDALNGTTILGQTVTV 132
           VE +S  +   A    +  ++  + + V
Sbjct: 66  VELESEDDVKLAL-KKDRESMGHRYIEV 92

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 12/90 (13%), Positives = 29/90 (32%), Gaps = 4/90 (4%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN---LDRRTGFLKGY 102
            +E           I+ + G+   A  +++   F ++  I         +    G   G 
Sbjct: 11  SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70

Query: 103 ALVEYDSYKEASAARDALNGTTILGQTVTV 132
           A V +   + A  A    +   +  + + +
Sbjct: 71  AFVLFACEEYAQNAL-RKHKDLLGKRYIEL 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	192
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.92
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.92
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.92
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.92
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.91
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.91
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.91
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.91
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.9
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.9
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.9
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.9
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.9
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.9
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.89
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.89
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.89
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.89
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.89
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.89
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.89
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.89
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.88
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.88
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.88
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.88
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.88
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.88
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.88
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.88
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.88
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.88
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.88
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.88
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.88
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.88
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.88
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.88
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.88
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.88
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.87
2div_A	99	TRNA selenocysteine associated protein; structural	99.87
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.87
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.87
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.87
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.87
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.87
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.87
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.87
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.87
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.87
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.87
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.86
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.86
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.86
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.86
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.86
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.86
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.86
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.86
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.86
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.86
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.86
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.86
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.85
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.85
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.85
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.85
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.85
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.85
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.85
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.85
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.85
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.85
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.84
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.84
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.84
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.84
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.84
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.84
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.84
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.84
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.84
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.84
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.83
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.83
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.83
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.83
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.83
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.83
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.83
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.83
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.83
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.82
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.82
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.82
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.82
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.82
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.82
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.82
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.71
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.82
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.82
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.81
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.81
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.81
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.81
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.81
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.81
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.81
1x5p_A	97	Negative elongation factor E; structure genomics,	99.81
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.81
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.81
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.81
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.81
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.8
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.8
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.8
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.8
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.8
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.8
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.8
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.79
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.79
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.79
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.79
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.78
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.77
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.77
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.77
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.77
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.77
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.76
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.76
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.75
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.75
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.73
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.72
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.72
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.72
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.7
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.66
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.65
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.64
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.62
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.6
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.59
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.58
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.52
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.45
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.35
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.31
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.16
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.15
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.6
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.12
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.96
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.94
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.79
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.74
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	97.26
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.23
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.91
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	96.79
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.76
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.69
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	96.64
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.63
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	96.58
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	96.43
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	96.43
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	96.37
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	96.24
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	96.22
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.21
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	96.04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	96.01
1x5o_A	114	RNA binding motif, single-stranded interacting pro	95.93
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	95.89
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	95.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	95.82
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	95.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	95.71
1x4e_A	85	RNA binding motif, single-stranded interacting pro	95.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	95.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	95.64
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	95.61
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	95.58
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	95.53
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	95.49
2div_A	99	TRNA selenocysteine associated protein; structural	95.47
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	95.45
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	95.41
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	95.4
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	95.39
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	95.39
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	95.36
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	95.35
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	95.33
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	95.32
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	95.32
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	95.31
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	95.31
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	95.26
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	95.26
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	95.24
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	95.23
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	95.22
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	95.19
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	95.19
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	95.16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	95.1
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	95.09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	95.09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	95.09
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	95.09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	95.08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	95.08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	95.05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	95.0
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	94.92
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	94.89
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	94.87
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	94.84
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	94.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	94.77
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	94.75
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	94.7
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	94.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	94.67
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	94.65
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	94.65
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	94.61
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	94.58
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	94.58
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	94.56
2dis_A	109	Unnamed protein product; structural genomics, RRM	94.53
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	94.52
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	94.49
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	94.45
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	94.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	94.39
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	94.37
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	94.19
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	94.18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	94.17
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	94.11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	94.08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	93.97
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	93.89
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	93.85
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	93.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	93.83
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	93.83
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	92.8
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	93.57
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	93.51
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	93.47
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	93.45
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	93.4
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	93.34
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	93.26
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	93.21
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	93.15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	93.05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	92.97
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	92.88
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	92.57
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.47
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	92.31
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	91.8
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	91.58
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	91.55
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	91.35
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	91.27
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	91.26
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	91.2
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	91.09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	90.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	90.37
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	90.36
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	89.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	89.73
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	89.64
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	88.47
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	88.38
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	87.84
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	87.63
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	84.43
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	83.95
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	83.64
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	82.51
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	81.79
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	80.95
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	80.87
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	80.37

>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=99.92  E-value=5.4e-25  Score=161.08  Aligned_cols=130  Identities=18%  Similarity=0.245  Sum_probs=101.7

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhHHH--hhhccc----CCC----------------CCCCCCCCCCCCCcEEEEcCC
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNEIR--EYESME----TDV----------------GDEEPGPQRSVEGWILFVTGV   66 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~~~--~~~~~~----~~~----------------~~~~~~~~~~~~~~~l~V~nL   66 (192)
                      .+.++.+..   +++|||||+|...+.+  +...++    .++                .............++|||+||
T Consensus         2 ~~kl~ln~~---~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl   78 (158)
T 2kn4_A            2 QYKLILNGK---TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNL   78 (158)
T ss_dssp             EEEEEEECS---SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESC
T ss_pred             cEEEEecCc---cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCC
Confidence            456677766   4899999999433322  222211    010                000111222344689999999


Q ss_pred             CCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCC
Q psy15152         67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK  141 (192)
Q Consensus        67 p~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~  141 (192)
                      |+++++++|+++|+.||.|..+.++.|+.+|.++|||||+|.+.++|++|++.|||..+.|+.|.|.++.++.++
T Consensus        79 ~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           79 TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             CTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            999999999999999999999999999889999999999999999999999999999999999999999876544

>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=99.92  E-value=6.6e-25  Score=148.89  Aligned_cols=82  Identities=28%  Similarity=0.458  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..+++|||+|||+++|+++|+++|++||.|.+++++.|+.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|+||
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q psy15152        136 FV  137 (192)
Q Consensus       136 ~~  137 (192)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.92  E-value=2.6e-24  Score=164.19  Aligned_cols=134  Identities=24%  Similarity=0.323  Sum_probs=105.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccC---CCCCCCCCCC---------------CCCCCcEEEEcCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMET---DVGDEEPGPQ---------------RSVEGWILFVTGV   66 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~---~~~~~~~~~~---------------~~~~~~~l~V~nL   66 (192)
                      +.+|.+++|+.+++ ++|||||+|...+  ..++..++.   .+........               .....++|||+||
T Consensus        55 i~~v~i~~~~~~g~-~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl  133 (216)
T 2qfj_A           55 IKSIDMSWDSVTMK-HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV  133 (216)
T ss_dssp             EEEEEECCC-CC-C-CCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECC
T ss_pred             EEEEEEeecCCCCc-cCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCC
Confidence            67899999999995 9999999994333  233332322   2211110000               1234579999999


Q ss_pred             CCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCC
Q psy15152         67 HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK  141 (192)
Q Consensus        67 p~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~  141 (192)
                      |.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+.+++..
T Consensus       134 p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          134 HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             CTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             CCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            999999999999999999999999999889999999999999999999999999999999999999999876433

>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=99.92  E-value=1.9e-24  Score=162.61  Aligned_cols=136  Identities=22%  Similarity=0.366  Sum_probs=101.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH-H-Hhhhcc--cCCCCC-----C-----CCCCCCCCCCcEEEEcCCCCCCc
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE-I-REYESM--ETDVGD-----E-----EPGPQRSVEGWILFVTGVHEEAQ   71 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~-~-~~~~~~--~~~~~~-----~-----~~~~~~~~~~~~l~V~nLp~~~t   71 (192)
                      .+.+|.+++|+.+++ +||||||+|...+ + .++...  ...+..     .     ...+......++|||+|||++++
T Consensus        39 ~i~~v~i~~~~~~g~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t  117 (196)
T 1l3k_A           39 TLTDCVVMRDPNTKR-SRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE  117 (196)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-----------CCSEEEEECCTTTCC
T ss_pred             CEEEEEEEEcCCCCC-ccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCC
Confidence            366899999999996 9999999993333 2 222221  111100     0     01112233458999999999999


Q ss_pred             HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCCCC
Q psy15152         72 EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKV  143 (192)
Q Consensus        72 ~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~~~  143 (192)
                      +++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|++. ++..+.|+.|.|.+|.++.....
T Consensus       118 ~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-------
T ss_pred             HHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHhcc
Confidence            999999999999999999999988999999999999999999999986 89999999999999988765443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.91  E-value=5.8e-25  Score=168.48  Aligned_cols=131  Identities=17%  Similarity=0.262  Sum_probs=103.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCC---CCCC-----CC-CCCCCCCCcEEEEcCCCCCCcHHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETD---VGDE-----EP-GPQRSVEGWILFVTGVHEEAQEDD   74 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~---~~~~-----~~-~~~~~~~~~~l~V~nLp~~~t~~~   74 (192)
                      .+.+|.+++|+.+++ ++|||||+|...+  ..++..++..   +...     .. .........+|||+|||+++++++
T Consensus        41 ~I~~v~i~~d~~tg~-~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~  119 (213)
T 4f02_A           41 PILSIRVCRDMITRR-SLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKA  119 (213)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHH
T ss_pred             CEEEEEEecccCCCC-ccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccccccccccccceECCcccccHHHH
Confidence            357899999999996 9999999994333  3333333322   1100     00 011122356899999999999999


Q ss_pred             HHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCC
Q psy15152         75 MHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        75 L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~  139 (192)
                      |+++|+.||.|..++|+.|.  +.++|||||+|.+.++|++|++.|||..|.|++|.|.+|.++.
T Consensus       120 l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          120 LYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             HHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             HHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            99999999999999999985  5589999999999999999999999999999999999998653

>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=99.91  E-value=4.5e-25  Score=162.07  Aligned_cols=130  Identities=20%  Similarity=0.312  Sum_probs=104.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcc-cCCCCCCCCCC----CCCCCCcEEEEcCCCCCCcHHHHHHhh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESM-ETDVGDEEPGP----QRSVEGWILFVTGVHEEAQEDDMHEKF   79 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~-~~~~~~~~~~~----~~~~~~~~l~V~nLp~~~t~~~L~~~F   79 (192)
                      +.+|.+++|+.+++ +||||||+|...+  ..+.... ...+.......    .......+|||+|||.++++++|+++|
T Consensus        30 i~~v~i~~~~~~g~-~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F  108 (167)
T 2cjk_A           30 VTDLKIMKDPATGR-SRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFF  108 (167)
T ss_dssp             EEEEECCCCTTTSS-CCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHHHHHCEEEEEEEECTTCCHHHHHHHH
T ss_pred             EEEEEEEECCCCCC-ccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhhccCCCeEEECCCCCCCCHHHHHHHH
Confidence            66899999999996 9999999993333  3333321 12221111111    112235789999999999999999999


Q ss_pred             ccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         80 SEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        80 ~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++..+.|+.|.|.||.++
T Consensus       109 ~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          109 SQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999999999999998899999999999999999999998 8999999999999999875

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.91  E-value=9.5e-24  Score=154.43  Aligned_cols=128  Identities=17%  Similarity=0.347  Sum_probs=103.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccCC---CC-----C-CCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMETD---VG-----D-EEPGPQRSVEGWILFVTGVHEEAQEDDM   75 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~~---~~-----~-~~~~~~~~~~~~~l~V~nLp~~~t~~~L   75 (192)
                      +.+|.+++|+. + +++|||||+|...+  ..+...++..   +.     . .........+.++|||+|||.++++++|
T Consensus        27 i~~v~i~~~~~-~-~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l  104 (166)
T 3md3_A           27 IANIKIMIDKN-N-KNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETL  104 (166)
T ss_dssp             EEEEEEECCCC---CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHH
T ss_pred             eEEEEEEECCC-C-CCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHH
Confidence            56888998875 4 39999999994333  2233233221   11     0 1112234456789999999999999999


Q ss_pred             HHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         76 HEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        76 ~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..++|+.|.|.||.
T Consensus       105 ~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          105 RNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             HHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            9999999999999999998899999999999999999999999999999999999999985

>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=99.91  E-value=8.4e-24  Score=156.08  Aligned_cols=135  Identities=68%  Similarity=1.186  Sum_probs=84.0

Q ss_pred             eEEeeccCcCCCCCCccCCCCChhHHHhhhcccC-CCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEE
Q psy15152         10 IARLKEKARKKKGRGFGTETSTRNEIREYESMET-DVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNL   88 (192)
Q Consensus        10 v~~~~d~~~~~k~rG~gfv~f~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~   88 (192)
                      +..+..+..++++||++-..-.......+..+.. ......+.+....++++|||+|||+.+++++|+++|++||.|..+
T Consensus        23 ~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v  102 (165)
T 1rk8_A           23 IVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI  102 (165)
T ss_dssp             -------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             chhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEE
Confidence            3444444555445554433222222334444321 111245667777888999999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCCCCCC
Q psy15152         89 HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVA  144 (192)
Q Consensus        89 ~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~~~~~  144 (192)
                      .|+.++.+|.++|||||+|.+.++|++|++.|||..|.|+.|.|.|+.++..+..+
T Consensus       103 ~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~~~  158 (165)
T 1rk8_A          103 HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK  158 (165)
T ss_dssp             EEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-----
T ss_pred             EEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCCCC
Confidence            99999989999999999999999999999999999999999999999987655443

>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=99.90  E-value=1.2e-23  Score=154.39  Aligned_cols=127  Identities=23%  Similarity=0.311  Sum_probs=103.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH--HhhhcccC---CCC-----CCCCCCCCCCCCcEEEEcCCCCCCcHHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI--REYESMET---DVG-----DEEPGPQRSVEGWILFVTGVHEEAQEDDMH   76 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~--~~~~~~~~---~~~-----~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   76 (192)
                      +.++.+++|+.+++ ++|||||+|...+.  .+...++.   .+.     ...+ .......++|||+|||.++++++|+
T Consensus        30 i~~v~i~~~~~~~~-~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~-~~~~~~~~~l~v~nl~~~~t~~~l~  107 (168)
T 1b7f_A           30 INTCRIMRDYKTGY-SYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP-GGESIKDTNLYVTNLPRTITDDQLD  107 (168)
T ss_dssp             EEEEECCEETTTTE-ECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC-CSSTTTTCEEEEESCCTTCCHHHHH
T ss_pred             eeEEEEEEeCCCCc-cceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC-CcccCCCCCEEEeCCCCCCCHHHHH
Confidence            56889999999996 99999999943332  22222322   121     1111 2233456899999999999999999


Q ss_pred             HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEec
Q psy15152         77 EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVDWC  135 (192)
Q Consensus        77 ~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a  135 (192)
                      ++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.||
T Consensus       108 ~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          108 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            999999999999999998899999999999999999999999999999988  99999986

>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=99.90  E-value=1.9e-23  Score=154.19  Aligned_cols=129  Identities=17%  Similarity=0.298  Sum_probs=101.9

Q ss_pred             eeeeeEEeeccCcC--CCCCCccCCCCChhH--HHhhhcccCCCCC-----------CCCCCCCCCCCcEEEEcCCCCCC
Q psy15152          6 RLKGIARLKEKARK--KKGRGFGTETSTRNE--IREYESMETDVGD-----------EEPGPQRSVEGWILFVTGVHEEA   70 (192)
Q Consensus         6 ~~~~v~~~~d~~~~--~k~rG~gfv~f~~~~--~~~~~~~~~~~~~-----------~~~~~~~~~~~~~l~V~nLp~~~   70 (192)
                      .+.++.+++|+.++  + +||||||+|...+  ..+...++...-.           ..+........++|||+|||+++
T Consensus        29 ~i~~v~i~~~~~~~~~~-~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  107 (175)
T 3nmr_A           29 AVYEINVLRDRSQNPPQ-SKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKC  107 (175)
T ss_dssp             CEEEEEEEEECSSSSCE-EEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCSCGGGSEEEEESCCTTC
T ss_pred             CEEEEEEEecCCCCCCC-cceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccccCCCCeEEEcCCCCcC
Confidence            35689999999987  5 9999999994333  3333333321100           01111223356899999999999


Q ss_pred             cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC---CeEEEEEecc
Q psy15152         71 QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL---GQTVTVDWCF  136 (192)
Q Consensus        71 t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~---g~~l~v~~a~  136 (192)
                      ++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|++|++.|||..+.   |++|.|.||.
T Consensus       108 t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          108 TENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999999999999996 7999999999999999999999999998876   4999999984

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.90  E-value=4.4e-23  Score=142.45  Aligned_cols=83  Identities=18%  Similarity=0.253  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|++||.|.++.|+.|+.||+++|||||+|.+.++|++|++.|||..+.|+.|.|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            644

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.90  E-value=4e-23  Score=141.42  Aligned_cols=93  Identities=75%  Similarity=1.399  Sum_probs=86.1

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy15152         48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG  127 (192)
Q Consensus        48 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g  127 (192)
                      ..+.+....++++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|
T Consensus        13 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   92 (106)
T 1p27_B           13 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG   92 (106)
T ss_dssp             --CCBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECC
Confidence            45666777788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEecccCCC
Q psy15152        128 QTVTVDWCFVKGP  140 (192)
Q Consensus       128 ~~l~v~~a~~~~~  140 (192)
                      +.|.|.|+.++++
T Consensus        93 ~~l~V~~a~~~~~  105 (106)
T 1p27_B           93 QPISVDWCFVRGP  105 (106)
T ss_dssp             SBCEEEESEESSC
T ss_pred             cEEEEEeecCCCC
Confidence            9999999987753

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.90  E-value=2.5e-22  Score=139.43  Aligned_cols=91  Identities=23%  Similarity=0.433  Sum_probs=83.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .....+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|++..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33445678999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEecccCCCCC
Q psy15152        132 VDWCFVKGPKK  142 (192)
Q Consensus       132 v~~a~~~~~~~  142 (192)
                      |.|+.++....
T Consensus        89 V~~a~~~~~~~   99 (115)
T 2dgo_A           89 TNWATRKPPAP   99 (115)
T ss_dssp             EEESSCCCCCS
T ss_pred             EEEccCCCCCC
Confidence            99998775543

>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=99.90  E-value=2.3e-23  Score=152.48  Aligned_cols=127  Identities=22%  Similarity=0.413  Sum_probs=102.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH--HhhhcccC---CCC-----CCCCCCCCCCCCcEEEEcCCCCCCcHHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI--REYESMET---DVG-----DEEPGPQRSVEGWILFVTGVHEEAQEDDMH   76 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~--~~~~~~~~---~~~-----~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   76 (192)
                      +.++.+++|+.+++ ++|||||+|...+.  .+...++.   .+.     ...+ ........+|||+|||.++++++|+
T Consensus        29 i~~v~~~~~~~~~~-~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~-~~~~~~~~~l~v~nl~~~~t~~~l~  106 (167)
T 1fxl_A           29 IESCKLVRDKITGQ-SLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP-SSASIRDANLYVSGLPKTMTQKELE  106 (167)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC-CCGGGTTCEEEEESCCTTCCHHHHH
T ss_pred             eEEEEEEeCCCCCc-ceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC-CcccCCCCcEEECCCCCcCCHHHHH
Confidence            56899999999995 99999999943332  22222322   121     1111 1223456789999999999999999


Q ss_pred             HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE--EEEEec
Q psy15152         77 EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT--VTVDWC  135 (192)
Q Consensus        77 ~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~--l~v~~a  135 (192)
                      ++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.  |.|.||
T Consensus       107 ~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          107 QLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            99999999999999999889999999999999999999999999999999964  888886

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.90  E-value=4.9e-24  Score=142.38  Aligned_cols=83  Identities=24%  Similarity=0.420  Sum_probs=76.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC-CCeeCCeEEEEEec
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN-GTTILGQTVTVDWC  135 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~-~~~~~g~~l~v~~a  135 (192)
                      +++|||+|||+++|+++|+++|++|| .|.++++++|+.+|.++|||||+|.+.++|++|++.++ +..++|++|.|+||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999999999999999999999999999999999874 56799999999999


Q ss_pred             ccCCC
Q psy15152        136 FVKGP  140 (192)
Q Consensus       136 ~~~~~  140 (192)
                      .+++.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87653

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.9e-22  Score=137.42  Aligned_cols=88  Identities=25%  Similarity=0.436  Sum_probs=82.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      |+.++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99876543

>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=99.89  E-value=6e-23  Score=141.50  Aligned_cols=94  Identities=77%  Similarity=1.316  Sum_probs=86.6

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy15152         48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG  127 (192)
Q Consensus        48 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g  127 (192)
                      ..+.+....++++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|+..|+|..+.|
T Consensus        16 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   95 (110)
T 1oo0_B           16 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG   95 (110)
T ss_dssp             --CCBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            45667777888999999999999999999999999999999999999899999999999999999999999999999999


Q ss_pred             eEEEEEecccCCCC
Q psy15152        128 QTVTVDWCFVKGPK  141 (192)
Q Consensus       128 ~~l~v~~a~~~~~~  141 (192)
                      +.|.|.|+.+++.+
T Consensus        96 ~~l~V~~a~~~~~~  109 (110)
T 1oo0_B           96 QTIQVDWCFVKGPK  109 (110)
T ss_dssp             EECEEEESEESSCC
T ss_pred             cEEEEEEcccCCCC
Confidence            99999999887543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=1.6e-22  Score=136.77  Aligned_cols=88  Identities=17%  Similarity=0.375  Sum_probs=81.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ |++..+.|+.|.|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            334556899999999999999999999999999999999999899999999999999999999998 9999999999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .++.++...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2dgs_A           84 KRAEPRDSK   92 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCccc
Confidence            999876544

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.89  E-value=2.5e-23  Score=139.98  Aligned_cols=83  Identities=23%  Similarity=0.316  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCC--eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC----eeCCe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGE--IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT----TILGQ  128 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~--i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~----~~~g~  128 (192)
                      ...-.+|||+|||+++|+++|+++|++||.  +.+|++++|+.||+++|||||+|.+.++|++|++.|||.    .|+|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            345578999999999999999999999995  679999999999999999999999999999999999997    48999


Q ss_pred             EEEEEeccc
Q psy15152        129 TVTVDWCFV  137 (192)
Q Consensus       129 ~l~v~~a~~  137 (192)
                      +|.|+||+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999964

>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=99.89  E-value=1.7e-22  Score=132.14  Aligned_cols=82  Identities=22%  Similarity=0.488  Sum_probs=78.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999986


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=3.1e-22  Score=135.59  Aligned_cols=89  Identities=28%  Similarity=0.377  Sum_probs=82.3

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        51 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ......+.++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.|++..+.|+.|
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   88 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENII   88 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34455667889999999999999999999999999999999998 99999999999999999999999999999999999


Q ss_pred             EEEecccCCC
Q psy15152        131 TVDWCFVKGP  140 (192)
Q Consensus       131 ~v~~a~~~~~  140 (192)
                      .|.++.++..
T Consensus        89 ~v~~a~~~~~   98 (100)
T 2do4_A           89 KVAISNSGPS   98 (100)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCCCCC
Confidence            9999987653

>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=99.89  E-value=1.3e-22  Score=133.87  Aligned_cols=83  Identities=23%  Similarity=0.397  Sum_probs=77.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||.++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|.|.|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            34678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            865

>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=99.89  E-value=1.8e-22  Score=136.44  Aligned_cols=87  Identities=28%  Similarity=0.371  Sum_probs=81.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9877543

>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=99.89  E-value=7e-23  Score=144.46  Aligned_cols=97  Identities=73%  Similarity=1.337  Sum_probs=88.0

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy15152         48 EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG  127 (192)
Q Consensus        48 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g  127 (192)
                      ..+.+....+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..|.|
T Consensus        12 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   91 (126)
T 3ex7_B           12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG   91 (126)
T ss_dssp             --CCBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            45667777888999999999999999999999999999999999998899999999999999999999999999999999


Q ss_pred             eEEEEEecccCCCCCCC
Q psy15152        128 QTVTVDWCFVKGPKKVA  144 (192)
Q Consensus       128 ~~l~v~~a~~~~~~~~~  144 (192)
                      +.|.|.|+.++......
T Consensus        92 ~~l~v~~a~~~~~~~~~  108 (126)
T 3ex7_B           92 QPISVDWCFVRGPPKGK  108 (126)
T ss_dssp             SBCEEEESEESSSCCC-
T ss_pred             eEEEEEEecCCCCCCCC
Confidence            99999999887655433

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=1.4e-22  Score=138.10  Aligned_cols=90  Identities=18%  Similarity=0.297  Sum_probs=83.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      +....+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34445678999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEecccCCCC
Q psy15152        132 VDWCFVKGPK  141 (192)
Q Consensus       132 v~~a~~~~~~  141 (192)
                      |.++.+....
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=2.5e-22  Score=134.68  Aligned_cols=86  Identities=27%  Similarity=0.377  Sum_probs=81.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            35678999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy15152        136 FVKGPK  141 (192)
Q Consensus       136 ~~~~~~  141 (192)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=1.5e-22  Score=137.59  Aligned_cols=88  Identities=28%  Similarity=0.535  Sum_probs=82.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q psy15152        135 CFVKGPKK  142 (192)
Q Consensus       135 a~~~~~~~  142 (192)
                      +.++..+.
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98775443

>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=99.88  E-value=3.1e-22  Score=136.72  Aligned_cols=90  Identities=24%  Similarity=0.361  Sum_probs=83.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      +....+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|++..+.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34445678999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEecccCCCC
Q psy15152        132 VDWCFVKGPK  141 (192)
Q Consensus       132 v~~a~~~~~~  141 (192)
                      |.++.++...
T Consensus        89 v~~a~~~~~~   98 (105)
T 1x5u_A           89 VNKASAHNKN   98 (105)
T ss_dssp             EEETTTTSCC
T ss_pred             EEECCCCCcC
Confidence            9999876543

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=4.1e-22  Score=137.38  Aligned_cols=91  Identities=21%  Similarity=0.387  Sum_probs=83.6

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC------CCe
Q psy15152         51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN------GTT  124 (192)
Q Consensus        51 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~------~~~  124 (192)
                      .+....+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|+      +..
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            34445567889999999999999999999999999999999999999999999999999999999999999      999


Q ss_pred             eCCeEEEEEecccCCCC
Q psy15152        125 ILGQTVTVDWCFVKGPK  141 (192)
Q Consensus       125 ~~g~~l~v~~a~~~~~~  141 (192)
                      +.|+.|.|.|+.++...
T Consensus        88 ~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           88 LDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SSSCEEEEECCCCCCCC
T ss_pred             EcCEEEEEEECCCCccC
Confidence            99999999999876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.6e-22  Score=135.96  Aligned_cols=87  Identities=29%  Similarity=0.484  Sum_probs=81.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNL-HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~-~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      .++++|||+|||+++++++|+++|++||.|..+ .++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456889999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q psy15152        135 CFVKGPKK  142 (192)
Q Consensus       135 a~~~~~~~  142 (192)
                      +.++..+.
T Consensus        83 a~~~~~~~   90 (96)
T 1x5t_A           83 AFKKDSKG   90 (96)
T ss_dssp             SCCCCCCC
T ss_pred             ecccCCCC
Confidence            98775443

>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=99.88  E-value=1.5e-22  Score=149.28  Aligned_cols=119  Identities=21%  Similarity=0.285  Sum_probs=93.0

Q ss_pred             CcCCCCCCccCCCCChhHHHhh-hcccCC---CCCC---CC-CCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEE
Q psy15152         17 ARKKKGRGFGTETSTRNEIREY-ESMETD---VGDE---EP-GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNL   88 (192)
Q Consensus        17 ~~~~k~rG~gfv~f~~~~~~~~-~~~~~~---~~~~---~~-~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~   88 (192)
                      ..++ +||||||+|...+.+.. ..++..   +...   .+ ........++|||+|||.++++++|+++|++||.|..+
T Consensus        46 ~~~~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v  124 (172)
T 2g4b_A           46 QINQ-DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF  124 (172)
T ss_dssp             EEET-TTTEEEEEESSHHHHHHHGGGTTCEETTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEE
T ss_pred             EecC-CCCEEEEEeCCHHHHHHHHHhCCcEecCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEE
Confidence            3343 79999999943333222 222221   1100   00 11122346889999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         89 HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        89 ~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|.|+||.
T Consensus       125 ~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            999998899999999999999999999999999999999999999973

>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=99.88  E-value=3.1e-22  Score=138.97  Aligned_cols=87  Identities=25%  Similarity=0.369  Sum_probs=81.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      +.++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9876543

>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=99.88  E-value=3e-23  Score=138.12  Aligned_cols=82  Identities=22%  Similarity=0.256  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+|||+|||+++++++|+++|++||  .|.+++++.++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy15152        137 VKGP  140 (192)
Q Consensus       137 ~~~~  140 (192)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7643

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.88  E-value=1e-21  Score=133.80  Aligned_cols=87  Identities=18%  Similarity=0.315  Sum_probs=80.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|+.|| |..+.++.++.+|.++|||||+|.+.++|++|+ .||+..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            3445578999999999999999999999997 999999999999999999999999999999999 89999999999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dng_A           88 DIAEGRKQD   96 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            999876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=1.9e-21  Score=134.63  Aligned_cols=88  Identities=23%  Similarity=0.267  Sum_probs=80.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            334556889999999999999999999999999999999997 7999999999999999999999999999999999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .++.....+
T Consensus        89 ~~a~~~~~~   97 (114)
T 2do0_A           89 KMDERALPK   97 (114)
T ss_dssp             EECSCCCCC
T ss_pred             EEcccCCCC
Confidence            999765444

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=8.4e-22  Score=134.15  Aligned_cols=87  Identities=21%  Similarity=0.378  Sum_probs=80.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.+  +|.++|||||+|.+.++|++|++.||+..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3446788999999999999999999999999999999998  89999999999999999999999999999999999999


Q ss_pred             ecccCCCCC
Q psy15152        134 WCFVKGPKK  142 (192)
Q Consensus       134 ~a~~~~~~~  142 (192)
                      |+.++..+.
T Consensus        89 ~a~~~~~~~   97 (103)
T 2d9p_A           89 LAQRKEERQ   97 (103)
T ss_dssp             ECSSCCCCC
T ss_pred             EecccccCC
Confidence            998775443

>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=99.88  E-value=9.2e-22  Score=134.34  Aligned_cols=87  Identities=26%  Similarity=0.370  Sum_probs=80.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC---eEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG---QTV  130 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g---~~l  130 (192)
                      ...+.++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.||+..+.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34557899999999999999999999999999999999997 89999999999999999999999999999998   999


Q ss_pred             EEEecccCCCC
Q psy15152        131 TVDWCFVKGPK  141 (192)
Q Consensus       131 ~v~~a~~~~~~  141 (192)
                      .|.|+.++..+
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999877544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1e-21  Score=136.60  Aligned_cols=90  Identities=23%  Similarity=0.382  Sum_probs=82.4

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        51 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      .+....+.++|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|++.|++ .+.|+.|
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l   88 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   88 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEE
Confidence            345556678999999999999999999999999999999999998999999999999999999999999998 8999999


Q ss_pred             EEEecccCCCC
Q psy15152        131 TVDWCFVKGPK  141 (192)
Q Consensus       131 ~v~~a~~~~~~  141 (192)
                      .|.++.+....
T Consensus        89 ~V~~a~~~~~~   99 (116)
T 2cqd_A           89 NVNLAYLGAKP   99 (116)
T ss_dssp             EEEESTTTCCC
T ss_pred             EEEEcccCCCc
Confidence            99999865433

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=3.5e-22  Score=135.78  Aligned_cols=88  Identities=26%  Similarity=0.444  Sum_probs=82.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34456889999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99876544

>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=99.88  E-value=3.8e-22  Score=134.24  Aligned_cols=83  Identities=20%  Similarity=0.397  Sum_probs=79.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ++++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.|+|..++|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            35789999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      +++
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.88  E-value=3.5e-22  Score=150.40  Aligned_cols=85  Identities=27%  Similarity=0.427  Sum_probs=80.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|.|.|+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q psy15152        136 FVKGP  140 (192)
Q Consensus       136 ~~~~~  140 (192)
                      .++..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.88  E-value=6.5e-22  Score=133.82  Aligned_cols=86  Identities=30%  Similarity=0.459  Sum_probs=80.4

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy15152         51 GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG  122 (192)
Q Consensus        51 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~--------~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~  122 (192)
                      .+......++|||+|||+++++++|+++|+.||.|..        +.++.++.+|.++|||||+|.+.++|++|++.|||
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g   85 (99)
T 2la6_A            6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   85 (99)
T ss_dssp             SCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            3445566789999999999999999999999999999        99999998999999999999999999999999999


Q ss_pred             CeeCCeEEEEEecc
Q psy15152        123 TTILGQTVTVDWCF  136 (192)
Q Consensus       123 ~~~~g~~l~v~~a~  136 (192)
                      ..+.|+.|+|++|.
T Consensus        86 ~~~~g~~l~V~~A~   99 (99)
T 2la6_A           86 KEFSGNPIKVSFAT   99 (99)
T ss_dssp             CBSSSSBCEEEECC
T ss_pred             CEeCCcEEEEEecC
Confidence            99999999999974

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=4.2e-22  Score=134.42  Aligned_cols=86  Identities=22%  Similarity=0.315  Sum_probs=79.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR---TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~---tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      .+.++|||+|||+++++++|+++|+.||.|..+.++.++.   |+.++|||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4567899999999999999999999999999999999876   6699999999999999999999999999999999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=7e-22  Score=132.43  Aligned_cols=85  Identities=25%  Similarity=0.387  Sum_probs=79.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus        10 ~~~~~~~~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           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            33455688999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             Eeccc
Q psy15152        133 DWCFV  137 (192)
Q Consensus       133 ~~a~~  137 (192)
                      .|+.+
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=5.9e-22  Score=135.69  Aligned_cols=90  Identities=22%  Similarity=0.428  Sum_probs=83.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCeE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLD-RRTGFLKGYALVEYDSYKEASAARDAL-NGTTILGQT  129 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~-~~tg~~~g~afV~f~~~~~a~~al~~l-~~~~~~g~~  129 (192)
                      +....+.++|||+|||+++++++|+++|+.||.|..+.++.+ +.+|.++|||||+|.+.++|++|++.| |+..+.|+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            344556789999999999999999999999999999999999 789999999999999999999999999 999999999


Q ss_pred             EEEEecccCCCC
Q psy15152        130 VTVDWCFVKGPK  141 (192)
Q Consensus       130 l~v~~a~~~~~~  141 (192)
                      |.|.|+.++...
T Consensus        89 l~v~~a~~~~~~  100 (107)
T 2cph_A           89 LVLEWADSEVTV  100 (107)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999876544

>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=99.88  E-value=8.3e-22  Score=134.45  Aligned_cols=88  Identities=18%  Similarity=0.268  Sum_probs=80.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT-GFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~t-g~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      +....+.++|||+|||+++++++|+++|+.|| |..+.++.++.+ |.++|||||+|.+.++|++|+ .|++..+.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34445678999999999999999999999999 999999999887 999999999999999999999 899999999999


Q ss_pred             EEEecccCCCC
Q psy15152        131 TVDWCFVKGPK  141 (192)
Q Consensus       131 ~v~~a~~~~~~  141 (192)
                      .|.++.++...
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999876544

>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=99.88  E-value=3.9e-22  Score=136.41  Aligned_cols=90  Identities=24%  Similarity=0.358  Sum_probs=82.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee---CCe
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI---LGQ  128 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~---~g~  128 (192)
                      +....+.++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+   .|+
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            44456678999999999999999999999999999999999998999999999999999999999999999997   899


Q ss_pred             EEEEEecccCCCC
Q psy15152        129 TVTVDWCFVKGPK  141 (192)
Q Consensus       129 ~l~v~~a~~~~~~  141 (192)
                      .|.|.++.++...
T Consensus        87 ~l~v~~a~~~~~~   99 (106)
T 2dgp_A           87 PIQVKPADSESRG   99 (106)
T ss_dssp             CCEEEECCCCSCC
T ss_pred             eEEEEECCccccc
Confidence            9999999876543

>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=99.88  E-value=3.7e-22  Score=131.09  Aligned_cols=81  Identities=30%  Similarity=0.587  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.||
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45688999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             c
Q psy15152        136 F  136 (192)
Q Consensus       136 ~  136 (192)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=4.6e-22  Score=138.31  Aligned_cols=81  Identities=20%  Similarity=0.347  Sum_probs=75.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..+|||+|||+++++++|+++|++||.|.+++|+.++  +.++|||||+|.+.++|++|++.|++..|.|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4679999999999999999999999999999999995  55899999999999999999999999999999999999986


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>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=99.88  E-value=3.8e-22  Score=158.63  Aligned_cols=132  Identities=17%  Similarity=0.257  Sum_probs=106.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccC---CCC-----CCC--CCCCCCCCCcEEEEcCCCCCC-cHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMET---DVG-----DEE--PGPQRSVEGWILFVTGVHEEA-QED   73 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~---~~~-----~~~--~~~~~~~~~~~l~V~nLp~~~-t~~   73 (192)
                      +.++.+++|+.+++ ++|||||+|...+  ..+...++.   .+.     ...  .........++|||+|||+++ +++
T Consensus       122 i~~~~i~~~~~~g~-~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~  200 (284)
T 3smz_A          122 LERCFLVYSERTGQ-SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVD  200 (284)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHH
T ss_pred             eeEEEEEeeCCCCc-cceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcccCCccEEEEecCCcccCCHH
Confidence            56888999999995 9999999994333  223323322   111     011  112233567899999999995 999


Q ss_pred             HHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCC
Q psy15152         74 DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP  140 (192)
Q Consensus        74 ~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~  140 (192)
                      +|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.|+.++..
T Consensus       201 ~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          201 ALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            999999999999999999997 899999999999999999999999999999999999999987654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=7.4e-22  Score=132.12  Aligned_cols=84  Identities=18%  Similarity=0.316  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|+|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            33455678999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             Eecc
Q psy15152        133 DWCF  136 (192)
Q Consensus       133 ~~a~  136 (192)
                      .||+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9984

>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=99.87  E-value=9.5e-22  Score=136.97  Aligned_cols=85  Identities=24%  Similarity=0.400  Sum_probs=79.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.|+|..+.|+.|.|.++
T Consensus         5 ~~~~~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            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345789999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy15152        136 FVKGPK  141 (192)
Q Consensus       136 ~~~~~~  141 (192)
                      .+....
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=5.7e-22  Score=133.98  Aligned_cols=85  Identities=22%  Similarity=0.378  Sum_probs=80.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCee-EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE----
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK-NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT----  129 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~-~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~----  129 (192)
                      ..+.++|||+|||+++++++|+++|++||.|. .+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34568899999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEEecccCC
Q psy15152        130 VTVDWCFVKG  139 (192)
Q Consensus       130 l~v~~a~~~~  139 (192)
                      |+|.||.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999997664

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.1e-21  Score=135.74  Aligned_cols=89  Identities=28%  Similarity=0.463  Sum_probs=82.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT  124 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--------~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~  124 (192)
                      ....+.++|||+|||+++++++|+++|+.||.|.        .+.++.++.+|.++|||||+|.+.++|++|++.||+..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            4456678999999999999999999999999998        69999998899999999999999999999999999999


Q ss_pred             eCCeEEEEEecccCCCC
Q psy15152        125 ILGQTVTVDWCFVKGPK  141 (192)
Q Consensus       125 ~~g~~l~v~~a~~~~~~  141 (192)
                      |.|+.|+|.++.++...
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999876543

>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=99.87  E-value=5.1e-22  Score=131.20  Aligned_cols=84  Identities=27%  Similarity=0.424  Sum_probs=78.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCC-cceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGF-LKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~-~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.++. ++|||||+|.+.++|++|++.|||..++|+.|.|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            3567899999999999999999999999999999999987766 899999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            97654

>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=99.87  E-value=4.3e-22  Score=141.27  Aligned_cols=88  Identities=27%  Similarity=0.485  Sum_probs=82.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|++..|.|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecccCCC
Q psy15152        133 DWCFVKGP  140 (192)
Q Consensus       133 ~~a~~~~~  140 (192)
                      .|+.++.+
T Consensus       121 ~~a~~~~p  128 (129)
T 2kxn_B          121 DFSITKRP  128 (129)
T ss_dssp             SCCSSSSC
T ss_pred             EEecCCCC
Confidence            99987653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.87  E-value=1.1e-22  Score=137.98  Aligned_cols=81  Identities=20%  Similarity=0.266  Sum_probs=78.0

Q ss_pred             CcEEEEcCCCC------CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC-eEE
Q psy15152         58 GWILFVTGVHE------EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG-QTV  130 (192)
Q Consensus        58 ~~~l~V~nLp~------~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g-~~l  130 (192)
                      +++|||+|||+      ++++++|+++|++||.|.++.++.++.||+++|||||+|.+.++|++|++.|||..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            57899999999      99999999999999999999999999999999999999999999999999999999999 999


Q ss_pred             EEEecccC
Q psy15152        131 TVDWCFVK  138 (192)
Q Consensus       131 ~v~~a~~~  138 (192)
                      .|.+|.+.
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99999764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.87  E-value=1.7e-21  Score=139.51  Aligned_cols=88  Identities=25%  Similarity=0.342  Sum_probs=82.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ....++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q psy15152        135 CFVKGPKK  142 (192)
Q Consensus       135 a~~~~~~~  142 (192)
                      +.++..+.
T Consensus       119 a~~~~~~~  126 (139)
T 1u6f_A          119 AASGHQRP  126 (139)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            98775443

>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=99.87  E-value=3.2e-22  Score=148.06  Aligned_cols=121  Identities=19%  Similarity=0.246  Sum_probs=93.1

Q ss_pred             EeeccCcCCCCCCccCCCCChhH-HHhhhcccC---CCC-----CCCC-CCCCCCCCcEEEEcCCCCCCcHHHHHHhhcc
Q psy15152         12 RLKEKARKKKGRGFGTETSTRNE-IREYESMET---DVG-----DEEP-GPQRSVEGWILFVTGVHEEAQEDDMHEKFSE   81 (192)
Q Consensus        12 ~~~d~~~~~k~rG~gfv~f~~~~-~~~~~~~~~---~~~-----~~~~-~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~   81 (192)
                      +++|..+++ +||||||+|...+ ......++.   .+.     ...+ ........++|||+|||.++++++|+++|++
T Consensus        44 ~~~~~~~~~-~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~  122 (175)
T 1fje_B           44 AVVDVRTGT-NRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFED  122 (175)
T ss_dssp             CCCEEEEET-TTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTT
T ss_pred             EEEECCCCc-cccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            456777785 9999999993333 222222321   121     1111 1222345689999999999999999999999


Q ss_pred             CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         82 YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        82 ~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ||.|..+     ..+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.||.++
T Consensus       123 ~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          123 ALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             cCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9988765     458999999999999999999999999999999999999999875

>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=99.87  E-value=9.7e-22  Score=135.22  Aligned_cols=86  Identities=27%  Similarity=0.441  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             ecccCC
Q psy15152        134 WCFVKG  139 (192)
Q Consensus       134 ~a~~~~  139 (192)
                      ++.++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            997653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=133.57  Aligned_cols=85  Identities=22%  Similarity=0.354  Sum_probs=79.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe-eCCeEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSE-YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT-ILGQTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~-~~g~~l~v~  133 (192)
                      .+.++|||+|||+++++++|+++|++ ||.|..+.++.++ +|.++|||||+|.+.++|++|++.|++.. +.|+.|.|.
T Consensus         7 ~~~~~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            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            45678999999999999999999999 9999999999998 99999999999999999999999999999 999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99766533

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.87  E-value=1.4e-21  Score=130.31  Aligned_cols=85  Identities=21%  Similarity=0.303  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.+..+  +|.++|||||+|.+.++|++|++.|++..+.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999885  89999999999999999999999999999999999999


Q ss_pred             ecccCCC
Q psy15152        134 WCFVKGP  140 (192)
Q Consensus       134 ~a~~~~~  140 (192)
                      ++.+...
T Consensus        82 ~a~~~~~   88 (92)
T 2dgv_A           82 IDRNASG   88 (92)
T ss_dssp             ECSCCSS
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.87  E-value=5.7e-21  Score=129.99  Aligned_cols=89  Identities=20%  Similarity=0.400  Sum_probs=80.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      +....+.++|||+|||+++++++|+++|+.||.|..+.++.++.  .++|||||+|.+.++|++|++.|++..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            44455678999999999999999999999999999999999863  3899999999999999999999999999999999


Q ss_pred             EEecccCCCCC
Q psy15152        132 VDWCFVKGPKK  142 (192)
Q Consensus       132 v~~a~~~~~~~  142 (192)
                      |.++.++....
T Consensus        87 v~~a~~~~~~~   97 (103)
T 2cq3_A           87 VNNATARVMTN   97 (103)
T ss_dssp             EEECCSSCCCC
T ss_pred             EEEcccCCCCC
Confidence            99998775443

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.87  E-value=4.2e-22  Score=141.59  Aligned_cols=89  Identities=17%  Similarity=0.321  Sum_probs=81.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC----ee
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT----TI  125 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~--~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~----~~  125 (192)
                      +......++|||+|||+++++++|+++|++||.|..  |+|+.|+.+|+++|||||+|.+. +|++|++.|||.    .+
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            344456789999999999999999999999999966  99999999999999999999999 999999999999    99


Q ss_pred             CCeEEEEEecccCCCC
Q psy15152        126 LGQTVTVDWCFVKGPK  141 (192)
Q Consensus       126 ~g~~l~v~~a~~~~~~  141 (192)
                      +|+.|.|.++.+....
T Consensus        96 ~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           96 DGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGCCCCCEECCCSCCC
T ss_pred             CCEEEEEEECCCCCCC
Confidence            9999999999876443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=133.76  Aligned_cols=89  Identities=20%  Similarity=0.338  Sum_probs=81.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .....+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++. ++..|.|+.|.
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   88 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNID   88 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEB
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEE
Confidence            33445678999999999999999999999999999999999998999999999999999999999998 99999999999


Q ss_pred             EEecccCCCC
Q psy15152        132 VDWCFVKGPK  141 (192)
Q Consensus       132 v~~a~~~~~~  141 (192)
                      |.++.++...
T Consensus        89 V~~a~~~~~~   98 (105)
T 2dh8_A           89 PKPCTPRGMQ   98 (105)
T ss_dssp             CCCSCCSSCC
T ss_pred             EEEccCCCCC
Confidence            9999876543

>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=99.86  E-value=1.8e-21  Score=128.87  Aligned_cols=81  Identities=19%  Similarity=0.335  Sum_probs=77.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|+ .|++..+.|+.|.|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            478999999999999999999999999999999999889999999999999999999999 8999999999999999976


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      ..
T Consensus        85 ~~   86 (89)
T 3ucg_A           85 NR   86 (89)
T ss_dssp             TS
T ss_pred             CC
Confidence            53

>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=99.86  E-value=7.1e-21  Score=129.53  Aligned_cols=87  Identities=25%  Similarity=0.411  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.  .++|||||+|.+.++|++|++.|++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            3445678999999999999999999999999999999999853  36899999999999999999999999999999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .|+.++..+
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            999876543

>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=99.86  E-value=2.5e-21  Score=129.74  Aligned_cols=85  Identities=22%  Similarity=0.336  Sum_probs=77.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      +....+.++|||+|||+++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|++|++.||+..+.|+.|.
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            3444567899999999999999999999999999999999997 599999999999999999999999999999999999


Q ss_pred             EEeccc
Q psy15152        132 VDWCFV  137 (192)
Q Consensus       132 v~~a~~  137 (192)
                      |.++..
T Consensus        89 V~~a~~   94 (95)
T 2ywk_A           89 VSGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EEEcCC
Confidence            999863

>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=99.86  E-value=3.7e-21  Score=131.73  Aligned_cols=83  Identities=24%  Similarity=0.384  Sum_probs=78.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+.+++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.|++..+.|+.|.|
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            344567899999999999999999999999999999999998 9999999999999999999999999999999999999


Q ss_pred             Eecc
Q psy15152        133 DWCF  136 (192)
Q Consensus       133 ~~a~  136 (192)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9985

>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=99.86  E-value=3.9e-21  Score=126.84  Aligned_cols=81  Identities=16%  Similarity=0.387  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++..+.|+.|.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            34566889999999999999999999999999999999999899999999999999999999996 58889999999999


Q ss_pred             ec
Q psy15152        134 WC  135 (192)
Q Consensus       134 ~a  135 (192)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.86  E-value=1.5e-21  Score=142.75  Aligned_cols=82  Identities=20%  Similarity=0.239  Sum_probs=77.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..++|||+|||+++++++|+++|+.||  .|.+++++.|+.+|+++|||||+|.+.++|++|++.|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      |.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.86  E-value=2.2e-21  Score=135.19  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=78.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecc
Q psy15152        134 WCF  136 (192)
Q Consensus       134 ~a~  136 (192)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            974

>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=99.86  E-value=2.7e-21  Score=130.36  Aligned_cols=83  Identities=23%  Similarity=0.151  Sum_probs=78.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|++.||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            44688999999999999999999999999998888888889999999999999999999999999999999999999998


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            654

>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=99.86  E-value=4.2e-21  Score=132.62  Aligned_cols=87  Identities=22%  Similarity=0.299  Sum_probs=79.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHH---HhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMH---EKFSEYGEIKNLHLNLDRRTG---FLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~---~~F~~~G~i~~~~i~~~~~tg---~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      .+....++|||+|||+++++++|+   ++|++||.|..+.++.++.++   .++|||||+|.+.++|++|++.||+..|+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            445567889999999999999999   999999999999999987654   56699999999999999999999999999


Q ss_pred             CeEEEEEecccCC
Q psy15152        127 GQTVTVDWCFVKG  139 (192)
Q Consensus       127 g~~l~v~~a~~~~  139 (192)
                      |+.|+|.||.++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999998775

>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=99.86  E-value=1.3e-20  Score=128.25  Aligned_cols=86  Identities=23%  Similarity=0.341  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++  ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            34456789999999999999999999999999999999999899999999999999999999998  4789999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99876543

>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=99.86  E-value=6.8e-21  Score=139.06  Aligned_cols=87  Identities=26%  Similarity=0.389  Sum_probs=81.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|++.|++..|.|+.|.|.||
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy15152        136 FVKGPKK  142 (192)
Q Consensus       136 ~~~~~~~  142 (192)
                      .+.....
T Consensus       117 ~~~~~~~  123 (156)
T 1h2v_Z          117 AGFKEGR  123 (156)
T ss_dssp             SCCCTTC
T ss_pred             CCCCCcC
Confidence            8765443

>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=99.86  E-value=1.1e-20  Score=129.78  Aligned_cols=84  Identities=17%  Similarity=0.192  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC-----e
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG-----Q  128 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g-----~  128 (192)
                      .....++|||+|||+++++++|+++|++||.|..+.++.+       |||||+|.+.++|++|++.||+..|.|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3455789999999999999999999999999999999876       799999999999999999999999999     9


Q ss_pred             EEEEEecccCCCCCCC
Q psy15152        129 TVTVDWCFVKGPKKVA  144 (192)
Q Consensus       129 ~l~v~~a~~~~~~~~~  144 (192)
                      .|+|.+|.++.....+
T Consensus        84 ~i~V~~a~~~~~~~~r   99 (108)
T 1x4c_A           84 YIRVKVDGPRSPSYGR   99 (108)
T ss_dssp             EEEEEESSCCSCCCCC
T ss_pred             EEEEEeCCCCCCCCCC
Confidence            9999999887654443

>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=99.86  E-value=3.7e-21  Score=132.20  Aligned_cols=86  Identities=23%  Similarity=0.391  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCC-eeEEEEe-ecCCCCCcceEEEEEecCHHHHHHHHHHhC--CCeeCCeEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLN-LDRRTGFLKGYALVEYDSYKEASAARDALN--GTTILGQTV  130 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~-i~~~~i~-~~~~tg~~~g~afV~f~~~~~a~~al~~l~--~~~~~g~~l  130 (192)
                      +.+.++|||+|||+++++++|+++|+.||. |..+.++ .++.+|.++|||||+|.+.++|++|++.|+  +..+.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            456789999999999999999999999998 9999998 888889999999999999999999999996  589999999


Q ss_pred             EEEecccCCC
Q psy15152        131 TVDWCFVKGP  140 (192)
Q Consensus       131 ~v~~a~~~~~  140 (192)
                      .|.||.++..
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.86  E-value=8.3e-22  Score=134.27  Aligned_cols=84  Identities=32%  Similarity=0.462  Sum_probs=79.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            35789999999999999999999999999999999999899999999999999999999999999999999999999997


Q ss_pred             cCCC
Q psy15152        137 VKGP  140 (192)
Q Consensus       137 ~~~~  140 (192)
                      +...
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            6643

>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=99.86  E-value=4.2e-21  Score=129.18  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=75.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMH----EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .+.++|||+|||+++++++|+    ++|++||.|.++.++.++.+   +|||||+|.+.++|++|++.|||..++|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            346789999999999999999    99999999999999999755   88999999999999999999999999999999


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |.+|.+..
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997664

>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=99.85  E-value=1.7e-21  Score=155.42  Aligned_cols=130  Identities=17%  Similarity=0.240  Sum_probs=95.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccC---CC-----CCCCCCC------CCCCCCcEEEEcCCCCC
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMET---DV-----GDEEPGP------QRSVEGWILFVTGVHEE   69 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~---~~-----~~~~~~~------~~~~~~~~l~V~nLp~~   69 (192)
                      .+.+|.+++|+. + +++|||||+|...+  ..+...++.   .+     ....+..      ......++|||+|||++
T Consensus       144 ~i~~v~i~~~~~-~-~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~  221 (292)
T 2ghp_A          144 VALSIRLPSLRF-N-TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTE  221 (292)
T ss_dssp             CCCEEECC---------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTT
T ss_pred             CeEEEEEEeCCC-C-CcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcc
Confidence            456788888887 5 39999999994333  222332322   11     1111111      22345689999999999


Q ss_pred             -CcHHHHHHhhccCCCeeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         70 -AQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        70 -~t~~~L~~~F~~~G~i~~~~i~~~~~-tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                       +++++|+++|+.||.|..+.++.+.. ||.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.||.++
T Consensus       222 ~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          222 LLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             cCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence             99999999999999999999999875 5999999999999999999999 99999999999999999876

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.85  E-value=9.4e-22  Score=140.55  Aligned_cols=89  Identities=22%  Similarity=0.358  Sum_probs=82.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|++..|.|+.|.|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456889999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecccCCCCC
Q psy15152        134 WCFVKGPKK  142 (192)
Q Consensus       134 ~a~~~~~~~  142 (192)
                      |+.+..+..
T Consensus       123 ~a~~~~~~~  131 (135)
T 2lea_A          123 MARYGRPPD  131 (135)
T ss_dssp             ECCCCCCCT
T ss_pred             ECCCCCCCc
Confidence            998765443

>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=99.85  E-value=1.4e-20  Score=130.26  Aligned_cols=85  Identities=14%  Similarity=0.273  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee-------
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI-------  125 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~-------  125 (192)
                      ....+.++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.|||..+       
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            344567899999999999999999999999999999999998 999999999999999999999999999999       


Q ss_pred             -CCeEEEEEecccC
Q psy15152        126 -LGQTVTVDWCFVK  138 (192)
Q Consensus       126 -~g~~l~v~~a~~~  138 (192)
                       .+++|.|.||.++
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             5788999999865

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=1.2e-20  Score=125.61  Aligned_cols=82  Identities=15%  Similarity=0.146  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ....++|||+|||+++++++|+++|+.| .|..+.++.+ .+|+++|||||+|.+.++|++|++ ||+..+.|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3456889999999999999999999999 9999999999 699999999999999999999999 999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      +.+++
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            97764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.85  E-value=5.4e-21  Score=134.37  Aligned_cols=82  Identities=27%  Similarity=0.394  Sum_probs=78.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|+ .|+|..|+|+.|.|.++.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            578999999999999999999999999999999999889999999999999999999999 7999999999999999986


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.9e-21  Score=132.63  Aligned_cols=80  Identities=19%  Similarity=0.283  Sum_probs=75.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ....+|||+|||+++|+++|+++|++||.|.++.++.++. |.++|||||+|.+.++|++|+. +++..+.|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4457899999999999999999999999999999999986 9999999999999999999999 8999999999999988


Q ss_pred             cc
Q psy15152        136 FV  137 (192)
Q Consensus       136 ~~  137 (192)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.85  E-value=4.8e-21  Score=131.92  Aligned_cols=85  Identities=16%  Similarity=0.307  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.+ +..+.|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345688999999999999999999999999999999999989999999999999999999999975 5899999999999


Q ss_pred             cccCCC
Q psy15152        135 CFVKGP  140 (192)
Q Consensus       135 a~~~~~  140 (192)
                      +.++..
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.85  E-value=2.8e-21  Score=129.53  Aligned_cols=81  Identities=22%  Similarity=0.167  Sum_probs=76.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45789999999999999999999999999999999998899999999999999999999999999999999999999875


Q ss_pred             c
Q psy15152        137 V  137 (192)
Q Consensus       137 ~  137 (192)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=1.7e-20  Score=127.18  Aligned_cols=84  Identities=25%  Similarity=0.389  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|   .++.+ .+|+++|||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   85 (101)
T 2fc9_A           10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRL   85 (101)
T ss_dssp             CCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            345567899999999999999999999999987   56666 58999999999999999999999999999999999999


Q ss_pred             EecccCCC
Q psy15152        133 DWCFVKGP  140 (192)
Q Consensus       133 ~~a~~~~~  140 (192)
                      .|+.++..
T Consensus        86 ~~a~~~~~   93 (101)
T 2fc9_A           86 ELQGPRGS   93 (101)
T ss_dssp             EECSSCCC
T ss_pred             EEcCCCCC
Confidence            99987643

>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=99.85  E-value=5.8e-21  Score=129.84  Aligned_cols=83  Identities=17%  Similarity=0.182  Sum_probs=73.5

Q ss_pred             CCCCCCCCCcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC--eeC
Q psy15152         50 PGPQRSVEGWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT--TIL  126 (192)
Q Consensus        50 ~~~~~~~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~--~~~  126 (192)
                      .......++++|||+|||+ ++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|++.  .|.
T Consensus         7 ~~~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A            7 GQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            3444455778999999999 9999999999999999999999876      479999999999999999999864  599


Q ss_pred             CeEEEEEecccC
Q psy15152        127 GQTVTVDWCFVK  138 (192)
Q Consensus       127 g~~l~v~~a~~~  138 (192)
                      |++|.|.||...
T Consensus        81 Gr~l~V~~a~~~   92 (102)
T 1x4d_A           81 GKPVRVHLSQKY   92 (102)
T ss_dssp             TEECEEEEECCC
T ss_pred             CcEEEEEECCCC
Confidence            999999999754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1e-21  Score=129.10  Aligned_cols=81  Identities=25%  Similarity=0.337  Sum_probs=76.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45678999999999999999999999999999999999989999999999999999999999999999999999988765


Q ss_pred             c
Q psy15152        136 F  136 (192)
Q Consensus       136 ~  136 (192)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.85  E-value=1.2e-20  Score=128.38  Aligned_cols=84  Identities=23%  Similarity=0.302  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      .....++|||+|||+++++++|+++|++||. ..+.|+.++ +|+++|||||+|.+.++|++||+ +|+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            3455689999999999999999999999994 599999998 99999999999999999999995 79999999999999


Q ss_pred             ecccCCC
Q psy15152        134 WCFVKGP  140 (192)
Q Consensus       134 ~a~~~~~  140 (192)
                      ++.+...
T Consensus        88 ~~~~~~~   94 (102)
T 1wez_A           88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             ECCCCCC
Confidence            9876543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.85  E-value=1.5e-21  Score=125.28  Aligned_cols=75  Identities=19%  Similarity=0.379  Sum_probs=72.4

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ |++..+.|+.|.|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998899999999999999999999998 9999999999999986

>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=99.85  E-value=2.3e-20  Score=128.32  Aligned_cols=85  Identities=18%  Similarity=0.285  Sum_probs=76.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++|++.||+..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34456789999999999999999999999999999998554   568999999999999999999999999999999999


Q ss_pred             EecccCCC
Q psy15152        133 DWCFVKGP  140 (192)
Q Consensus       133 ~~a~~~~~  140 (192)
                      .|+.+...
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4a_A           94 EFPRSGRG  101 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EEcccCCC
Confidence            99987643

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=3.4e-20  Score=125.88  Aligned_cols=86  Identities=35%  Similarity=0.575  Sum_probs=77.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .....+.++|||+|||+++++++|+++|+.|+   .+.++.++.++.++|||||+|.+.++|++|++.||+..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34455678899999999999999999999874   678888888999999999999999999999999999999999999


Q ss_pred             EEecccCCC
Q psy15152        132 VDWCFVKGP  140 (192)
Q Consensus       132 v~~a~~~~~  140 (192)
                      |.|+.++..
T Consensus        86 V~~a~~~~~   94 (102)
T 2fc8_A           86 LDWAKPKGE   94 (102)
T ss_dssp             EEECCCCCS
T ss_pred             EEEecCCCC
Confidence            999987654

>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=99.84  E-value=1.8e-21  Score=132.02  Aligned_cols=85  Identities=18%  Similarity=0.271  Sum_probs=75.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDR-RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~-~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ......++|||+|||+++++++|+++|+.|| |.++.++.++ .+|+++|||||+|.+.++|++|+ .|+|..+.|+.|.
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            3345678999999999999999999999999 9999999998 58999999999999999999999 8999999999999


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |.++.++.
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99997653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.84  E-value=2.3e-20  Score=131.25  Aligned_cols=84  Identities=23%  Similarity=0.360  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..++++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3556899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      |.+..
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            97654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=9.5e-21  Score=131.64  Aligned_cols=84  Identities=20%  Similarity=0.346  Sum_probs=78.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++. ++..|.|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            348999999999999999999999999999999999998999999999999999999999997 9999999999999998


Q ss_pred             cCCCC
Q psy15152        137 VKGPK  141 (192)
Q Consensus       137 ~~~~~  141 (192)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            77543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=5.1e-21  Score=130.45  Aligned_cols=81  Identities=16%  Similarity=0.252  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG--TTILGQTVTV  132 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~--~~~~g~~l~v  132 (192)
                      ..+.++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|++  ..+.|++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345688999999999999999999999999999999865      68999999999999999998864  6899999999


Q ss_pred             EecccCCCC
Q psy15152        133 DWCFVKGPK  141 (192)
Q Consensus       133 ~~a~~~~~~  141 (192)
                      .||.++...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.84  E-value=1.4e-20  Score=134.67  Aligned_cols=82  Identities=29%  Similarity=0.596  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ec
Q psy15152        134 WC  135 (192)
Q Consensus       134 ~a  135 (192)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            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

Probab=99.84  E-value=2.1e-20  Score=127.58  Aligned_cols=84  Identities=17%  Similarity=0.158  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN-LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~-~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      .....++|||+|||+++++++|+++|+.||.|.. +.++.+ .+|+++|||||+|.+.++|++|++. ++..++|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3455689999999999999999999999999987 889888 6999999999999999999999997 999999999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .++.+..
T Consensus        89 ~~~~~~~   95 (104)
T 1wg5_A           89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9986543

>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=99.84  E-value=5.2e-20  Score=125.02  Aligned_cols=83  Identities=14%  Similarity=0.171  Sum_probs=73.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCeEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL--NGTTILGQTV  130 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l--~~~~~~g~~l  130 (192)
                      ....++++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|  ++..+.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            33456789999999999999999999999999999988765      689999999999999999987  4678999999


Q ss_pred             EEEecccCCCC
Q psy15152        131 TVDWCFVKGPK  141 (192)
Q Consensus       131 ~v~~a~~~~~~  141 (192)
                      .|.|+.++...
T Consensus        84 ~V~~a~~~~~~   94 (101)
T 2cq1_A           84 YIQYSNHKELK   94 (101)
T ss_dssp             EEEECSCSSCC
T ss_pred             EEEEcCcccCc
Confidence            99999876544

>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=99.84  E-value=5.5e-21  Score=132.46  Aligned_cols=82  Identities=22%  Similarity=0.372  Sum_probs=78.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|+ .||+..|.|+.|.|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3479999999999999999999999999999999999989999999999999999999999 899999999999999998


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            754

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.84  E-value=1.3e-21  Score=129.91  Aligned_cols=80  Identities=29%  Similarity=0.407  Sum_probs=74.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|||+|||.++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.+ |++|+..|||..+.|+.|.|++|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999999989999999999999999 99999999999999999999999876


Q ss_pred             C
Q psy15152        139 G  139 (192)
Q Consensus       139 ~  139 (192)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.84  E-value=9.9e-21  Score=137.33  Aligned_cols=82  Identities=20%  Similarity=0.398  Sum_probs=75.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ......++|||+|||+++++++|+++|++||.|.+++++.+     ++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  142 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV  142 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999877     4899999999999999999999999999999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .|+.++.
T Consensus       143 ~~a~~~~  149 (150)
T 2i2y_A          143 ELSNGEK  149 (150)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9997763

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.6e-20  Score=129.22  Aligned_cols=83  Identities=20%  Similarity=0.426  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||.++++++|+++|++||.|..+.+..++  +.++|||||+|.+.++|++|++.|+|..++|+.|.|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999985  4589999999999999999999999999999999999


Q ss_pred             ecccC
Q psy15152        134 WCFVK  138 (192)
Q Consensus       134 ~a~~~  138 (192)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99765

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=3e-21  Score=124.43  Aligned_cols=76  Identities=16%  Similarity=0.290  Sum_probs=73.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.++ ..+.|+.|.|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            469999999999999999999999999999999999899999999999999999999999988 9999999999987

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.84  E-value=1.8e-20  Score=126.61  Aligned_cols=78  Identities=22%  Similarity=0.324  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe--eCCeEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT--ILGQTVTV  132 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~--~~g~~l~v  132 (192)
                      ..++.+|||+|||+++++++|+++|++||.|.++.++.+      ||||||+|.+.++|.+|++.|++..  +.|++|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            345678999999999999999999999999999998753      6899999999999999999999875  78999999


Q ss_pred             EecccC
Q psy15152        133 DWCFVK  138 (192)
Q Consensus       133 ~~a~~~  138 (192)
                      .|+.++
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            999765

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.83  E-value=1.1e-20  Score=133.46  Aligned_cols=83  Identities=14%  Similarity=0.282  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMH----EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      ...++++|||+|||+.+++++|+    ++|++||.|.+|.+.   .+|+++|||||+|.+.++|+.|++.|||..+.|+.
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34557899999999999999876    699999999998774   36889999999999999999999999999999999


Q ss_pred             EEEEecccCC
Q psy15152        130 VTVDWCFVKG  139 (192)
Q Consensus       130 l~v~~a~~~~  139 (192)
                      |+|.||.++.
T Consensus       102 l~V~~a~~~~  111 (127)
T 2a3j_A          102 LVITFSETPQ  111 (127)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCcc
Confidence            9999997654

>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=99.83  E-value=3.8e-20  Score=124.59  Aligned_cols=83  Identities=18%  Similarity=0.314  Sum_probs=74.8

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC--CeE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL--GQT  129 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~--g~~  129 (192)
                      .....+.++|||+|||+++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.||+..+.  |+.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~   84 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRR   84 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCB
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcE
Confidence            344556688999999999999999999999999999988754      689999999999999999999999999  999


Q ss_pred             EEEEecccCCC
Q psy15152        130 VTVDWCFVKGP  140 (192)
Q Consensus       130 l~v~~a~~~~~  140 (192)
                      |.|.|+.+++.
T Consensus        85 l~V~~a~~~~~   95 (97)
T 1why_A           85 LRVDFAKSGPS   95 (97)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.83  E-value=1.7e-20  Score=128.21  Aligned_cols=82  Identities=26%  Similarity=0.310  Sum_probs=75.2

Q ss_pred             CCCCcEEEEcCCCCCC------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy15152         55 SVEGWILFVTGVHEEA------QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ  128 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~------t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~  128 (192)
                      ...+++|||+|||+.+      ++++|+++|++||.|..+.++  +.+|.++|||||+|.+.++|++|++.|||..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3446889999999999      789999999999999999988  35899999999999999999999999999999998


Q ss_pred             -EEEEEecccC
Q psy15152        129 -TVTVDWCFVK  138 (192)
Q Consensus       129 -~l~v~~a~~~  138 (192)
                       .|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998654

>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=99.83  E-value=5.8e-20  Score=125.45  Aligned_cols=83  Identities=22%  Similarity=0.263  Sum_probs=73.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC--eeCCeEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT--TILGQTV  130 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~--~~~g~~l  130 (192)
                      ....++++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|++.  .+.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l   83 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            34456789999999999999999999999999999988754      689999999999999999988764  5999999


Q ss_pred             EEEecccCCCC
Q psy15152        131 TVDWCFVKGPK  141 (192)
Q Consensus       131 ~v~~a~~~~~~  141 (192)
                      .|.|+..+...
T Consensus        84 ~V~~a~~~~~~   94 (104)
T 1wex_A           84 FFNYSTSKRIT   94 (104)
T ss_dssp             EEEECSSSSCC
T ss_pred             EEEEccCcccc
Confidence            99999866443

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=6.4e-20  Score=121.79  Aligned_cols=79  Identities=23%  Similarity=0.331  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.||+..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3456889999999999999999999999999999986        57999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      +.++...
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.83  E-value=3.1e-20  Score=147.55  Aligned_cols=118  Identities=21%  Similarity=0.265  Sum_probs=95.7

Q ss_pred             CCCCccCCCCChhHH--HhhhcccCC---CCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCC
Q psy15152         21 KGRGFGTETSTRNEI--REYESMETD---VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR   95 (192)
Q Consensus        21 k~rG~gfv~f~~~~~--~~~~~~~~~---~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~   95 (192)
                      +++|||||+|...+.  .+...++..   +....  .......++|||+|||+++++++|+++|+.||.|..+.++.++.
T Consensus        55 ~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~--v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~  132 (284)
T 3smz_A           55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELS--VQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER  132 (284)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECE--EEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             cCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEE--EEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCC
Confidence            489999999944333  333333222   21111  11234567899999999999999999999999999999999988


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCC
Q psy15152         96 TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP  140 (192)
Q Consensus        96 tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~  140 (192)
                      +|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+...
T Consensus       133 ~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            999999999999999999999999999999999999999987643

>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=99.83  E-value=3.8e-20  Score=129.00  Aligned_cols=83  Identities=16%  Similarity=0.244  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCeEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG--TTILGQTVT  131 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~--~~~~g~~l~  131 (192)
                      ...++++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|++  ..+.|++|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3445788999999999999999999999999999999876      68999999999999999998874  689999999


Q ss_pred             EEecccCCCCC
Q psy15152        132 VDWCFVKGPKK  142 (192)
Q Consensus       132 v~~a~~~~~~~  142 (192)
                      |.||.++..+.
T Consensus       101 V~~a~~k~~~~  111 (119)
T 2ad9_A          101 IQFSNHKELKT  111 (119)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEccCCCCCc
Confidence            99998765443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.83  E-value=1.9e-20  Score=122.66  Aligned_cols=74  Identities=20%  Similarity=0.257  Sum_probs=69.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+.-|||+||++.+|+++|+++|.+||+|.++.+..      ++|||||+|.+.++|++|++.||+..+.|+.|+|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            456699999999999999999999999999999865      48999999999999999999999999999999999984

>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=99.83  E-value=1.5e-20  Score=130.39  Aligned_cols=83  Identities=14%  Similarity=0.151  Sum_probs=77.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCe-eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEI-KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i-~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ..+.++|||+|||+++++++|+++|+.||.| ..+.|+.++ +|+++|||||+|.+.++|++|++. |+..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3456889999999999999999999999999 899999998 999999999999999999999987 9999999999999


Q ss_pred             ecccCC
Q psy15152        134 WCFVKG  139 (192)
Q Consensus       134 ~a~~~~  139 (192)
                      ++.++.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            997664

>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=99.83  E-value=8.4e-20  Score=124.26  Aligned_cols=81  Identities=21%  Similarity=0.434  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|++|++.|++..|.|+.|.|.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            456789999999999999999999999999999886        459999999999999999999999999999999999


Q ss_pred             ccCCCCCCC
Q psy15152        136 FVKGPKKVA  144 (192)
Q Consensus       136 ~~~~~~~~~  144 (192)
                      .++......
T Consensus        81 ~~~~~~~~~   89 (103)
T 2dgu_A           81 KPPDQKRKE   89 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCcccchh
Confidence            877654433

>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=99.83  E-value=8.9e-21  Score=131.46  Aligned_cols=87  Identities=18%  Similarity=0.334  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|++|++.|++..+.|+.|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34568999999999999999999999999984433322223789999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      +.++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.83  E-value=3e-20  Score=129.70  Aligned_cols=83  Identities=18%  Similarity=0.228  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGE---IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~---i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ..+.++|||+|||+++++++|+++|+.||.   |..++++.++. |+++|||||+|.+.++|++|++ ||+..|+|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345688999999999999999999999999   89999999985 9999999999999999999999 999999999999


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |.++..+.
T Consensus        92 V~~a~~~~   99 (118)
T 2db1_A           92 VFKSHRTE   99 (118)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99986543

>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=99.82  E-value=1e-19  Score=122.94  Aligned_cols=85  Identities=20%  Similarity=0.411  Sum_probs=76.0

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         50 PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        50 ~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      +......+.++|||+|||+++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|++..+.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~   80 (99)
T 2cpj_A            7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQ   80 (99)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCce
Confidence            33444556789999999999999999999999999999998755      689999999999999999999999999999


Q ss_pred             EEEEecccCCC
Q psy15152        130 VTVDWCFVKGP  140 (192)
Q Consensus       130 l~v~~a~~~~~  140 (192)
                      |.|.|+.++..
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpj_A           81 LRVRFACHSAS   91 (99)
T ss_dssp             CEEEESSCCSC
T ss_pred             EEEEEcCCCCC
Confidence            99999987643

>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=99.82  E-value=2e-20  Score=133.60  Aligned_cols=82  Identities=18%  Similarity=0.210  Sum_probs=76.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGE---IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~---i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ..+.++|||+|||+++|+++|+++|+.||.   |..+.++.|+. |+++|||||+|.+.++|++|++ ||+..|+|+.|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            345689999999999999999999999999   88999999985 9999999999999999999999 999999999999


Q ss_pred             EEecccC
Q psy15152        132 VDWCFVK  138 (192)
Q Consensus       132 v~~a~~~  138 (192)
                      |.++.++
T Consensus       119 V~~a~~~  125 (136)
T 2hgl_A          119 VFKSHRT  125 (136)
T ss_dssp             EEECCHH
T ss_pred             EEECChH
Confidence            9998654

>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=99.82  E-value=1.3e-20  Score=132.57  Aligned_cols=83  Identities=16%  Similarity=0.160  Sum_probs=76.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++||+ ||+..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999999886666766799999999999999999999999 999999999999999


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      +.++
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            9754

>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=99.82  E-value=2.1e-20  Score=149.12  Aligned_cols=128  Identities=12%  Similarity=0.080  Sum_probs=95.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH-HHhhhcccCCCCCCCCC--CCCCCCCcEEEEcCCCCCCcHHHHHHhhccC
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE-IREYESMETDVGDEEPG--PQRSVEGWILFVTGVHEEAQEDDMHEKFSEY   82 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~   82 (192)
                      .+.+|.+++|+.+   ++|||||+|...+ +.....+  ++......  .......++|||+|||+++++++|+++|+.|
T Consensus        67 ~i~~v~i~~~~~~---~~g~afV~f~~~~~A~~A~~~--~~~~~~g~~i~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~  141 (292)
T 2ghp_A           67 PIIHVDVADSLKK---NFRFARIEFARYDGALAAITK--THKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDI  141 (292)
T ss_dssp             CEEEEEEEECTTS---SSEEEEEEESSHHHHHHHHTT--TTCEETTEECEEEECCSCEEEEECCCTTCCHHHHHHHHHHT
T ss_pred             CeEEEEEEECCCC---CcEEEEEEECCHHHHHHHHHh--CCcEeCCcEEEEEECCCCEEEEECCCCCCCHHHHHHHHHHh
Confidence            3568888888753   5799999994333 2222222  22111111  1122356889999999999999999999999


Q ss_pred             C-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCC
Q psy15152         83 G-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        83 G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~  139 (192)
                      | .|..+.++.++ .|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+..
T Consensus       142 G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          142 NVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             TCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             CCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence            9 99999999987 48899999999999999999999999999999999999998654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=8.3e-20  Score=122.97  Aligned_cols=82  Identities=18%  Similarity=0.234  Sum_probs=73.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ......++|||+|||+++++++|+++|+.||.|. +.++.+    .++|||||+|.+.++|++|++.|||..+.|+.|.|
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3445578999999999999999999999999996 666644    57899999999999999999999999999999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (97)
T 2e5j_A           89 ALARQQR   95 (97)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998764

>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=99.82  E-value=2.2e-20  Score=144.66  Aligned_cols=81  Identities=22%  Similarity=0.276  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYG--EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G--~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..++|||+|||+++++++|+++|+.||  .|.+|+|+.|+.+|+++|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            457899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy15152        135 CFV  137 (192)
Q Consensus       135 a~~  137 (192)
                      |.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.82  E-value=3.7e-20  Score=125.50  Aligned_cols=78  Identities=23%  Similarity=0.438  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++|++.|++..+.|+.|.|.++.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999877     5899999999999999999999999999999999999877


Q ss_pred             CCC
Q psy15152        139 GPK  141 (192)
Q Consensus       139 ~~~  141 (192)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.82  E-value=3.2e-21  Score=130.76  Aligned_cols=84  Identities=18%  Similarity=0.296  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ....++|||+|||+++++++|+++|+.||.|.. .++.++.+|.++|||||+|.+.++|++|++ |++..+.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345689999999999999999999999999888 677777789999999999999999999998 999999999999999


Q ss_pred             cccCCC
Q psy15152        135 CFVKGP  140 (192)
Q Consensus       135 a~~~~~  140 (192)
                      +.++..
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            987643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=7e-22  Score=137.45  Aligned_cols=87  Identities=30%  Similarity=0.453  Sum_probs=80.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKN--------LHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~--------~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      ..+.++|||+|||+++++++|+++|++||.|..        +.++.++.+|.++|||||+|.+.++|++|++.||+..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345678999999999999999999999999998        899999889999999999999999999999999999999


Q ss_pred             CeEEEEEecccCCCC
Q psy15152        127 GQTVTVDWCFVKGPK  141 (192)
Q Consensus       127 g~~l~v~~a~~~~~~  141 (192)
                      |+.|.|.++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=2.6e-19  Score=119.29  Aligned_cols=80  Identities=21%  Similarity=0.337  Sum_probs=72.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++        ++||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            344567899999999999999999999999999999986        349999999999999999999999999999999


Q ss_pred             EecccCCC
Q psy15152        133 DWCFVKGP  140 (192)
Q Consensus       133 ~~a~~~~~  140 (192)
                      .++.++..
T Consensus        77 ~~a~~~~~   84 (92)
T 2dgt_A           77 QLSTSRLR   84 (92)
T ss_dssp             EESSCCCS
T ss_pred             EEccCCCC
Confidence            99987643

>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=99.82  E-value=1.1e-19  Score=124.91  Aligned_cols=80  Identities=25%  Similarity=0.449  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.+      +|||||+|.+.++|++|++.|+|..+.|+.|.|.|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            45678999999999999999999999999999999876      689999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy15152        136 FVKGPK  141 (192)
Q Consensus       136 ~~~~~~  141 (192)
                      .++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4g_A           97 KESPDM  102 (109)
T ss_dssp             CCCCSS
T ss_pred             CCCCCC
Confidence            876543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.82  E-value=5.4e-20  Score=123.50  Aligned_cols=83  Identities=24%  Similarity=0.345  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|+.||.|..+     ..+|.++|||||+|.+.++|++|++.|+|..+.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34456899999999999999999999999988766     2478999999999999999999999999999999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (96)
T 1fjc_A           87 YTGEKGGT   94 (96)
T ss_dssp             ECSSSCCC
T ss_pred             EcCCCCCC
Confidence            99876543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=5.2e-20  Score=126.69  Aligned_cols=80  Identities=23%  Similarity=0.259  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+..+|||+|||+++++++|+++|+.| .|.++.|+.|+ +|+++|||||+|.+.++|++|+ .||+..|+|+.|.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            345789999999999999999999999 89999999997 5999999999999999999999 68999999999999888


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      .+.
T Consensus        91 ~~~   93 (109)
T 2dnn_A           91 TER   93 (109)
T ss_dssp             CHH
T ss_pred             Ccc
Confidence            643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.81  E-value=1.9e-20  Score=122.03  Aligned_cols=73  Identities=29%  Similarity=0.408  Sum_probs=67.9

Q ss_pred             CcEEEEcCCCCCC------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCe-EE
Q psy15152         58 GWILFVTGVHEEA------QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ-TV  130 (192)
Q Consensus        58 ~~~l~V~nLp~~~------t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~-~l  130 (192)
                      +++|||+|||..+      ++++|+++|++||.|..+.++  +.+|+++|||||+|.+.++|++|++.|||..+.|+ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      789999999999999999987  35899999999999999999999999999999999 88


Q ss_pred             EE
Q psy15152        131 TV  132 (192)
Q Consensus       131 ~v  132 (192)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=4.6e-20  Score=127.31  Aligned_cols=79  Identities=18%  Similarity=0.155  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..++|||+|||+++++++|+++|++|| .|..+.+..    +.++|||||+|.+.++|++|++.|||..+.|+.|.|+++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            457899999999999999999999999 899998753    347899999999999999999999999999999999998


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      ...+
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7543

>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=99.81  E-value=1e-19  Score=144.39  Aligned_cols=75  Identities=32%  Similarity=0.471  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEec
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL-GQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~-g~~l~v~~a  135 (192)
                      +.++|||+|||.++++++|+++|++||.|.+++++.++     +|||||+|.+.++|++|++.|||..+. |+.|+|.||
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            46889999999999999999999999999999998664     689999999999999999999999999 999999998


Q ss_pred             c
Q psy15152        136 F  136 (192)
Q Consensus       136 ~  136 (192)
                      +
T Consensus       281 k  281 (282)
T 3pgw_A          281 K  281 (282)
T ss_pred             c
Confidence            5

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.9e-19  Score=119.54  Aligned_cols=81  Identities=21%  Similarity=0.345  Sum_probs=72.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccC--CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEY--GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~--G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      .....+.++|||+|||+++++++|+++|++|  |.|..+.+.        +|||||+|.+.++|++|++.||+..+.|+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3444567899999999999999999999999  899988764        579999999999999999999999999999


Q ss_pred             EEEEecccCCC
Q psy15152        130 VTVDWCFVKGP  140 (192)
Q Consensus       130 l~v~~a~~~~~  140 (192)
                      |.|.|+.++..
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpd_A           81 IEVTLAKPVDK   91 (99)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987653

>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=99.81  E-value=2.7e-19  Score=123.17  Aligned_cols=76  Identities=26%  Similarity=0.423  Sum_probs=70.5

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ...++|||+|||++ +++++|+++|++||.|..+.+        ++|||||+|.+.++|++|++.|++..+.|+.|.|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34579999999999 999999999999999999988        478999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      +.+..
T Consensus        97 a~~~~  101 (110)
T 1wf1_A           97 AGEPK  101 (110)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            97544

>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=99.81  E-value=3.3e-20  Score=124.72  Aligned_cols=82  Identities=15%  Similarity=0.383  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMH----EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ..++++|||+|||.++++++|+    ++|++||.|..+.+..   +|.++|||||+|.+.++|++|++.|||..+.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999    9999999999998863   57889999999999999999999999999999999


Q ss_pred             EEEecccCC
Q psy15152        131 TVDWCFVKG  139 (192)
Q Consensus       131 ~v~~a~~~~  139 (192)
                      .|.|+.++.
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998764

>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=99.81  E-value=1.1e-19  Score=125.44  Aligned_cols=80  Identities=21%  Similarity=0.216  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCeEEE
Q psy15152         55 SVEGWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG--TTILGQTVT  131 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~--~~~~g~~l~  131 (192)
                      ..++++|||+|||++ +++++|+++|++||.|.++.++..      +|||||+|.+.++|++|++.|++  ..+.|++|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456789999999998 999999999999999999998743      78999999999999999998864  569999999


Q ss_pred             EEecccCCC
Q psy15152        132 VDWCFVKGP  140 (192)
Q Consensus       132 v~~a~~~~~  140 (192)
                      |.||..+..
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999976543

>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=99.81  E-value=1.8e-19  Score=118.22  Aligned_cols=78  Identities=21%  Similarity=0.413  Sum_probs=71.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCeEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL-NGTTILGQTVT  131 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l-~~~~~~g~~l~  131 (192)
                      ....+.++|||+|||.++++++|+++|++||.|..+.++.+      +|||||+|.+.++|++|++.| ++..+.|+.|+
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            33455678999999999999999999999999999999865      689999999999999999999 99999999999


Q ss_pred             EEecc
Q psy15152        132 VDWCF  136 (192)
Q Consensus       132 v~~a~  136 (192)
                      |+||+
T Consensus        81 v~~ak   85 (85)
T 2ytc_A           81 VKWGR   85 (85)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99974

>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=99.81  E-value=8.9e-20  Score=121.79  Aligned_cols=79  Identities=23%  Similarity=0.350  Sum_probs=69.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCC-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC-CeeCCeEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG-TTILGQTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~-i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~-~~~~g~~l~v~  133 (192)
                      ...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||+ ..+.|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            34578999999999999999999999999 5555542       378999999999999999999999 99999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      |+.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876543

>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=99.81  E-value=1.1e-20  Score=121.11  Aligned_cols=75  Identities=16%  Similarity=0.400  Sum_probs=71.8

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++. ++..+.|+.|.|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999998999999999999999999999985 899999999999875

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=5.5e-19  Score=118.89  Aligned_cols=85  Identities=22%  Similarity=0.318  Sum_probs=74.1

Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy15152         49 EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ  128 (192)
Q Consensus        49 ~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~  128 (192)
                      .+......+.++|||+||  ++++++|+++|++||.|..+.+.      .++|||||+|.+.++|++|++.|++..+.|+
T Consensus         6 ~~~~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   77 (97)
T 1x5p_A            6 SGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESV   77 (97)
T ss_dssp             SSCCCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCccCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            344444556789999996  89999999999999999999884      4578999999999999999999999999999


Q ss_pred             EEEEEecccCCCC
Q psy15152        129 TVTVDWCFVKGPK  141 (192)
Q Consensus       129 ~l~v~~a~~~~~~  141 (192)
                      .|.|.|+.++...
T Consensus        78 ~l~v~~a~~~~~~   90 (97)
T 1x5p_A           78 QLKVNIARKQPML   90 (97)
T ss_dssp             EEEEECCSSCCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.81  E-value=1.8e-19  Score=123.85  Aligned_cols=78  Identities=23%  Similarity=0.452  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.|+|..+.|+.|.|.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4556899999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             cccCCC
Q psy15152        135 CFVKGP  140 (192)
Q Consensus       135 a~~~~~  140 (192)
                      +.+...
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.81  E-value=4.9e-20  Score=125.13  Aligned_cols=81  Identities=22%  Similarity=0.420  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++  ++..+.|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            345789999999999999999999999999999999998 99999999999999999999998  999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .++.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            8764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.4e-19  Score=119.25  Aligned_cols=78  Identities=19%  Similarity=0.288  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++++++|+++|+.||.|.+|  +.++.+|.   ||||+|.+.++|++|++ |++..+.|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345789999999999999999999999999987  66666665   99999999999999999 9999999999999988


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .++.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6554

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.81  E-value=2.6e-19  Score=136.93  Aligned_cols=83  Identities=29%  Similarity=0.359  Sum_probs=77.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|++||.|.+|+|+.|+.+|+++|||||+|.+.++|++|++.+++..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ...
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

>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=99.81  E-value=2.4e-20  Score=127.96  Aligned_cols=82  Identities=20%  Similarity=0.201  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGE---IKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~---i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ....++|||+|||+++++++|+++|+.||.   |..+.++.++. |+++|||||+|.+.++|++|++ |++..++|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            345688999999999999999999999988   89999999986 9999999999999999999999 999999999999


Q ss_pred             EEecccC
Q psy15152        132 VDWCFVK  138 (192)
Q Consensus       132 v~~a~~~  138 (192)
                      |.++.++
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998754

>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=99.80  E-value=3.4e-19  Score=120.12  Aligned_cols=77  Identities=16%  Similarity=0.329  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         54 RSVEGWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ...++++|||+|||+ ++++++|+++|+.||.|..+.+.        +|||||+|.+.++|++|++.|+|..+.|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999998 99999999999999999999882        789999999999999999999999999999999


Q ss_pred             EecccC
Q psy15152        133 DWCFVK  138 (192)
Q Consensus       133 ~~a~~~  138 (192)
                      .++.++
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            999765

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.1e-19  Score=123.13  Aligned_cols=76  Identities=20%  Similarity=0.319  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||.++++++|+++|+.||.|.++.+.      .++|||||+|.+.++|++|++.|||..++|+.|+|.|+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            35789999999999999999999999999999987      347999999999999999999999999999999999987


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.3e-19  Score=121.89  Aligned_cols=79  Identities=14%  Similarity=0.315  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         55 SVEGWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        55 ~~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ..+.++|||+|||+ ++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.|++..+.|+.|.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999998 99999999999999999999883        6899999999999999999999999999999999


Q ss_pred             ecccCCCC
Q psy15152        134 WCFVKGPK  141 (192)
Q Consensus       134 ~a~~~~~~  141 (192)
                      ++.++...
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.3e-19  Score=118.34  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++        ++||||+|.+.++|++|++.||+..+.|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3456789999999999999999999999999999986        34999999999999999999999999999999999


Q ss_pred             cccCCC
Q psy15152        135 CFVKGP  140 (192)
Q Consensus       135 a~~~~~  140 (192)
                      +.+...
T Consensus        78 a~~~~~   83 (90)
T 2dnp_A           78 STKGQK   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=99.80  E-value=5.7e-19  Score=128.96  Aligned_cols=82  Identities=27%  Similarity=0.385  Sum_probs=78.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57899999999999999999999999999999999988999999999999999999999999999999999999999976


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.80  E-value=1.9e-19  Score=134.14  Aligned_cols=84  Identities=23%  Similarity=0.374  Sum_probs=79.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...++++|||+|||+.+++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.++|++|++.|++..|.|+.|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34557899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             ecccC
Q psy15152        134 WCFVK  138 (192)
Q Consensus       134 ~a~~~  138 (192)
                      ||...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            99754

>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=99.80  E-value=2e-19  Score=141.70  Aligned_cols=117  Identities=18%  Similarity=0.230  Sum_probs=90.5

Q ss_pred             CCCccCCCCChhHHHh--hhcccCC---CCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCC
Q psy15152         22 GRGFGTETSTRNEIRE--YESMETD---VGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT   96 (192)
Q Consensus        22 ~rG~gfv~f~~~~~~~--~~~~~~~---~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~t   96 (192)
                      +||||||+|...+.+.  ...++..   +...  ......++.+|||+|||..+++++|+++|+.||.|..+.++.+. +
T Consensus        57 ~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l--~v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~  133 (261)
T 3sde_A           57 DRGFGFIRLESRTLAEIAKAELDGTILKSRPL--RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-R  133 (261)
T ss_dssp             TTTEEEEECSSHHHHHHHHHHHTTCEETTEEC--EEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-T
T ss_pred             CCcEEEEEECCHHHHHHHHHHcCCcEECCcee--EeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-C
Confidence            6899999994443322  2223222   2111  11122346789999999999999999999999999999999994 9


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCC-CeeC---CeEEEEEecccCCCC
Q psy15152         97 GFLKGYALVEYDSYKEASAARDALNG-TTIL---GQTVTVDWCFVKGPK  141 (192)
Q Consensus        97 g~~~g~afV~f~~~~~a~~al~~l~~-~~~~---g~~l~v~~a~~~~~~  141 (192)
                      |.++|||||+|.+.++|.+|+..|++ ..+.   +++|.|.++.+....
T Consensus       134 g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~~  182 (261)
T 3sde_A          134 GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDE  182 (261)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEESS
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCcc
Confidence            99999999999999999999999954 4444   999999999876433

>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=99.80  E-value=2.1e-20  Score=133.94  Aligned_cols=84  Identities=23%  Similarity=0.306  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      .....++|||+|||+++++++|+++|++|| |.+|.|+.|+. |+++|||||+|.+.++|++|| .+|+..|.|+.|.|.
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            334567899999999999999999999999 77999999974 999999999999999999999 789999999999999


Q ss_pred             ecccCCC
Q psy15152        134 WCFVKGP  140 (192)
Q Consensus       134 ~a~~~~~  140 (192)
                      ++.+...
T Consensus       119 ~a~~~~~  125 (139)
T 2hgn_A          119 LNSTTGA  125 (139)
T ss_dssp             ECCCSCC
T ss_pred             ECCCCCC
Confidence            9876654

>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=99.80  E-value=2.7e-19  Score=124.03  Aligned_cols=81  Identities=21%  Similarity=0.345  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .++++|||+|||+++++++|+++|+.||.|..+.++.+   +.++|||||+|.+.++|++|++.|||..+.|+.|.|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            34678999999999999999999999999999999866   455899999999999999999999999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .+..
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            8654

>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=99.80  E-value=2.1e-19  Score=136.92  Aligned_cols=77  Identities=19%  Similarity=0.229  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCe--eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCe----EE
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEI--KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQ----TV  130 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i--~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~----~l  130 (192)
                      ++++|||+|||+++++++|+++|++||.|  ..+++..+.  |.++|||||+|.+.++|.+|+..|||..|.|+    ++
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            45789999999999999999999999999  899988774  56679999999999999999999999999886    67


Q ss_pred             EEEec
Q psy15152        131 TVDWC  135 (192)
Q Consensus       131 ~v~~a  135 (192)
                      .|++|
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            88776

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=2.9e-19  Score=119.89  Aligned_cols=80  Identities=23%  Similarity=0.234  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNL-HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~-~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ...++|||+|||+++++++|+++|+.||.|..+ .++.++.+|    .|||+|.+.++|++|++.|||..+.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            446789999999999999999999999999999 588886554    399999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      +.++.
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            98763

>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=99.79  E-value=5.9e-20  Score=132.18  Aligned_cols=87  Identities=22%  Similarity=0.343  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEE--E---eecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLH--L---NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~--i---~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.  +   +....+|.++|||||+|.+.++|++|++.|||..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            34568899999999999999999999999987641  1   111237899999999999999999999999999999999


Q ss_pred             EEEEecccCCCC
Q psy15152        130 VTVDWCFVKGPK  141 (192)
Q Consensus       130 l~v~~a~~~~~~  141 (192)
                      |.|.+|.+...+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999876543

>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=99.79  E-value=2e-19  Score=124.91  Aligned_cols=80  Identities=18%  Similarity=0.232  Sum_probs=67.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE-----E
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT-----V  130 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~-----l  130 (192)
                      ...++|||+|||+++++++|+++|++||.|..+.++.+       |||||+|.+.++|++||+.||+..|+|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45688999999999999999999999999999998765       89999999999999999999999999998     7


Q ss_pred             EEEecccCCCCC
Q psy15152        131 TVDWCFVKGPKK  142 (192)
Q Consensus       131 ~v~~a~~~~~~~  142 (192)
                      +|..+.+.....
T Consensus        87 ~v~~~~~~~~~~   98 (115)
T 3beg_B           87 RVKVDGPRSPSY   98 (115)
T ss_dssp             EEEECC----CC
T ss_pred             EeccCCCCCCCC
Confidence            888776654433

>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=99.79  E-value=5.5e-19  Score=129.38  Aligned_cols=83  Identities=24%  Similarity=0.402  Sum_probs=78.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.|++..+.|+.|.|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            45789999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.79  E-value=2e-19  Score=135.66  Aligned_cols=78  Identities=19%  Similarity=0.254  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL-GQTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~-g~~l~v~  133 (192)
                      .++++|||+|||..+++++|+++|++|| .|..+.+..+.     +|+|||+|.+.++|.+|++.|||..+. |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            3478999999999999999999999999 99999986642     789999999999999999999999999 9999999


Q ss_pred             ecccC
Q psy15152        134 WCFVK  138 (192)
Q Consensus       134 ~a~~~  138 (192)
                      |+.++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99754

>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=99.79  E-value=7.6e-19  Score=147.70  Aligned_cols=85  Identities=29%  Similarity=0.465  Sum_probs=80.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|++||..|||..|.|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q psy15152        136 FVKGP  140 (192)
Q Consensus       136 ~~~~~  140 (192)
                      .+...
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            87654

>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=99.79  E-value=3.3e-19  Score=123.07  Aligned_cols=77  Identities=17%  Similarity=0.210  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|++.|||..+.|+.|.|.||.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            457899999999999999999999999999998864      46899999999999999999999999999999999997


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ...
T Consensus        83 ~~~   85 (111)
T 1whx_A           83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.79  E-value=5.6e-19  Score=136.51  Aligned_cols=77  Identities=19%  Similarity=0.249  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEe
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYG-EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL-GQTVTVDW  134 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G-~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~-g~~l~v~~  134 (192)
                      ++++|||+|||.++++++|+++|++|| .|..+.++.+     .+|||||+|.+.++|.+|++.|+|..+. |+.|.|.|
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            468999999999999999999999999 9999998653     2689999999999999999999999999 99999999


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      +.++
T Consensus       225 a~~~  228 (229)
T 2adc_A          225 SKST  228 (229)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            9764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.5e-19  Score=126.94  Aligned_cols=81  Identities=14%  Similarity=0.072  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCe----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEI----KNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i----~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .+..+|||+|||+++|+++|+++|++||.|    ..|.|+.++ +|+++|||||+|.+.++|++|++. |+..|.|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            446789999999999999999999999975    689999995 999999999999999999999986 99999999999


Q ss_pred             EEecccC
Q psy15152        132 VDWCFVK  138 (192)
Q Consensus       132 v~~a~~~  138 (192)
                      |..+.++
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988644

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.78  E-value=3.7e-19  Score=124.16  Aligned_cols=78  Identities=22%  Similarity=0.248  Sum_probs=71.0

Q ss_pred             cEEEEcCC----CCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecC----HHH----HHHHHH--HhCCCe
Q psy15152         59 WILFVTGV----HEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS----YKE----ASAARD--ALNGTT  124 (192)
Q Consensus        59 ~~l~V~nL----p~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~----~~~----a~~al~--~l~~~~  124 (192)
                      ..|||+||    |+.+++++|+++|+.||+|.++.++.|+.||.++|||||+|.+    +++    |.+|+.  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999996    333    888888  789999


Q ss_pred             eCCeEEEEEecc
Q psy15152        125 ILGQTVTVDWCF  136 (192)
Q Consensus       125 ~~g~~l~v~~a~  136 (192)
                      |+|+.|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999754

>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=99.78  E-value=2.7e-19  Score=126.02  Aligned_cols=82  Identities=21%  Similarity=0.219  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCee--EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK--NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ......+|||+|||+++++++|+++|+.| .|.  +|.|+.|+. |+++|||||+|.+.++|++|++. ++..|+|+.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            33456889999999999999999999999 677  899999985 99999999999999999999985 78999999999


Q ss_pred             EEecccC
Q psy15152        132 VDWCFVK  138 (192)
Q Consensus       132 v~~a~~~  138 (192)
                      |.++.++
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988643

>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=99.77  E-value=1.1e-18  Score=115.33  Aligned_cols=75  Identities=15%  Similarity=0.199  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|++| .|..+.+.      +++|||||+|.+.++|++|++.|||..+.|++|+|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            45789999999999999999999999 99999884      568999999999999999999999999999999999986


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=114.74  Aligned_cols=74  Identities=14%  Similarity=0.274  Sum_probs=66.3

Q ss_pred             CCcE-EEEcCCCCCCcHHH----HHHhhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         57 EGWI-LFVTGVHEEAQEDD----MHEKFSEY-GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        57 ~~~~-l~V~nLp~~~t~~~----L~~~F~~~-G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      +..+ |||+|||+.+++++    |+++|++| |+|.+|       +|   |+|||.|.+.++|++|++.|+|..+.|++|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            4455 99999999999987    56899999 599998       44   999999999999999999999999999999


Q ss_pred             EEEecccCCC
Q psy15152        131 TVDWCFVKGP  140 (192)
Q Consensus       131 ~v~~a~~~~~  140 (192)
                      +|.||..++.
T Consensus        77 ~v~~A~~~sd   86 (96)
T 2diu_A           77 IVSFTPKNRE   86 (96)
T ss_dssp             EEESSCCSCC
T ss_pred             EEEecCCCcc
Confidence            9999987654

>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=99.77  E-value=2.2e-18  Score=129.34  Aligned_cols=86  Identities=20%  Similarity=0.362  Sum_probs=78.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ....+.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++. ++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            3445578999999999999999999999999999999999998999999999999999999999986 999999999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .++.+..
T Consensus        87 ~~~~~~~   93 (196)
T 1l3k_A           87 KRAVSRE   93 (196)
T ss_dssp             EECCC--
T ss_pred             ecccCcc
Confidence            9987653

>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=99.77  E-value=1.1e-18  Score=120.57  Aligned_cols=78  Identities=18%  Similarity=0.265  Sum_probs=69.7

Q ss_pred             CCCcEEEE--cCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee-----CCe
Q psy15152         56 VEGWILFV--TGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI-----LGQ  128 (192)
Q Consensus        56 ~~~~~l~V--~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~-----~g~  128 (192)
                      .++.+|||  +||++++++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|||..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34678999  779999999999999999999999887532      68999999999999999999999998     689


Q ss_pred             EEEEEecccCC
Q psy15152        129 TVTVDWCFVKG  139 (192)
Q Consensus       129 ~l~v~~a~~~~  139 (192)
                      +|.|.|+...+
T Consensus        97 ~l~v~~a~~~p  107 (114)
T 2cq2_A           97 TLYLNFVEKVQ  107 (114)
T ss_dssp             ECEEEEESCCC
T ss_pred             EEEEEecccCc
Confidence            99999997543

>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=99.77  E-value=3.7e-18  Score=124.82  Aligned_cols=78  Identities=21%  Similarity=0.281  Sum_probs=71.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEec
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVDWC  135 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a  135 (192)
                      ..+|||+||++.+++++|+++|++||.|.+|.+..+.    ++|||||+|.+.++|++|++.|||..|.|  +.|+|.|+
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----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            4679999999999999999999999999999986442    57999999999999999999999999966  99999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      +++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.77  E-value=4.7e-18  Score=119.91  Aligned_cols=76  Identities=21%  Similarity=0.361  Sum_probs=69.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGY-ALVEYDSYKEASAARDALNGTTILG--QTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~-afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a  135 (192)
                      -.|||+||++.+|+++|+++|++||.|.+|.+..+.     +|| |||+|.+.++|++|++.|||..|.|  +.|+|.|+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            568899999999999999999999999999887653     677 9999999999999999999999988  89999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      ++..
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            8764

>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=99.76  E-value=2.8e-18  Score=113.82  Aligned_cols=76  Identities=24%  Similarity=0.421  Sum_probs=63.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe--eCCeEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT--ILGQTVTV  132 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~--~~g~~l~v  132 (192)
                      ..+.++|||+|||+++++++|+++|++||.|.++.++.+     ++|||||+|.+.++|++    |++..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            345678999999999999999999999999999999875     68999999999999983    45655  56999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .+|.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.76  E-value=4e-18  Score=124.33  Aligned_cols=80  Identities=29%  Similarity=0.514  Sum_probs=74.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|||+|||.++++++|+++|++||.|.++.++.++ +|+++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999997 6889999999999999999999999999999999999999765


Q ss_pred             C
Q psy15152        139 G  139 (192)
Q Consensus       139 ~  139 (192)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=5.1e-18  Score=117.55  Aligned_cols=78  Identities=19%  Similarity=0.223  Sum_probs=68.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCC---CCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRT---GFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~t---g~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3457899999999999999999999999999 888888776   7999999999999999999999984  377777777


Q ss_pred             Eecc
Q psy15152        133 DWCF  136 (192)
Q Consensus       133 ~~a~  136 (192)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=2.4e-17  Score=115.62  Aligned_cols=75  Identities=23%  Similarity=0.313  Sum_probs=67.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGY-ALVEYDSYKEASAARDALNGTTILG--QTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~-afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~~a  135 (192)
                      -.|||+||++.+++++|+++|++||.|.++.+.. +     .|| |||+|.+.++|++|++.|||..|.|  +.|+|.||
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 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            3478999999999999999999999999999864 2     276 9999999999999999999999987  69999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8764

>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=99.75  E-value=6.1e-18  Score=128.82  Aligned_cols=79  Identities=22%  Similarity=0.310  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCC-CCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVH-EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp-~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      .++++|||+||| +.+++++|+++|++||.|.+++++.++     +|||||+|.+.++|++|++.|||..+.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            356789999999 899999999999999999999998763     79999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      +....
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            97543

>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=99.74  E-value=3e-18  Score=113.19  Aligned_cols=79  Identities=20%  Similarity=0.314  Sum_probs=66.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++|+..  ...+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35688999999999999999999999999999998765     589999999999999864331  34468999999999


Q ss_pred             ccCCCC
Q psy15152        136 FVKGPK  141 (192)
Q Consensus       136 ~~~~~~  141 (192)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=7.9e-18  Score=128.11  Aligned_cols=82  Identities=26%  Similarity=0.350  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +.++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.|++..+.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            34789999999999999999999999999999999998899999999999999999999999999999999999998875


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      ..
T Consensus       107 ~~  108 (216)
T 2qfj_A          107 NI  108 (216)
T ss_dssp             CC
T ss_pred             Cc
Confidence            44

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.73  E-value=2.8e-17  Score=112.25  Aligned_cols=82  Identities=16%  Similarity=0.157  Sum_probs=72.9

Q ss_pred             CCCcEEEEcCCCC-----CCcHHHHHHhhccCCCeeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         56 VEGWILFVTGVHE-----EAQEDDMHEKFSEYGEIKNLHLNLDRRT-GFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        56 ~~~~~l~V~nLp~-----~~t~~~L~~~F~~~G~i~~~~i~~~~~t-g~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      .++.+|+|.||..     +-++++|++.|++||.|.++.++.++.+ +.++|||||+|.+.++|++|++.|||..+.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4567899999963     2368999999999999999999998654 689999999999999999999999999999999


Q ss_pred             EEEEeccc
Q psy15152        130 VTVDWCFV  137 (192)
Q Consensus       130 l~v~~a~~  137 (192)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>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=99.73  E-value=1.9e-17  Score=121.80  Aligned_cols=83  Identities=24%  Similarity=0.365  Sum_probs=75.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCCeeC---CeEEE
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTG--FLKGYALVEYDSYKEASAARDALNGTTIL---GQTVT  131 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg--~~~g~afV~f~~~~~a~~al~~l~~~~~~---g~~l~  131 (192)
                      +.++|||+|||+++++++|+++|++||.|.++.++.++.+|  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            46789999999999999999999999999999999998776  89999999999999999999999998876   67888


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      +.++.+..
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88877654

>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=99.72  E-value=3.7e-17  Score=123.37  Aligned_cols=79  Identities=18%  Similarity=0.257  Sum_probs=72.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|++||.|..++++.+. +|.++|||||+|.+.++|++|++.+ +..+.|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4789999999999999999999999999999999996 6999999999999999999999865 5699999999998764


Q ss_pred             C
Q psy15152        138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      -
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.72  E-value=1.3e-17  Score=121.99  Aligned_cols=80  Identities=19%  Similarity=0.445  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            467899999999999999999999999999999999988999999999999999999999984  678999999999886


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      +.
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            54

>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=99.72  E-value=2e-17  Score=108.74  Aligned_cols=71  Identities=25%  Similarity=0.449  Sum_probs=65.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEY----G-------EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~----G-------~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      +.++|||+|||+++++++|+++|+.|    |       .|.++.+..+      +|||||+|.+.++|++|+ .||+..+
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-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            46789999999999999999999999    8       8999988755      689999999999999999 9999999


Q ss_pred             CCeEEEEEe
Q psy15152        126 LGQTVTVDW  134 (192)
Q Consensus       126 ~g~~l~v~~  134 (192)
                      .|+.|+|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999973

>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=99.70  E-value=8.1e-17  Score=127.64  Aligned_cols=82  Identities=15%  Similarity=0.389  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMH----EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ..+.++|||+|||+++++++|+    ++|+.||.|.+|.+..   +|+++|||||+|.+.++|++|++.|||..+.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            3457899999999999999966    8999999999998875   68899999999999999999999999999999999


Q ss_pred             EEEecccCC
Q psy15152        131 TVDWCFVKG  139 (192)
Q Consensus       131 ~v~~a~~~~  139 (192)
                      +|.|+....
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999997654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.70  E-value=3.4e-17  Score=126.94  Aligned_cols=80  Identities=21%  Similarity=0.354  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCC---------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         55 SVEGWILFVTGVHEEA---------QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~---------t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      ....++|||+||+..+         ++++|+++|++||.|.+|+++.+      +|||||+|.+.++|+.|++.|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3457899999999998         79999999999999999999854      79999999999999999999999999


Q ss_pred             ------------CCeEEEEEecccCCC
Q psy15152        126 ------------LGQTVTVDWCFVKGP  140 (192)
Q Consensus       126 ------------~g~~l~v~~a~~~~~  140 (192)
                                  .|+.|.|+||...+.
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999986643

>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=99.69  E-value=1.8e-16  Score=122.41  Aligned_cols=82  Identities=18%  Similarity=0.349  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         53 QRSVEGWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ....++++|||+|||+ ++++++|+++|+.||.|.++.++.++     +|||||+|.+.++|++|++.|++..+.|+.|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            4456678999999999 99999999999999999999999885     78999999999999999999999999999999


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |.++.+..
T Consensus       104 v~~a~~~~  111 (229)
T 2adc_A          104 ITLSKHQN  111 (229)
T ss_dssp             EECCSCCC
T ss_pred             EEEecCcc
Confidence            99998653

>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=99.68  E-value=7.9e-16  Score=106.12  Aligned_cols=83  Identities=22%  Similarity=0.338  Sum_probs=70.8

Q ss_pred             CCCCCCcEEEEcCCCCCCc-----------HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy15152         53 QRSVEGWILFVTGVHEEAQ-----------EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN  121 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t-----------~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~  121 (192)
                      ....++.+|+|.||.....           +++|+++|++||.|.++.| .++   .++|||||+|.+.++|++|++.||
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            3445678899999954432           5799999999999999955 554   379999999999999999999999


Q ss_pred             CCeeCCeEEEEEecccCC
Q psy15152        122 GTTILGQTVTVDWCFVKG  139 (192)
Q Consensus       122 ~~~~~g~~l~v~~a~~~~  139 (192)
                      |..++|+.|.|.++.++.
T Consensus        86 g~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CCEECCcEEEEEEeCCCC
Confidence            999999999999997754

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=2.2e-16  Score=118.84  Aligned_cols=78  Identities=19%  Similarity=0.374  Sum_probs=72.9

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         57 EGWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+++|||+|||+ ++++++|+++|+.||.|.++.++.++     +|||||+|.+.++|++|++.|+|..+.|+.|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            457899999999 99999999999999999999998875     789999999999999999999999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .+..
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8654

>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=99.66  E-value=2.8e-17  Score=121.27  Aligned_cols=84  Identities=18%  Similarity=0.304  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ...+.++|||+|||+++++++|+++|+.||.+.. .++.+..+|.++|||||+|.+.++|++|++ |++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3445789999999999999999999999998766 334444588999999999999999999995 99999999999999


Q ss_pred             ecccCC
Q psy15152        134 WCFVKG  139 (192)
Q Consensus       134 ~a~~~~  139 (192)
                      ++.+..
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            997654

>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=99.65  E-value=7.6e-16  Score=121.12  Aligned_cols=82  Identities=24%  Similarity=0.497  Sum_probs=73.6

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         50 PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        50 ~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      |........++|||+|||+++|+++|+++|+.||.|..+.+..+      +|||||+|.+.++|++|+..|+|..+.|+.
T Consensus        14 p~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~   87 (261)
T 3sde_A           14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRP   87 (261)
T ss_dssp             TTCCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCce
Confidence            33444456789999999999999999999999999999998644      689999999999999999999999999999


Q ss_pred             EEEEeccc
Q psy15152        130 VTVDWCFV  137 (192)
Q Consensus       130 l~v~~a~~  137 (192)
                      |.|.++.+
T Consensus        88 l~v~~a~~   95 (261)
T 3sde_A           88 LRIRFATH   95 (261)
T ss_dssp             CEEEECCC
T ss_pred             eEeeeccc
Confidence            99999864

>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=99.64  E-value=1.3e-16  Score=108.83  Aligned_cols=72  Identities=21%  Similarity=0.389  Sum_probs=65.0

Q ss_pred             EcCCCCCCcHHHHHHhh------------ccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         63 VTGVHEEAQEDDMHEKF------------SEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        63 V~nLp~~~t~~~L~~~F------------~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      +.||++.+++++|++.|            ++||.|.++.++.++ +|.++|||||+|.+.++|++|++.|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56778888888777666            999999999999886 58999999999999999999999999999999999


Q ss_pred             EEEec
Q psy15152        131 TVDWC  135 (192)
Q Consensus       131 ~v~~a  135 (192)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.62  E-value=1.3e-15  Score=104.00  Aligned_cols=82  Identities=21%  Similarity=0.282  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCC--CCCCc--------HHHHHHhhccCCCeeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCC
Q psy15152         56 VEGWILFVTGV--HEEAQ--------EDDMHEKFSEYGEIKNLHLNLDRRT--GFLKGYALVEYDSYKEASAARDALNGT  123 (192)
Q Consensus        56 ~~~~~l~V~nL--p~~~t--------~~~L~~~F~~~G~i~~~~i~~~~~t--g~~~g~afV~f~~~~~a~~al~~l~~~  123 (192)
                      .++..|.+.|+  |.+..        +++|++.|++||.|.++.|+.++.+  +.++|+|||+|.+.++|++|++.|||.
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            35678999998  33332        3689999999999999999988754  468999999999999999999999999


Q ss_pred             eeCCeEEEEEeccc
Q psy15152        124 TILGQTVTVDWCFV  137 (192)
Q Consensus       124 ~~~g~~l~v~~a~~  137 (192)
                      .++|+.|.|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999864

>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=99.61  E-value=4.6e-15  Score=103.23  Aligned_cols=81  Identities=17%  Similarity=0.296  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCC--C---CcHHHHHHhhccCCCeeEEEEeecCC----CCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy15152         57 EGWILFVTGVHE--E---AQEDDMHEKFSEYGEIKNLHLNLDRR----TGFLKGYALVEYDSYKEASAARDALNGTTILG  127 (192)
Q Consensus        57 ~~~~l~V~nLp~--~---~t~~~L~~~F~~~G~i~~~~i~~~~~----tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g  127 (192)
                      ++.+|++.|+-.  +   -.+++|++.|++||.|.++.|+.++.    ++.++|++||+|.+.++|.+|++.|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            567899999842  2   23689999999999999999999864    46788999999999999999999999999999


Q ss_pred             eEEEEEeccc
Q psy15152        128 QTVTVDWCFV  137 (192)
Q Consensus       128 ~~l~v~~a~~  137 (192)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999854

>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=99.60  E-value=3.4e-15  Score=109.55  Aligned_cols=75  Identities=23%  Similarity=0.346  Sum_probs=66.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEY----G-------EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~----G-------~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      +.++|||+|||+++++++|+++|++|    |       .|.++.+.      .++|||||+|.+.++|++|+ .|++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            45789999999999999999999999    6       67776654      34799999999999999999 8999999


Q ss_pred             CCeEEEEEecccC
Q psy15152        126 LGQTVTVDWCFVK  138 (192)
Q Consensus       126 ~g~~l~v~~a~~~  138 (192)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.59  E-value=8.1e-15  Score=109.87  Aligned_cols=77  Identities=22%  Similarity=0.342  Sum_probs=66.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEY----G-------EIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~----G-------~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+      +.++|||||+|.+.++|++|+ .|+|..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            45789999999999999999999999    4       5555554      455899999999999999999 8999999


Q ss_pred             CCeEEEEEecccCCC
Q psy15152        126 LGQTVTVDWCFVKGP  140 (192)
Q Consensus       126 ~g~~l~v~~a~~~~~  140 (192)
                      .|+.|.|.++.....
T Consensus        76 ~g~~i~v~~~~~~~~   90 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQP   90 (198)
T ss_dssp             TTEEEEEECCCCCCC
T ss_pred             cCceEEEeCCCCCCC
Confidence            999999999876543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=3e-14  Score=96.22  Aligned_cols=66  Identities=24%  Similarity=0.358  Sum_probs=58.1

Q ss_pred             CCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCCC
Q psy15152         68 EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGP  140 (192)
Q Consensus        68 ~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~~  140 (192)
                      ..+++++|+++|++||.|.++.++     ++++|||||+|.+.++|+.|++.+++  +.|++|+|.|+.+++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            458999999999999999999987     46799999999999999999997544  6899999999976653

>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=99.52  E-value=2.6e-14  Score=116.20  Aligned_cols=76  Identities=21%  Similarity=0.327  Sum_probs=65.5

Q ss_pred             CCCCcEEEEcC--CCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC---Ce-
Q psy15152         55 SVEGWILFVTG--VHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL---GQ-  128 (192)
Q Consensus        55 ~~~~~~l~V~n--Lp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~---g~-  128 (192)
                      +.++.+|||+|  |++.+++++|+++|++||+|.++.+..      +||||||+|.+.++|++|++.|||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45667899999  578999999999999999999887643      4799999999999999999999999873   44 


Q ss_pred             -EEEEEecc
Q psy15152        129 -TVTVDWCF  136 (192)
Q Consensus       129 -~l~v~~a~  136 (192)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             67788774

>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=99.45  E-value=4.9e-13  Score=92.35  Aligned_cols=77  Identities=19%  Similarity=0.285  Sum_probs=64.8

Q ss_pred             CCcEEEEcCCCCCC----------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         57 EGWILFVTGVHEEA----------QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        57 ~~~~l~V~nLp~~~----------t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      ++..|.+.|+=..-          .+++|++.|++||.|.++.+..+.    ++|++||+|.+.++|++|++.|||..++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45678888873321          135789999999999999886653    4899999999999999999999999999


Q ss_pred             CeEEEEEeccc
Q psy15152        127 GQTVTVDWCFV  137 (192)
Q Consensus       127 g~~l~v~~a~~  137 (192)
                      |+.|.|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999854

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=4.4e-12  Score=83.01  Aligned_cols=77  Identities=22%  Similarity=0.355  Sum_probs=65.0

Q ss_pred             CCCCcEEEEcCCCC----CCcH----HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         55 SVEGWILFVTGVHE----EAQE----DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        55 ~~~~~~l~V~nLp~----~~t~----~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      .++..||+|.-.+.    .+-.    .+|.+.|++||.|..+++..++        +||+|.+.++|.+|++ |||..+.
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            34566799987762    2333    5789999999999999998874        8999999999999998 9999999


Q ss_pred             CeEEEEEecccCCC
Q psy15152        127 GQTVTVDWCFVKGP  140 (192)
Q Consensus       127 g~~l~v~~a~~~~~  140 (192)
                      |+.|+|+++.+...
T Consensus        75 Gr~LkV~lkt~dW~   88 (91)
T 2dnr_A           75 NRTITIALKSPSGP   88 (91)
T ss_dssp             TEEEEEEECCCSSC
T ss_pred             CeEEEEEeCCCCcc
Confidence            99999999987654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=1.1e-11  Score=85.90  Aligned_cols=78  Identities=22%  Similarity=0.279  Sum_probs=68.3

Q ss_pred             CCCCCCCcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecC-HHHHHHHHHHhC--CCeeCC
Q psy15152         52 PQRSVEGWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS-YKEASAARDALN--GTTILG  127 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~-~~~a~~al~~l~--~~~~~g  127 (192)
                      ...-..++.|||+||+.+ +++++|+++|++||+|..|.+..+..      .|||.|.+ .++|..|++.|+  +..|.|
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            344567899999999999 99999999999999999999988863      59999999 899999999994  677899


Q ss_pred             eEEEEEec
Q psy15152        128 QTVTVDWC  135 (192)
Q Consensus       128 ~~l~v~~a  135 (192)
                      ..++++..
T Consensus        86 ~~~~~evL   93 (121)
T 1owx_A           86 KEVTWEVL   93 (121)
T ss_dssp             SSEEEEEC
T ss_pred             cEEEEEEC
Confidence            88888754

>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=99.16  E-value=1.1e-10  Score=89.38  Aligned_cols=69  Identities=19%  Similarity=0.290  Sum_probs=61.5

Q ss_pred             CCcHHHHHHhhccCCCeeEEEEeecC----CCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         69 EAQEDDMHEKFSEYGEIKNLHLNLDR----RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        69 ~~t~~~L~~~F~~~G~i~~~~i~~~~----~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +-.+++|.+.|++||.|.++.+..+.    .++.++|++||+|.+.++|++|++.|||..+.||.|.+.++..
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            34567899999999999999998554    4558999999999999999999999999999999999999753

>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=99.15  E-value=8.2e-11  Score=77.37  Aligned_cols=74  Identities=18%  Similarity=0.256  Sum_probs=62.5

Q ss_pred             CCCCCcEEEEcCCCCC------CcH---HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe
Q psy15152         54 RSVEGWILFVTGVHEE------AQE---DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT  124 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~------~t~---~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~  124 (192)
                      ..++..||+|.-++.+      .++   .+|.+.|+.||.|..+++..|+        +||+|.+.++|.+||+ |+|..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            3456678999888743      222   4688999999999999999884        9999999999999998 99999


Q ss_pred             eCCeEEEEEecc
Q psy15152        125 ILGQTVTVDWCF  136 (192)
Q Consensus       125 ~~g~~l~v~~a~  136 (192)
                      +.|+.|+|++..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.60  E-value=2.7e-07  Score=61.94  Aligned_cols=70  Identities=16%  Similarity=0.196  Sum_probs=64.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccC-----CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEY-----GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~-----G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      .++|-+-|||..+++..++.+..++     |.+..+.+..|-      |-|+|+|.+...|-+|.-+|+|..+.|+.|++
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            4568888999999999999999999     999999988883      57999999999999999999999999999998


Q ss_pred             E
Q psy15152        133 D  133 (192)
Q Consensus       133 ~  133 (192)
                      .
T Consensus        95 g   95 (117)
T 2l9w_A           95 G   95 (117)
T ss_dssp             E
T ss_pred             c
Confidence            5

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.12  E-value=4.7e-05  Score=50.58  Aligned_cols=76  Identities=11%  Similarity=0.112  Sum_probs=61.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhcc-----CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSE-----YGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~-----~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ..+.+|.|.|||..++++.|.-+|+.     -|+|..+....        +-|+|+|.+.+.|++.|+. ..+.|.|..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            34578999999999999999999986     25787876643        3699999999999999974 5788999999


Q ss_pred             EEEecccCCC
Q psy15152        131 TVDWCFVKGP  140 (192)
Q Consensus       131 ~v~~a~~~~~  140 (192)
                      .|....+..+
T Consensus        77 sV~P~~~~~~   86 (104)
T 2dhx_A           77 SLRPAPPRAP   86 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEcCCCCCc
Confidence            9987655443

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.04  E-value=1.7e-05  Score=52.84  Aligned_cols=74  Identities=14%  Similarity=0.159  Sum_probs=62.5

Q ss_pred             cEEEEcCCCCCC-c----HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         59 WILFVTGVHEEA-Q----EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        59 ~~l~V~nLp~~~-t----~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ++|+|.||+.++ .    .+.++++|..|+++....++..-      .-..|.|.+.++|.+|-..||+..+.|+.++|-
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            569999998864 2    25678999999999887776653      146899999999999999999999999999999


Q ss_pred             ecccC
Q psy15152        134 WCFVK  138 (192)
Q Consensus       134 ~a~~~  138 (192)
                      ++.+.
T Consensus        80 Fgq~~   84 (104)
T 1wey_A           80 FAQTL   84 (104)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99844

>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=97.96  E-value=1.1e-06  Score=60.01  Aligned_cols=65  Identities=12%  Similarity=0.127  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccC---CCC-----CCCCC-------CCCCCCCcEEEEcCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMET---DVG-----DEEPG-------PQRSVEGWILFVTGVHEE   69 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~---~~~-----~~~~~-------~~~~~~~~~l~V~nLp~~   69 (192)
                      +.+|.+++|+.  + +||||||+|...+  ..++..++.   .+.     ...+.       ........+|||+|||++
T Consensus        32 v~~v~i~~d~~--~-~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~  108 (115)
T 4f25_A           32 ILSCKVVCDEN--G-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPG  108 (115)
T ss_dssp             EEEEEEEEETT--E-EEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC-----------------------
T ss_pred             EEEEEEeecCC--C-CCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccccccccccCCCCceEeCCCCCC
Confidence            56888999863  2 7899999994333  333333322   211     01111       112233467999999999


Q ss_pred             CcHHH
Q psy15152         70 AQEDD   74 (192)
Q Consensus        70 ~t~~~   74 (192)
                      +|++.
T Consensus       109 ~T~~a  113 (115)
T 4f25_A          109 STRAA  113 (115)
T ss_dssp             -----
T ss_pred             ccccc
Confidence            99864

>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=97.94  E-value=4.9e-05  Score=49.94  Aligned_cols=55  Identities=22%  Similarity=0.303  Sum_probs=47.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN  121 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~  121 (192)
                      .+.+++ +.|..+...||.++|++||.| .|+++-|.       -|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            366777 999999999999999999954 77888874       79999999999999998763

>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=0.00023  Score=46.50  Aligned_cols=68  Identities=10%  Similarity=0.222  Sum_probs=55.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHHHhCCCeeC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGF--LKGYALVEYDSYKEASAARDALNGTTIL  126 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~--~~g~afV~f~~~~~a~~al~~l~~~~~~  126 (192)
                      ++|.|++||+.+|++++.+.++....+..........+.+  .-.-|||.|.+.+++....+.++|..+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4689999999999999999999988776666554433222  2367999999999999999999999864

>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=97.74  E-value=7.1e-05  Score=49.31  Aligned_cols=54  Identities=20%  Similarity=0.270  Sum_probs=47.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN  121 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~  121 (192)
                      +.+++ +.|..+...||.++|++||. ..|+++-|.       -|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            55667 99999999999999999994 478888884       79999999999999999774

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=97.26  E-value=6.4e-05  Score=49.54  Aligned_cols=36  Identities=17%  Similarity=0.320  Sum_probs=27.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCC--hhHHHhhhccc
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETST--RNEIREYESME   42 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~--~~~~~~~~~~~   42 (192)
                      .+.+|.+++|+.|++ +||||||+|.  .++..+...++
T Consensus        37 ~v~~v~i~~d~~tg~-srG~aFV~f~~~~~A~~Ai~~ln   74 (95)
T 2lkz_A           37 AVNNIRLIKDKQTQQ-NRGFAFVQLSSAMDASQLLQILQ   74 (95)
T ss_dssp             CGGGEECCCCSSSSS-CSSEEEEECSSSHHHHHHHHHHH
T ss_pred             cEEEEEEEecCCCCC-CceEeEEEECCHHHHHHHHHHhc
Confidence            456899999999996 9999999993  33444444443

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.23  E-value=0.0019  Score=44.10  Aligned_cols=70  Identities=19%  Similarity=0.271  Sum_probs=56.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC-eEEEEEec
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG-QTVTVDWC  135 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g-~~l~v~~a  135 (192)
                      .+-|.|-+.|... ...+.+.|++||.|.+....    ++  ..+-.|.|.++.+|++||.. ||..+.| -.|-|...
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEEC
Confidence            4568888999985 56677889999999987752    12  35899999999999999985 9999985 67777764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.91  E-value=0.0029  Score=41.59  Aligned_cols=78  Identities=10%  Similarity=0.218  Sum_probs=53.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHHHhCCCeeCC-----eEE
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGF--LKGYALVEYDSYKEASAARDALNGTTILG-----QTV  130 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~--~~g~afV~f~~~~~a~~al~~l~~~~~~g-----~~l  130 (192)
                      +-+|.|+.||+.+|++++.+.++..-.+..........+.+  .-.-|||.|.+.++.....+..+|..+.+     .+-
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            34699999999999999998888754432222111111111  12468999999999999999999988643     244


Q ss_pred             EEEec
Q psy15152        131 TVDWC  135 (192)
Q Consensus       131 ~v~~a  135 (192)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56665

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=96.79  E-value=0.00025  Score=46.10  Aligned_cols=28  Identities=14%  Similarity=0.316  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.++. +||||||+|...+
T Consensus        28 ~v~~v~i~~d~~t~~-~rg~aFV~F~~~~   55 (91)
T 2lxi_A           28 QAREVRLMRNKSSGQ-SRGFAFVEFSHLQ   55 (91)
T ss_dssp             CCSBCCSSSCSSSCC-CSSEEEEECSSHH
T ss_pred             EeEEEEEEecCCCCC-cCceEEEEecCHH
Confidence            356889999999995 9999999994433

>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=96.76  E-value=0.0016  Score=46.32  Aligned_cols=36  Identities=19%  Similarity=0.105  Sum_probs=29.9

Q ss_pred             EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCe
Q psy15152         87 NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTT  124 (192)
Q Consensus        87 ~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~  124 (192)
                      .+.+.++.  .+++|||||+|.+.++|++|++.+++..
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            45677774  4689999999999999999999887654

>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=96.69  E-value=0.0013  Score=46.46  Aligned_cols=42  Identities=21%  Similarity=0.047  Sum_probs=37.9

Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCeEEEEEecccC
Q psy15152         96 TGFLKGYALVEYDSYKEASAARDAL-NGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        96 tg~~~g~afV~f~~~~~a~~al~~l-~~~~~~g~~l~v~~a~~~  138 (192)
                      ..+.+|+++|+|.+.++|++|++.| ||..++| .+.+.++...
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            4567899999999999999999999 9999999 9999988653

>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=96.64  E-value=0.0004  Score=44.80  Aligned_cols=27  Identities=15%  Similarity=0.266  Sum_probs=22.6

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      .+.++.+++|+.+++ +||||||+|...
T Consensus        29 ~v~~v~i~~~~~~g~-~kG~afV~f~~~   55 (90)
T 3p5t_L           29 DILEIKFFENRANGQ-SKGFALVGVGSE   55 (90)
T ss_dssp             CCCCEEEEECTTTCC-EEEEEEECC-CH
T ss_pred             ceEEEEEEecCCCCc-cCcEEEEEECCH
Confidence            467899999999995 999999999433

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.63  E-value=0.0028  Score=43.93  Aligned_cols=76  Identities=20%  Similarity=0.169  Sum_probs=54.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeE-EEEeec------------CCCC-CcceEEEEEecCHHHHHHHHHHhCCCe
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKN-LHLNLD------------RRTG-FLKGYALVEYDSYKEASAARDALNGTT  124 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~-~~i~~~------------~~tg-~~~g~afV~f~~~~~a~~al~~l~~~~  124 (192)
                      .-|.|-+.|++... .+.+.|++||.|.+ .....+            +..+ ....+-.|.|++..+|.+||.. ||..
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            34667788887654 46677999999865 211110            0000 1245889999999999999985 9999


Q ss_pred             eCCeEEEEEecc
Q psy15152        125 ILGQTVTVDWCF  136 (192)
Q Consensus       125 ~~g~~l~v~~a~  136 (192)
                      +.|..|-|.+..
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988888764

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=96.58  E-value=0.00041  Score=46.81  Aligned_cols=28  Identities=14%  Similarity=0.094  Sum_probs=23.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+.|++ +||||||+|...+.
T Consensus        33 i~~v~i~~d~~tg~-~rG~aFV~f~~~~~   60 (110)
T 3s8s_A           33 VEEVEILLHPRTRK-HLGLARVLFTSTRG   60 (110)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESSHHH
T ss_pred             eeEEEEEECCCCCc-eeeEEEEEECCHHH
Confidence            57899999999995 99999999944443

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=96.43  E-value=0.00055  Score=45.18  Aligned_cols=27  Identities=15%  Similarity=0.097  Sum_probs=23.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.|++ +||||||+|...+
T Consensus        39 i~~v~i~~d~~tg~-~kG~afV~f~~~~   65 (100)
T 3ns6_A           39 VVNMEFPIDEATGK-TKGFLFVECGSMN   65 (100)
T ss_dssp             EEEEECCEETTTTE-ECSEEEEEESSHH
T ss_pred             EeEEEEEEcCCCCc-cceEEEEEECCHH
Confidence            56899999999996 9999999994443

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=96.43  E-value=0.00079  Score=44.26  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=15.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCCh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      +.+|.+++|      ++|||||+|..
T Consensus        27 i~~v~i~~~------~~g~afV~f~~   46 (101)
T 2hvz_A           27 LRTVWIARN------PPGFAFVEFED   46 (101)
T ss_dssp             CSEEEEESS------SSSEEEEECSS
T ss_pred             eEEEEEeeC------CCCEEEEEECC
Confidence            456777776      78999999933

>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=96.37  E-value=0.00067  Score=44.78  Aligned_cols=28  Identities=11%  Similarity=0.270  Sum_probs=23.4

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ +||||||+|...+
T Consensus        45 ~I~~v~i~~d~~tg~-~kG~afV~f~~~~   72 (99)
T 4fxv_A           45 EVESAKLIRDKVAGH-SLGYGFVNYVTAK   72 (99)
T ss_dssp             CEEEEEEEECSSSCC-EEEEEEEEESSHH
T ss_pred             CEEEeEeeecCCCCc-ccccEEEEECCHH
Confidence            367899999999996 9999999994443

>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=96.24  E-value=0.0011  Score=44.53  Aligned_cols=64  Identities=13%  Similarity=0.076  Sum_probs=39.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH--HhhhcccCCCCCCCCCCCCCCCCcEEEE---------cCCCCCCcHHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI--REYESMETDVGDEEPGPQRSVEGWILFV---------TGVHEEAQEDDM   75 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~l~V---------~nLp~~~t~~~L   75 (192)
                      +.++.+++|   + +++|||||+|...+.  .+...++...  ..        +..|.|         .+++...++++|
T Consensus        35 v~~v~i~~~---~-~~~g~afV~f~~~~~A~~A~~~l~g~~--~~--------g~~l~v~~a~~~~~~~~~~~~~~~~~l  100 (115)
T 3lqv_A           35 IRQIRVGNT---P-ETRGTAYVVYEDIFDAKNAVDHLSGFN--VS--------NRYLVVLYYNANRAFQKMDTKKKEEQL  100 (115)
T ss_dssp             EEEEEEECS---T-TTTTCEEEEESSHHHHHHHHHHHTTCB--SS--------SCBCEEEECCHHHHTTTSCHHHHHHHH
T ss_pred             eEEEEEeeC---C-CCCcEEEEEECCHHHHHHHHHHcCCCE--EC--------CeEEEEEEecCChhhhhhhHhHhHHHH
Confidence            456777765   3 369999999944433  3333332221  11        111222         467777889999


Q ss_pred             HHhhccCCC
Q psy15152         76 HEKFSEYGE   84 (192)
Q Consensus        76 ~~~F~~~G~   84 (192)
                      .++|++||-
T Consensus       101 ~~~~~~~g~  109 (115)
T 3lqv_A          101 KLLKEKYGI  109 (115)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHHHHhCC
Confidence            999999984

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=96.22  E-value=0.0011  Score=47.66  Aligned_cols=29  Identities=7%  Similarity=0.204  Sum_probs=24.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.+++ +||||||+|...+.
T Consensus        83 ~v~~v~i~~d~~tg~-skGfaFV~f~~~~~  111 (156)
T 3n9u_C           83 DVVELKFAENRANGQ-SKGYAEVVVASENS  111 (156)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESCHHH
T ss_pred             cEEEEEEEecCCCCc-cceEEEEEECCHHH
Confidence            578999999999996 99999999944443

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.21  E-value=0.0025  Score=53.58  Aligned_cols=56  Identities=20%  Similarity=0.339  Sum_probs=41.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA  119 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~  119 (192)
                      .+.|+|. .|...++.+|.++|++||.|.++.+-.+.  |   -||.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhc
Confidence            3679997 79999999999999999999998765442  2   6999999999999977653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=96.04  E-value=0.0014  Score=45.30  Aligned_cols=32  Identities=16%  Similarity=0.242  Sum_probs=23.9

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChh-HHHhhhcc
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRN-EIREYESM   41 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~-~~~~~~~~   41 (192)
                      +|.+++|+.+++ +||||||+|... +..++..+
T Consensus        54 ~v~i~~d~~tg~-~rG~aFV~f~~~~a~~Ai~~l   86 (131)
T 2m2b_A           54 NVRVIKDKQTQL-NRGFAFIQLSTIEAAQLLQIL   86 (131)
T ss_dssp             TEECCBCSSSSS-BCSCEEEECCHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCC-cceEEEEEECCHHHHHHHHHh
Confidence            489999999996 999999999444 33333433

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.01  E-value=0.0038  Score=38.51  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      +.++.+++|+.+++ +||||||+|.
T Consensus        27 v~~v~i~~~~~~~~-~~g~afV~f~   50 (77)
T 1uaw_A           27 VKECLVMRDPLTKR-SRGFGFVTFM   50 (77)
T ss_dssp             CCCEEEECCCCSSS-CSSEEEECCC
T ss_pred             EEEEEEecCCCCCC-cCceEEEEEc
Confidence            56889999999995 9999999993

>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=95.93  E-value=0.0031  Score=42.26  Aligned_cols=27  Identities=19%  Similarity=0.307  Sum_probs=21.8

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+ +++ +||||||+|...+
T Consensus        51 ~i~~~~i~~~~-~g~-~~g~afV~f~~~~   77 (114)
T 1x5o_A           51 QVISTRILRDS-SGT-SRGVGFARMESTE   77 (114)
T ss_dssp             CEEEEEEEECS-SSC-EEEEEEEEESCHH
T ss_pred             CEEEEEEEECC-CCC-cceEEEEEECCHH
Confidence            36789999998 885 9999999994444

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=95.89  E-value=0.0036  Score=41.83  Aligned_cols=28  Identities=25%  Similarity=0.395  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        51 ~i~~v~i~~~~~tg~-~kg~afV~f~~~~   78 (109)
T 2rs2_A           51 EVKECLVMRDPLTKR-SRGFGFVTFMDQA   78 (109)
T ss_dssp             CEEEEEECCCTTTCC-CTTCEEEEESSHH
T ss_pred             CeEEEEEEECCCCCC-cCcEEEEEECCHH
Confidence            356899999999996 9999999994443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.83  E-value=0.0038  Score=41.41  Aligned_cols=26  Identities=15%  Similarity=-0.087  Sum_probs=21.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+. ++ +||||||+|...+
T Consensus        38 v~~v~i~~d~~-g~-~rG~aFV~F~~~e   63 (103)
T 1s79_A           38 VLNIQMRRTLH-KA-FKGSIFVVFDSIE   63 (103)
T ss_dssp             EEEEEEECCCT-TS-CCCEEEEEESSHH
T ss_pred             EEEEEEEECCC-CC-CccEEEEEECCHH
Confidence            57899999988 75 9999999994444

>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=95.82  E-value=0.0041  Score=39.74  Aligned_cols=27  Identities=19%  Similarity=0.358  Sum_probs=22.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ ++|||||+|...+
T Consensus        28 i~~v~i~~~~~~~~-~~g~afV~f~~~~   54 (90)
T 2ki2_A           28 VFNVKLIYDRETKK-PKGFGFVEMQEES   54 (90)
T ss_dssp             CSEEEECCCSSSCC-CCEEEEEEECTTH
T ss_pred             EEEEEEEEcCCCCC-cceEEEEEECCHH
Confidence            56889999999995 9999999994444

>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=95.73  E-value=0.0031  Score=48.08  Aligned_cols=28  Identities=14%  Similarity=0.256  Sum_probs=23.8

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        96 ~v~~v~i~~d~~tg~-skGfaFV~f~~~~  123 (229)
T 3q2s_C           96 DILEIKFFENRANGQ-SKGFALVGVGSEA  123 (229)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESCTT
T ss_pred             ceEEEEEEecCCCCc-cceEEEEEECCHH
Confidence            578999999999996 9999999994433

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=95.71  E-value=0.0033  Score=41.35  Aligned_cols=28  Identities=14%  Similarity=0.274  Sum_probs=23.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        40 gi~~v~i~~~~~~g~-~~g~afV~f~~~~   67 (103)
T 2dng_A           40 SIRSVRLVRDKDTDK-FKGFCYVEFDEVD   67 (103)
T ss_dssp             CEEEEEEEECSSSCS-EEEEEEEEESSHH
T ss_pred             CceEEEEeecCCCCc-cceEEEEEECCHH
Confidence            477899999999996 9999999994444

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.70  E-value=0.0051  Score=38.80  Aligned_cols=28  Identities=14%  Similarity=0.297  Sum_probs=22.9

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.++.|+.+++ +||||||+|...+
T Consensus        31 ~i~~~~i~~~~~~~~-~~g~afV~f~~~~   58 (85)
T 1x4e_A           31 KIVSTKAILDKTTNK-CKGYGFVDFDSPS   58 (85)
T ss_dssp             CEEEEEEECCSSSCS-CCSEEEEEESCHH
T ss_pred             CeEEEEEEecCCCCC-cCcEEEEEECCHH
Confidence            356889999999996 9999999994333

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=95.64  E-value=0.004  Score=41.56  Aligned_cols=29  Identities=7%  Similarity=-0.223  Sum_probs=22.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+.+..++|||+||+|...+.
T Consensus        40 V~~v~i~~~~~~~~~~~G~~FV~f~~~~~   68 (105)
T 2pe8_A           40 VGKCVIFEIPGAPDDEAVRIFLEFERVES   68 (105)
T ss_dssp             EEEEEEEECSSCCTTTSEEEEEEESSHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEECCHHH
Confidence            56889999987633599999999954443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=95.64  E-value=0.0038  Score=38.42  Aligned_cols=28  Identities=25%  Similarity=0.411  Sum_probs=22.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|+.+++ +||||||+|...+.
T Consensus        26 i~~v~i~~~~~~~~-~~g~afV~f~~~~~   53 (75)
T 2mss_A           26 VDDAMLMFDKTTNR-HRGFGFVTFESEDI   53 (75)
T ss_dssp             CSEECCCBCSSSTT-SCBEEEEECSCHHH
T ss_pred             EEEEEEEecCCCCC-cCcEEEEEECCHHH
Confidence            45788899999995 99999999944443

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.61  E-value=0.0051  Score=40.05  Aligned_cols=28  Identities=18%  Similarity=0.368  Sum_probs=23.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +|||+||+|...+
T Consensus        36 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   63 (99)
T 2dgs_A           36 VVTEVVMIYDAEKQR-PRGFGFITFEDEQ   63 (99)
T ss_dssp             CEEEEEECCCTTTCS-CCSEEEEEESSHH
T ss_pred             CeEEEEEEeCCCCCC-CCceEEEEECCHH
Confidence            356899999999995 9999999994333

>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=95.58  E-value=0.0033  Score=38.65  Aligned_cols=26  Identities=23%  Similarity=0.257  Sum_probs=21.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      +.++.+++|+.+++ ++|||||+|...
T Consensus        26 i~~v~i~~~~~~~~-~~g~afV~f~~~   51 (75)
T 1iqt_A           26 VESIELPMDNKTNK-RRGFCFITFKEE   51 (75)
T ss_dssp             CSEECCCCSCCCSS-SCCCEEEECSSS
T ss_pred             eEEEEEEecCCCCC-cCCEEEEEECCH
Confidence            45788899999995 999999999433

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.53  E-value=0.0053  Score=41.23  Aligned_cols=27  Identities=19%  Similarity=0.298  Sum_probs=21.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+. ++ +||||||+|...+
T Consensus        41 ~v~~v~i~~d~~-g~-~~G~afV~F~~~~   67 (109)
T 2dnn_A           41 RVDAVHLLKDHV-GR-NNGNGLVKFLSPQ   67 (109)
T ss_dssp             CCCEEEECCCTT-CC-CCSEEEEECSSHH
T ss_pred             CeeEEEEEECCC-CC-CCeEEEEEECCHH
Confidence            467899999986 75 9999999994444

>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=95.49  E-value=0.0069  Score=38.43  Aligned_cols=28  Identities=18%  Similarity=0.241  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ ++|||||+|...+
T Consensus        32 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   59 (89)
T 3ucg_A           32 SVNRVTILCDKFSGH-PKGFAYIEFSDKE   59 (89)
T ss_dssp             CEEEEEEEESCSSSS-CCEEEEEEESSTH
T ss_pred             CEEEEEEEecCCCCC-cceEEEEEECCHH
Confidence            356899999999995 9999999994443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.47  E-value=0.004  Score=40.56  Aligned_cols=25  Identities=4%  Similarity=0.042  Sum_probs=21.5

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      ++.+++|+.+++ ++||+||+|...+
T Consensus        39 ~v~i~~~~~~g~-~~g~afV~f~~~~   63 (99)
T 2div_A           39 SVKIIRNRLTGI-PAGYCFVEFADLA   63 (99)
T ss_dssp             EEEEEECSSSCC-EEEEEEEECSCHH
T ss_pred             EEEEeecCCCCC-cCCEEEEEeCCHH
Confidence            889999999995 9999999994444

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=95.45  E-value=0.0078  Score=40.49  Aligned_cols=24  Identities=13%  Similarity=0.140  Sum_probs=21.4

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCC
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETS   30 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f   30 (192)
                      .+.+|.+++|+.+++ +|||+||+|
T Consensus        66 ~i~~~~i~~~~~~g~-~~g~afV~f   89 (118)
T 2khc_A           66 NVISAKVFIDKQTSL-SKCFGFVSF   89 (118)
T ss_dssp             EEEEEEECCCSSSSC-CCCEEEEEE
T ss_pred             CEEEEEEEeCCCCCC-cCcEEEEEE
Confidence            367899999999995 999999999

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.41  E-value=0.008  Score=40.35  Aligned_cols=29  Identities=17%  Similarity=0.351  Sum_probs=23.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.+++ +|||+||+|...+.
T Consensus        43 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~~   71 (116)
T 2cqd_A           43 DIEEAVVITDRQTGK-SRGYGFVTMADRAA   71 (116)
T ss_dssp             CEEEEEESCCSSSCC-CCSEEEEEESSHHH
T ss_pred             CeeEEEEEEcCCCCc-cceEEEEEECCHHH
Confidence            367899999999995 99999999944443

>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=95.40  E-value=0.0036  Score=41.33  Aligned_cols=27  Identities=19%  Similarity=0.198  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++ +||||||+|...+
T Consensus        40 i~~v~i~~~~~~g~-~~g~afV~f~~~~   66 (106)
T 2dgp_A           40 IYELTVLKDRFTGM-HKGCAFLTYCERE   66 (106)
T ss_dssp             CCEEECCCCSSSCS-CCSEEEEEESSHH
T ss_pred             eeEEEEEecCCCCC-cceEEEEEECCHH
Confidence            56889999999995 9999999994443

>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=95.39  E-value=0.0039  Score=40.45  Aligned_cols=27  Identities=7%  Similarity=0.140  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ ++|||||+|...+
T Consensus        29 i~~v~i~~~~~~g~-~~g~afV~f~~~~   55 (96)
T 2x1f_A           29 VINLKMMFDPQTGR-SKGYAFIEFRDLE   55 (96)
T ss_dssp             EEEEECCBCTTTCC-BCSEEEEEESSHH
T ss_pred             EEEEEEEeCCCCCc-cceEEEEEECCHH
Confidence            56889999999995 9999999994444

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.39  E-value=0.0057  Score=40.14  Aligned_cols=25  Identities=24%  Similarity=0.255  Sum_probs=21.8

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      .+.+|.+++|+.+++ ++|||||+|.
T Consensus        39 ~i~~v~i~~~~~~~~-~~g~afV~f~   63 (103)
T 2dnm_A           39 RVGDVYIPREPHTKA-PRGFAFVRFH   63 (103)
T ss_dssp             CEEEEECCBCSSSCS-BCSCEEEEES
T ss_pred             CEEEEEEEeCCCCCC-CCeEEEEEEC
Confidence            357899999999995 9999999993

>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=95.36  E-value=0.005  Score=42.53  Aligned_cols=22  Identities=18%  Similarity=0.021  Sum_probs=19.2

Q ss_pred             eeEEeeccCcCCCCCCccCCCCCh
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      +|.+++|+. ++ +||||||+|..
T Consensus        72 ~v~i~~d~~-Gr-srGfaFV~F~~   93 (126)
T 2hgm_A           72 GITLPVDPE-GK-ITGEAFVQFAS   93 (126)
T ss_dssp             EEECCCCSS-SS-SCSEEEEEESS
T ss_pred             EEEEEECCC-CC-CceEEEEEECC
Confidence            899999988 75 99999999933

>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=95.35  E-value=0.0054  Score=39.90  Aligned_cols=28  Identities=25%  Similarity=0.189  Sum_probs=23.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++||+||+|...+
T Consensus        34 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   61 (99)
T 1whw_A           34 PLSELHYPIDSLTKK-PKGFAFVTFMFPE   61 (99)
T ss_dssp             CEEEEECCCCTTTCC-CCSEEEEEESSHH
T ss_pred             CEeEEEEEecCCCCC-cCeEEEEEECCHH
Confidence            356899999999995 9999999994444

>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=95.33  E-value=0.0061  Score=40.80  Aligned_cols=27  Identities=4%  Similarity=0.276  Sum_probs=22.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      .+.+|.+++|+.+++ +||||||+|...
T Consensus        51 ~i~~v~i~~~~~~g~-~~g~afV~f~~~   77 (114)
T 2cq4_A           51 KVRDVRIISDRNSRR-SKGIAYVEFCEI   77 (114)
T ss_dssp             CEEEEEECCSCCSSS-CCCCEEEEESCG
T ss_pred             CEeEEEEEecCCCCc-cCcEEEEEeCcH
Confidence            367899999999995 999999999433

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.32  E-value=0.0089  Score=38.45  Aligned_cols=28  Identities=21%  Similarity=0.478  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++||+||+|...+
T Consensus        31 ~v~~v~i~~~~~~~~-~~g~afV~f~~~~   58 (95)
T 2dnz_A           31 KIDNIVLMKDSDTGR-SKGYGFITFSDSE   58 (95)
T ss_dssp             CEEEEEEECCSSSCC-CCSEEEEEESCHH
T ss_pred             CEeEEEEeecCCCCc-eeeEEEEEECCHH
Confidence            367899999999995 9999999994443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.32  E-value=0.0064  Score=39.24  Aligned_cols=28  Identities=4%  Similarity=0.126  Sum_probs=22.4

Q ss_pred             eeee-EEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGI-ARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v-~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++ .+++|+.++. ++|||||+|...+.
T Consensus        32 i~~~~~i~~~~~~g~-~~g~afV~f~~~~~   60 (96)
T 1x5t_A           32 ILQTPKIMRDPDTGN-SKGYAFINFASFDA   60 (96)
T ss_dssp             BSSCCEECCCTTTCS-CCSEEEEEBSSHHH
T ss_pred             eeEEEEEEEcCCCCC-cCeEEEEEECCHHH
Confidence            4567 8999999996 99999999944443

>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=95.31  E-value=0.0042  Score=39.42  Aligned_cols=28  Identities=14%  Similarity=0.159  Sum_probs=23.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ ++|||||+|...+
T Consensus        37 ~i~~v~i~~~~~~g~-~~g~afV~f~~~~   64 (87)
T 3s7r_A           37 EVVDCTIKMDPNTGR-SRGFGFILFKDAA   64 (87)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSTH
T ss_pred             CEEEEEEeecCCCCc-cccEEEEEECCHH
Confidence            357899999999995 9999999994333

>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=95.31  E-value=0.0059  Score=40.15  Aligned_cols=28  Identities=14%  Similarity=0.210  Sum_probs=23.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +|||+||+|...+
T Consensus        41 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   68 (105)
T 1x5u_A           41 PVVNTHMPKDRVTGQ-HQGYGFVEFLSEE   68 (105)
T ss_dssp             CEEEEECCBCSSSCS-BCSCEEEEESSHH
T ss_pred             CeEEEEEEecCCCCc-CCcEEEEEECCHH
Confidence            356889999999995 9999999994444

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.26  E-value=0.0051  Score=40.23  Aligned_cols=28  Identities=21%  Similarity=0.191  Sum_probs=22.8

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++||+||+|...+
T Consensus        38 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   65 (102)
T 2cqb_A           38 DITDIQIPLDYETEK-HRGFAFVEFELAE   65 (102)
T ss_dssp             CCCCEECCCCSSSCC-CSSEEEECCSSHH
T ss_pred             CEEEEEEEecCCCCC-cceEEEEEECCHH
Confidence            356889999999995 9999999994433

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.26  E-value=0.0081  Score=38.58  Aligned_cols=28  Identities=14%  Similarity=0.281  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++||+||+|...+
T Consensus        42 ~v~~v~i~~~~~~~~-~~g~afV~f~~~~   69 (94)
T 2e5h_A           42 KVVKVTIMKDKDTRK-SKGVAFILFLDKD   69 (94)
T ss_dssp             CEEEEEECCCSSSCC-CTTCEEEEESCHH
T ss_pred             CeEEEEEEeCCCCCC-cccEEEEEECCHH
Confidence            356899999999995 9999999994444

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.24  E-value=0.0082  Score=40.29  Aligned_cols=27  Identities=30%  Similarity=0.457  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++ +||||||+|...+
T Consensus        54 i~~v~i~~~~~~g~-~~g~afV~f~~~~   80 (116)
T 1x4b_A           54 LTDCVVMRDPASKR-SRGFGFVTFSSMA   80 (116)
T ss_dssp             CSEEEEECCTTTSS-CCSEEEEECSSHH
T ss_pred             EEEEEEEECCCCCC-cCceEEEEeCCHH
Confidence            56889999999996 9999999994444

>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=95.23  E-value=0.007  Score=39.62  Aligned_cols=27  Identities=15%  Similarity=0.283  Sum_probs=21.9

Q ss_pred             eeeeEEeecc-CcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEK-ARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~-~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ .+++ +||||||+|...+
T Consensus        45 i~~v~i~~~~~~~g~-~~g~afV~f~~~~   72 (100)
T 2j76_E           45 ISAVRLPREPSNPER-LKGFGYAEFEDLD   72 (100)
T ss_dssp             EEEEECSCCTTTTCC-CCSCEEEEECCHH
T ss_pred             CeEEEEEecCCcCCc-cCeEEEEEECCHH
Confidence            6788999998 5785 9999999994433

>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=95.22  E-value=0.0065  Score=40.82  Aligned_cols=26  Identities=12%  Similarity=0.146  Sum_probs=20.9

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+|.+++|+ +++ +||||||+|...+.
T Consensus        44 ~~v~i~~d~-~g~-~~G~afV~F~~~~~   69 (114)
T 2cpy_A           44 NAVHVLVDN-NGQ-GLGQALVQFKNEDD   69 (114)
T ss_dssp             TTEEECCCT-TSS-CSSCEEEECSSHHH
T ss_pred             CeEEEEECC-CCC-cceEEEEEECCHHH
Confidence            458899999 885 99999999954443

>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=95.19  E-value=0.0039  Score=39.44  Aligned_cols=27  Identities=19%  Similarity=0.259  Sum_probs=22.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ ++|||||+|...+
T Consensus        33 i~~v~i~~~~~~~~-~~g~afV~f~~~~   59 (87)
T 3bs9_A           33 ISDARVVKDMATGK-SKGYGFVSFFNKW   59 (87)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESSHH
T ss_pred             EeEEEEEecCCCCc-cceEEEEEECCHH
Confidence            57899999999995 9999999994444

>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=95.19  E-value=0.0074  Score=39.69  Aligned_cols=27  Identities=15%  Similarity=0.315  Sum_probs=22.4

Q ss_pred             eeeeEEeeccCc-CCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKAR-KKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~-~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+ ++ ++|||||+|...+
T Consensus        41 i~~v~i~~~~~~~g~-~~g~afV~f~~~~   68 (104)
T 1wi8_A           41 ISAVRLPREPSNPER-LKGFGYAEFEDLD   68 (104)
T ss_dssp             EEEEECCBCSSCTTS-BCSCEEEEESSHH
T ss_pred             ceEEEEecCCCCCCC-cCeEEEEEECCHH
Confidence            678999999998 74 9999999994443

>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=95.16  E-value=0.0067  Score=40.28  Aligned_cols=27  Identities=15%  Similarity=0.155  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++ ++|||||+|...+
T Consensus        42 i~~v~i~~~~~~g~-~~g~afV~f~~~~   68 (111)
T 1x4h_A           42 LKYVRVVLHPDTEH-SKGCAFAQFMTQE   68 (111)
T ss_dssp             EEEEECCBCSSSCC-BCSEEEEEESSHH
T ss_pred             eEEEEEEecCCCCC-CccEEEEEECCHH
Confidence            57899999999995 9999999994333

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=95.10  E-value=0.0044  Score=40.87  Aligned_cols=28  Identities=11%  Similarity=0.089  Sum_probs=23.3

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++|||||+|...+
T Consensus        49 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   76 (106)
T 1p27_B           49 EIKNIHLNLDRRTGY-LKGYTLVEYETYK   76 (106)
T ss_dssp             CEEEEEEEECTTTSS-EEEEEEEEESCHH
T ss_pred             CeEEEEEEecCCCCc-eeeEEEEEECCHH
Confidence            357899999999995 9999999994443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=95.09  E-value=0.0037  Score=43.51  Aligned_cols=24  Identities=0%  Similarity=-0.143  Sum_probs=22.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      +.++.++.|+.|++ +||||||+|.
T Consensus        33 V~~~~li~Dp~Tg~-slGfgfVef~   56 (136)
T 2j8a_A           33 ISHFEAFNDPNSAL-PLHVYLIKYA   56 (136)
T ss_dssp             CSEEEEEECTTTCC-EEEEEEEECC
T ss_pred             eEEEEEEecCCCCc-eeeEEEEEEC
Confidence            56899999999997 9999999996

>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=95.09  E-value=0.0042  Score=38.91  Aligned_cols=27  Identities=15%  Similarity=0.174  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ ++|||||+|...+
T Consensus        28 i~~~~i~~~~~~~~-~~g~afV~f~~~~   54 (83)
T 3md1_A           28 YLSGHVMWDMQTGS-SRGYGFVSFTSQD   54 (83)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESCHH
T ss_pred             eeEEEEEEcCCCCC-ccceEEEEECCHH
Confidence            56889999999995 9999999994444

>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=95.09  E-value=0.0051  Score=40.63  Aligned_cols=25  Identities=4%  Similarity=-0.174  Sum_probs=20.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      +.+|.+++|+ +++ +|||+||+|...
T Consensus        41 ~~~v~i~~d~-~g~-~~G~afV~F~~~   65 (102)
T 1wez_A           41 PMRVHIEIGP-DGR-VTGEADVEFATH   65 (102)
T ss_dssp             CSEEEEEESS-SSC-EEEEEEEECSSS
T ss_pred             ceEEEEEECC-CCC-EeeEEEEEECCH
Confidence            4589999998 775 999999999433

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.09  E-value=0.0075  Score=39.43  Aligned_cols=27  Identities=22%  Similarity=0.479  Sum_probs=22.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++ ++||+||+|...+
T Consensus        39 i~~v~i~~~~~~~~-~~g~afV~f~~~~   65 (102)
T 1x5s_A           39 ISEVVVVKDRETQR-SRGFGFVTFENID   65 (102)
T ss_dssp             CCEEEECCCSSSCS-CCSEEEEECSSHH
T ss_pred             eEEEEEEeCCCCCC-cccEEEEEECCHH
Confidence            56889999999995 9999999994443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=95.08  E-value=0.0045  Score=40.35  Aligned_cols=24  Identities=17%  Similarity=0.113  Sum_probs=20.6

Q ss_pred             eEEeeccCcCCCCCCccCCCCChhH
Q psy15152         10 IARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus        10 v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+++|+.+++ +||||||+|...+
T Consensus        51 v~i~~~~~~g~-~~G~afV~f~~~~   74 (99)
T 2la6_A           51 INLYTDRETGK-LKGEATVSFDDPP   74 (99)
T ss_dssp             EEEEECTTTCS-EEEEEEEEBSSHH
T ss_pred             EEEEecCCCCC-eeeEEEEEECCHH
Confidence            88999999996 9999999994444

>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=95.08  E-value=0.0079  Score=41.50  Aligned_cols=28  Identities=11%  Similarity=0.280  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        72 ~I~~v~i~~d~~tg~-~~G~afV~F~~~~   99 (129)
T 2kxn_B           72 PIADVSIVYDQQSRR-SRGFAFVYFENVD   99 (129)
T ss_dssp             CEEEEEEECCSSSSC-CCCEEEEEESCHH
T ss_pred             CeEEEEEEecCCCCc-cceEEEEEECCHH
Confidence            367899999999995 9999999994433

>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=95.05  E-value=0.0061  Score=39.98  Aligned_cols=28  Identities=21%  Similarity=0.233  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        41 ~i~~v~i~~~~~~g~-~~g~afV~f~~~~   68 (103)
T 2cqg_A           41 EVLMVQVKKDLKTGH-SKGFGFVRFTEYE   68 (103)
T ss_dssp             CEEEEEEEECSSSCS-EEEEEEEEESSHH
T ss_pred             CeEEEEEEecCCCCC-ccceEEEEECCHH
Confidence            356899999999995 9999999994433

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.00  E-value=0.006  Score=40.01  Aligned_cols=28  Identities=25%  Similarity=0.350  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.++. ++||+||+|...+
T Consensus        41 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   68 (103)
T 2cq0_A           41 SISRIYLAKDKTTGQ-SKGFAFISFHRRE   68 (103)
T ss_dssp             CEEEEEEEECSSSCS-EEEEEEEEESSHH
T ss_pred             CeEEEEEeecCCCCc-eeeEEEEEECCHH
Confidence            367899999999995 9999999994444

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=94.92  E-value=0.0097  Score=40.39  Aligned_cols=28  Identities=14%  Similarity=0.182  Sum_probs=23.2

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+.+++ ++|||||+|...+.
T Consensus        63 i~~v~i~~~~~~~~-~~g~afV~f~~~~~   90 (124)
T 2jwn_A           63 INRITILCDKFSGH-PKGYAYIEFAERNS   90 (124)
T ss_dssp             EEEEEEEEECTTSS-CEEEEEEEESSHHH
T ss_pred             EEEEEEEecCCCCC-cccEEEEEECCHHH
Confidence            56899999999996 99999999944443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.89  E-value=0.006  Score=40.17  Aligned_cols=25  Identities=24%  Similarity=0.407  Sum_probs=21.9

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      .+.+|.+++|+.+++ +|||+||+|.
T Consensus        42 ~v~~v~i~~~~~~g~-~~g~afV~f~   66 (105)
T 2dh8_A           42 EVVDCVIMKDKTTNQ-SRGFGFVKFK   66 (105)
T ss_dssp             CEEEEEEEECSSSCC-EEEEEEEEES
T ss_pred             CeEEEEEeeCCCCCC-cceEEEEEEC
Confidence            356899999999995 9999999993

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.87  E-value=0.0061  Score=40.01  Aligned_cols=26  Identities=15%  Similarity=0.216  Sum_probs=21.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ +++ +||||||+|...+
T Consensus        37 v~~v~i~~~~-~g~-~~g~afV~f~~~~   62 (104)
T 2dhg_A           37 CRGGKVVLDQ-TGV-SKGYGFVKFTDEL   62 (104)
T ss_dssp             EEEEEEEECT-TCC-EEEEEEEEESCHH
T ss_pred             eEEEEEEECC-CCC-ccceEEEEECCHH
Confidence            5689999999 885 9999999994333

>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=94.84  E-value=0.0053  Score=38.63  Aligned_cols=29  Identities=21%  Similarity=0.141  Sum_probs=23.4

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.++.+++|+.+++ ++|||||+|...+.
T Consensus        33 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~~   61 (85)
T 3mdf_A           33 DITDIQIPLDYETEK-HRGFAFVEFELAED   61 (85)
T ss_dssp             CEEEEECCEETTTTE-ECSEEEEEESSHHH
T ss_pred             CEEEEEEEECCCCCc-cccEEEEEECCHHH
Confidence            356889999999996 99999999944443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=94.78  E-value=0.0071  Score=40.49  Aligned_cols=28  Identities=21%  Similarity=0.305  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++|||||+|...+
T Consensus        41 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   68 (115)
T 2dgo_A           41 RISDARVVKDMATGK-SKGYGFVSFFNKW   68 (115)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHH
T ss_pred             CeEEEEEEEcCCCCC-cceEEEEEECCHH
Confidence            367899999999995 9999999994433

>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=94.77  E-value=0.0075  Score=40.03  Aligned_cols=27  Identities=11%  Similarity=0.183  Sum_probs=22.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.++. ++|||||+|...+
T Consensus        53 i~~v~i~~~~~~~~-~~g~afV~f~~~~   79 (110)
T 1oo0_B           53 IKNIHLNLDRRTGF-SKGYALVEYETHK   79 (110)
T ss_dssp             EEEEECCBCTTTSS-BCSEEEEEESSHH
T ss_pred             EEEEEEEecCCCCC-cceEEEEEECCHH
Confidence            56889999999995 9999999994444

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.75  E-value=0.0064  Score=39.10  Aligned_cols=28  Identities=11%  Similarity=0.280  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +|||+||+|...+
T Consensus        41 ~v~~v~i~~~~~~~~-~~g~afV~f~~~~   68 (95)
T 2cqc_A           41 PIADVSIVYDQQSRR-SRGFAFVYFENVD   68 (95)
T ss_dssp             CEEEEEEEECSSSSS-EEEEEEEEESSHH
T ss_pred             CeeEEEEEEcCCCCC-cccEEEEEECCHH
Confidence            367899999999995 9999999994443

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=94.70  E-value=0.0064  Score=42.19  Aligned_cols=27  Identities=11%  Similarity=0.373  Sum_probs=22.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++ +||||||+|...+
T Consensus        69 i~~v~i~~~~~~~~-~~g~afV~f~~~~   95 (139)
T 1u6f_A           69 IESVKIVCDRETRQ-SRGYGFVKFQSGS   95 (139)
T ss_dssp             EEEEEEEEETTTTE-EEEEEEEEESSHH
T ss_pred             eEEEEEEEcCCCCC-cceEEEEEECCHH
Confidence            57899999999995 9999999994444

>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=94.70  E-value=0.0063  Score=40.79  Aligned_cols=27  Identities=11%  Similarity=0.114  Sum_probs=22.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++ +|||+||+|...+
T Consensus        52 i~~v~i~~~~~~g~-~~g~afV~f~~~~   78 (115)
T 2cpz_A           52 VVSAKVFIDKQTNL-SKCFGFVSYDNPV   78 (115)
T ss_dssp             CSEEEEEECSSSCS-EEEEEEEECSSHH
T ss_pred             eEEEEEEECCCCCC-cCccEEEEECCHH
Confidence            56889999999995 9999999994333

>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=94.67  E-value=0.012  Score=39.61  Aligned_cols=26  Identities=23%  Similarity=0.381  Sum_probs=21.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ ++. ++|||||+|...+
T Consensus        34 i~~v~i~~~~-~g~-~~g~afV~F~~~~   59 (116)
T 2fy1_A           34 ISEVLLIKDR-TSK-SRGFAFITFENPA   59 (116)
T ss_dssp             CSEEEEECST-TTT-CCCEEEEECSSHH
T ss_pred             EEEEEEEECC-CCC-cccEEEEEECCHH
Confidence            5688999998 784 9999999994443

>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=94.65  E-value=0.0062  Score=39.94  Aligned_cols=28  Identities=14%  Similarity=0.255  Sum_probs=23.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|+.+++ ++|||||+|...+.
T Consensus        35 i~~~~i~~~~~~g~-~~g~afV~f~~~~~   62 (104)
T 1p1t_A           35 VVSFRLVYDRETGK-PKGYGFCEYQDQET   62 (104)
T ss_dssp             CSEEEEEEETTTTE-EEEEEEEECSCHHH
T ss_pred             eeEEEEEeCCCCCc-cceEEEEEECCHHH
Confidence            56889999999996 99999999944443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=94.65  E-value=0.024  Score=39.33  Aligned_cols=28  Identities=14%  Similarity=0.192  Sum_probs=23.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+.++. +|||+||+|...+.
T Consensus        74 i~~v~i~~~~~~g~-~~G~afV~F~~~~~  101 (135)
T 2lea_A           74 VGDVYIPRDRYTKE-SRGFAFVRFHDKRD  101 (135)
T ss_dssp             CSEEECCCCSSSSS-CCSCCEEECSCHHH
T ss_pred             EEEEEEEecCCCCc-cceEEEEEECCHHH
Confidence            56888999999995 99999999954443

>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=94.61  E-value=0.0079  Score=39.90  Aligned_cols=27  Identities=22%  Similarity=0.140  Sum_probs=21.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+. ++ +||||||+|...+.
T Consensus        41 v~~v~i~~~~~-g~-~~G~afV~F~~~~~   67 (107)
T 2lmi_A           41 ENGIHFLLNRD-GK-RRGDALIEMESEQD   67 (107)
T ss_dssp             TTTEECCCCTT-ST-TCSEEEEEBSSHHH
T ss_pred             cceEEEEECCC-CC-EeeEEEEEECCHHH
Confidence            46788999988 75 99999999944443

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.58  E-value=0.0081  Score=41.26  Aligned_cols=26  Identities=15%  Similarity=0.011  Sum_probs=20.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ +++ +||||||+|..++
T Consensus        54 v~~v~i~~d~-~gr-~~G~aFV~F~~~~   79 (123)
T 2dha_A           54 KEGILFVTYP-DGR-PTGDAFVLFACEE   79 (123)
T ss_dssp             GGGEEEEECT-TSC-EEEEEEECCSSHH
T ss_pred             cceEEEEECC-CCC-EeeEEEEEECCHH
Confidence            4689999994 785 9999999994444

>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=94.58  E-value=0.022  Score=39.95  Aligned_cols=27  Identities=7%  Similarity=-0.154  Sum_probs=21.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+. ++ +|||+||+|...+.
T Consensus        72 i~~v~i~~d~~-g~-srGfaFV~F~~~e~   98 (139)
T 2hgn_A           72 PVRVHIEIGPD-GR-VTGEADVEFATHEE   98 (139)
T ss_dssp             CSEEECCCSSS-SC-SSCCCEEECSHHHH
T ss_pred             CeEEEEEECCC-CC-CceEEEEEeCCHHH
Confidence            45889999987 74 99999999955544

>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=94.56  E-value=0.0081  Score=39.89  Aligned_cols=27  Identities=11%  Similarity=-0.067  Sum_probs=20.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|.. + ++||||||+|...+.
T Consensus        54 V~~v~i~~~~~-~-~~~G~~fV~f~~~~~   80 (104)
T 1jmt_A           54 VEEMNVCDNLG-D-HLVGNVYVKFRREED   80 (104)
T ss_dssp             EEEEEECCSSS-S-SSEEEEEEEESCHHH
T ss_pred             eEEEEEEeCCC-C-CccEEEEEEECCHHH
Confidence            56788888775 5 499999999944443

>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=94.53  E-value=0.014  Score=38.54  Aligned_cols=28  Identities=14%  Similarity=0.211  Sum_probs=22.1

Q ss_pred             eeeeEEe-eccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARL-KEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~-~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.++ +|+.+++ +||||||+|...+.
T Consensus        36 v~~v~i~~~~~~~g~-~~g~afV~f~~~~~   64 (109)
T 2dis_A           36 VLDVIVYASAADKMK-NRGFAFVEYESHRA   64 (109)
T ss_dssp             EEEEECCSSSCTTTT-TCCEEEEEESSHHH
T ss_pred             ceEEEEEccCCCCCC-cCcEEEEEecCHHH
Confidence            5678888 8888885 99999999944443

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=94.52  E-value=0.0095  Score=41.17  Aligned_cols=29  Identities=21%  Similarity=0.141  Sum_probs=23.4

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.+++ +||||||+|...+.
T Consensus        89 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~~  117 (140)
T 2ku7_A           89 DITDIQIPLDYETEK-HRGFAFVEFELAED  117 (140)
T ss_dssp             CEEEEECCCCTTTCC-CCSEEEEEESCHHH
T ss_pred             CEEEEEEeecCCCCC-cCcEEEEEECCHHH
Confidence            356889999999995 99999999944443

>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=94.49  E-value=0.0064  Score=40.53  Aligned_cols=28  Identities=21%  Similarity=0.456  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ ++|||||+|...+
T Consensus        52 ~i~~v~i~~~~~~g~-~~g~afV~F~~~~   79 (108)
T 2jrs_A           52 RIESIQLMMDSETGR-SKGYGFITFSDSE   79 (108)
T ss_dssp             CEEEEEEEEETTTTE-EEEEEEEEESCHH
T ss_pred             CeEEEEEEEcCCCCc-cceEEEEEECCHH
Confidence            356899999999996 9999999994444

>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=94.45  E-value=0.0076  Score=42.16  Aligned_cols=27  Identities=7%  Similarity=0.042  Sum_probs=21.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+. ++ +||||||+|...+.
T Consensus        74 v~~v~i~~d~~-g~-srG~aFV~F~~~e~  100 (136)
T 2hgl_A           74 AAGVHFIYTRE-GR-QSGEAFVELGSEDD  100 (136)
T ss_dssp             STTEEEEECSS-SC-EEEEEEEECSSHHH
T ss_pred             eeEEEEEECCC-CC-CCeEEEEEECCHHH
Confidence            56899999998 75 99999999954443

>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=94.43  E-value=0.014  Score=38.47  Aligned_cols=24  Identities=13%  Similarity=0.080  Sum_probs=18.9

Q ss_pred             eEEeeccCcCCCCCCccCCCCChhHH
Q psy15152         10 IARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus        10 v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      |.+++| .+++ ++|||||+|...+.
T Consensus        46 v~i~~~-~~g~-~~G~afV~F~~~~~   69 (104)
T 1wg5_A           46 MTLPVD-FQGR-STGEAFVQFASQEI   69 (104)
T ss_dssp             EECCBC-SSSC-BCSEEEEEESSHHH
T ss_pred             EEEEEC-CCCC-cceEEEEEECCHHH
Confidence            778888 7885 99999999944443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=94.39  E-value=0.017  Score=36.05  Aligned_cols=28  Identities=7%  Similarity=-0.084  Sum_probs=18.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIRE   37 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~   37 (192)
                      +.++.++  +.+++ +||||||+|...+.+.
T Consensus        34 i~~v~i~--~~~g~-~~g~afV~f~~~~~A~   61 (81)
T 2krb_A           34 ITNDFYP--EEDGK-TKGYIFLEYASPAHAV   61 (81)
T ss_dssp             EEEEECC--CBTTB-CCCEEEEEESSHHHHH
T ss_pred             eEEEEec--CCCCc-EeEEEEEEECCHHHHH
Confidence            4456655  46774 9999999995444433

>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=94.37  E-value=0.012  Score=40.08  Aligned_cols=28  Identities=11%  Similarity=0.089  Sum_probs=22.9

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.++. ++|||||+|...+
T Consensus        48 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   75 (126)
T 3ex7_B           48 EIKNIHLNLDRRTGY-LKGYTLVEYETYK   75 (126)
T ss_dssp             CEEEEECCBCTTTSS-BCSCEEEEESSHH
T ss_pred             CeEEEEEEecCCCCc-cceEEEEEECCHH
Confidence            356889999999995 9999999994443

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.19  E-value=0.013  Score=39.22  Aligned_cols=24  Identities=4%  Similarity=0.029  Sum_probs=18.4

Q ss_pred             eEEeeccCc---CCCCCCccCCCCChhH
Q psy15152         10 IARLKEKAR---KKKGRGFGTETSTRNE   34 (192)
Q Consensus        10 v~~~~d~~~---~~k~rG~gfv~f~~~~   34 (192)
                      +.++.|+.+   ++ +||||||+|...+
T Consensus        37 ~~~~~~~~~~~~g~-~~G~aFV~f~~~~   63 (114)
T 2dnl_A           37 VDWPHKAESKSYFP-PKGYAFLLFQEES   63 (114)
T ss_dssp             EECTTSSSSCCCSC-TTSEEEECCSSHH
T ss_pred             EEEeecCCCCCCCC-cccEEEEEECCHH
Confidence            677778877   54 9999999994443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.18  E-value=0.012  Score=37.52  Aligned_cols=27  Identities=15%  Similarity=0.170  Sum_probs=21.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++| .+++ ++|||||+|...+
T Consensus        35 ~i~~v~i~~~-~~g~-~~g~afV~f~~~~   61 (91)
T 2dgw_A           35 KPVAIRIVRN-AHGN-KTGYIFVDFSNEE   61 (91)
T ss_dssp             CCSEEEEEEC-TTSC-EEEEEEEECSSHH
T ss_pred             CceEEEEEEC-CCCC-CceEEEEEECCHH
Confidence            4668899999 7775 9999999994444

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=94.17  E-value=0.018  Score=37.88  Aligned_cols=27  Identities=26%  Similarity=0.319  Sum_probs=21.9

Q ss_pred             eeeeEEeec-cCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKE-KARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d-~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++| +.+++ ++||+||+|...+
T Consensus        42 i~~v~i~~~~~~~~~-~~g~afV~f~~~~   69 (107)
T 2cph_A           42 LKTVRLPKKMTGTGA-HRGFGFVDFITKQ   69 (107)
T ss_dssp             EEEEECCCCCSSSCS-SCSEEEEEESSHH
T ss_pred             eEEEEEecCCCCCCC-cCceEEEEECCHH
Confidence            568889999 78885 9999999994333

>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=94.11  E-value=0.0066  Score=38.39  Aligned_cols=29  Identities=14%  Similarity=0.146  Sum_probs=23.2

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|+.++.+++|||||+|...+.
T Consensus        31 i~~~~i~~~~~~~~~~~g~afV~f~~~~~   59 (88)
T 4a8x_A           31 IKMIDMPVERMHPHLSKGYAYVEFENPDE   59 (88)
T ss_dssp             EEEEECCEETTEEEEECSEEEEEESSHHH
T ss_pred             EEEEEEEeCCCCCCCCCcEEEEEEecHHH
Confidence            56888999998875699999999944443

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.08  E-value=0.011  Score=38.58  Aligned_cols=26  Identities=15%  Similarity=0.268  Sum_probs=21.4

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      ..|.+++|+.+++ +||||||+|...+
T Consensus        40 ~~~~~~~~~~~~~-~~g~afV~f~~~~   65 (102)
T 2fc8_A           40 VRARIVTDRETGS-SKGFGFVDFNSEE   65 (102)
T ss_dssp             SEEEEEECSSSCS-EEEEEEEECSSHH
T ss_pred             eEEEEEecCCCCC-cCcEEEEEECCHH
Confidence            4788999999995 9999999994444

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=93.97  E-value=0.011  Score=39.95  Aligned_cols=27  Identities=7%  Similarity=0.091  Sum_probs=21.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++|+. ++ +||||||+|...+.
T Consensus        47 v~~v~i~~~~~-g~-~~G~afV~F~~~~~   73 (118)
T 2db1_A           47 VAGVHFIYTRE-GR-QSGEAFVELESEDD   73 (118)
T ss_dssp             GGGEEEEECSS-SC-EEEEEEEEBSSHHH
T ss_pred             ceeEEEEECCC-CC-CCeEEEEEECCHHH
Confidence            46889999988 74 99999999954443

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=93.89  E-value=0.0089  Score=39.08  Aligned_cols=23  Identities=13%  Similarity=0.348  Sum_probs=20.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      +.++.+++|+ +++ +||||||+|.
T Consensus        36 i~~v~i~~~~-~g~-~~g~afV~f~   58 (102)
T 2xs2_A           36 VKEVKIITDR-TGV-SKGYGFVSFY   58 (102)
T ss_dssp             EEEEEEEECT-TSC-EEEEEEEEES
T ss_pred             eEEEEEEECC-CCC-ccceEEEEEC
Confidence            5689999998 885 9999999993

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.85  E-value=0.014  Score=38.84  Aligned_cols=25  Identities=20%  Similarity=0.070  Sum_probs=21.0

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .|.+++|+.+++ +|||+||+|...+
T Consensus        52 ~v~i~~~~~~g~-~~g~afV~f~~~~   76 (113)
T 2cpe_A           52 MIHIYLDKETGK-PKGDATVSYEDPP   76 (113)
T ss_dssp             SEECCBCTTTCS-BCSEEEEEBSSHH
T ss_pred             CEEEEEeCCCCC-eeeEEEEEECCHH
Confidence            588999999995 9999999994433

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=93.85  E-value=0.017  Score=39.21  Aligned_cols=26  Identities=19%  Similarity=0.123  Sum_probs=21.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ +++ +||||||+|...+
T Consensus        62 v~~v~i~~~~-~g~-~~g~afV~f~~~~   87 (124)
T 2kt5_A           62 LKKAAVDYDR-SGR-SLGTADVHFERRA   87 (124)
T ss_dssp             CSEEEEECCS-SSS-CCSEEEEEESSHH
T ss_pred             eeEEEEEECC-CCC-EeeEEEEEECCHH
Confidence            5688999999 885 9999999994444

>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=93.83  E-value=0.013  Score=38.53  Aligned_cols=26  Identities=8%  Similarity=0.118  Sum_probs=20.9

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ ++ +++|||||+|...+
T Consensus        42 i~~v~i~~~~-~g-~~~g~afV~f~~~~   67 (105)
T 2dnh_A           42 IDECTVLRGP-DG-SSKGCAFVKFSSHT   67 (105)
T ss_dssp             EEEEEEEECS-SS-CEEEEEEEEESSHH
T ss_pred             eEEEEEEECC-CC-CcCcEEEEEeCCHH
Confidence            6788999998 67 49999999994444

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.83  E-value=0.012  Score=38.27  Aligned_cols=26  Identities=12%  Similarity=0.230  Sum_probs=21.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ +++ +||||||+|...+
T Consensus        44 i~~v~i~~~~-~g~-~~g~afV~f~~~~   69 (100)
T 2do4_A           44 VKDLRLVTNR-AGK-PKGLAYVEYENES   69 (100)
T ss_dssp             EEEEEEEECT-TSC-EEEEEEEEESSHH
T ss_pred             eEEEEEEECC-CCC-EEeEEEEEECCHH
Confidence            5688999998 774 9999999994433

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=92.80  E-value=0.012  Score=39.57  Aligned_cols=24  Identities=17%  Similarity=0.113  Sum_probs=20.1

Q ss_pred             eEEeeccCcCCCCCCccCCCCChhH
Q psy15152         10 IARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus        10 v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      |.+++|+.+++ +||||||+|...+
T Consensus        45 v~i~~~~~~g~-~~g~afV~f~~~~   68 (116)
T 2lcw_A           45 INLYTDRETGK-LKGEATVSFDDPP   68 (116)
Confidence            78899999995 9999999994443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=93.57  E-value=0.046  Score=35.27  Aligned_cols=47  Identities=13%  Similarity=0.164  Sum_probs=26.6

Q ss_pred             CCCccCCCCChhHHHhhhcccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHhhc
Q psy15152         22 GRGFGTETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFS   80 (192)
Q Consensus        22 ~rG~gfv~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~   80 (192)
                      +||||||+|..++.+..+...+++        ....+++|.|. .+   ++.++..+|.
T Consensus        42 ~kGfaFVey~~~~eA~~Ai~~Ln~--------~~l~gr~I~V~-~A---~e~~~~~~~~   88 (89)
T 2wbr_A           42 NQGIALCKYTTREEANKAQMALNN--------CVLANTTIFAE-SP---SENEVQSIMQ   88 (89)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTT--------EEETTEEEEEE-CC---CHHHHHHHHC
T ss_pred             CCcEEEEEECCHHHHHHHHHHhcC--------CEECCcEEEEE-EC---CHHHHHHHhh
Confidence            899999999444333333323332        11234556662 22   7777877765

>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=93.51  E-value=0.018  Score=40.72  Aligned_cols=29  Identities=21%  Similarity=0.106  Sum_probs=23.8

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.++. ++||+||+|...+.
T Consensus        65 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~~   93 (156)
T 1h2v_Z           65 DIKKIIMGLDKMKKT-ACGFCFVEYYSRAD   93 (156)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHH
T ss_pred             CeEEEEEEecCCCCc-cceEEEEEECCHHH
Confidence            367899999999995 99999999944443

>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=93.47  E-value=0.021  Score=37.88  Aligned_cols=36  Identities=14%  Similarity=-0.019  Sum_probs=24.2

Q ss_pred             eeeeEEeeccCcC-CCCCCccCCCCChhH--HHhhhccc
Q psy15152          7 LKGIARLKEKARK-KKGRGFGTETSTRNE--IREYESME   42 (192)
Q Consensus         7 ~~~v~~~~d~~~~-~k~rG~gfv~f~~~~--~~~~~~~~   42 (192)
                      +.+|.+++|+.+. .+++||+||+|...+  ..++..++
T Consensus        42 V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~ln   80 (105)
T 3v4m_A           42 VKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT   80 (105)
T ss_dssp             EEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHT
T ss_pred             EEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhC
Confidence            5688888888763 148999999994444  33444443

>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=93.45  E-value=0.025  Score=37.69  Aligned_cols=28  Identities=11%  Similarity=-0.001  Sum_probs=20.8

Q ss_pred             eeeeEEeeccCcCC--CCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKK--KGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~--k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+++  ++||||||+|...+
T Consensus        45 i~~v~i~~~~~~~~~~~~~G~afV~f~~~~   74 (111)
T 2cpi_A           45 IHKVVINNSTSYAGSQGPSASAYVTYIRSE   74 (111)
T ss_dssp             EEEEEEECCSSCCSSSCCCEEEEEEESSHH
T ss_pred             EEEEEEecCCCcCccCCCCeEEEEEECcHH
Confidence            56888898887542  37799999994443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=93.40  E-value=0.014  Score=37.84  Aligned_cols=27  Identities=26%  Similarity=0.258  Sum_probs=21.5

Q ss_pred             eeeeEEeeccC---cCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKA---RKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~---~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.   |++ ++||+||+|...+
T Consensus        32 i~~v~i~~~~~~~gt~~-~~g~afV~f~~~~   61 (98)
T 2cpf_A           32 IKSCTISKKKNKAGVLL-SMGFGFVEYKKPE   61 (98)
T ss_dssp             EEEEEEEEEECTTCCEE-EEEEEEEEESSHH
T ss_pred             eEEEEEEecCCCCCCcC-cccEEEEEECCHH
Confidence            56888999887   665 9999999994444

>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=93.34  E-value=0.022  Score=36.52  Aligned_cols=27  Identities=22%  Similarity=0.294  Sum_probs=21.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+. + ++|||+||+|...+
T Consensus        42 ~i~~v~i~~~~~-g-~~~g~afV~f~~~~   68 (95)
T 2ywk_A           42 PLTKVTICKDRE-G-KPKSFGFVCFKHPE   68 (95)
T ss_dssp             CEEEEEEEECTT-S-CEEEEEEEEESSTH
T ss_pred             CEEEEEEEECCC-C-CCceEEEEEECCHH
Confidence            356889999986 6 49999999994333

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=93.26  E-value=0.031  Score=36.78  Aligned_cols=22  Identities=9%  Similarity=-0.020  Sum_probs=16.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      +.+|.++  +.+++ +||||||+|.
T Consensus        48 v~~v~i~--~~~g~-~~G~afV~f~   69 (105)
T 2nlw_A           48 ITNDFYP--EEDGK-TKGYIFLEYA   69 (105)
T ss_dssp             EEEEECC--CBTTB-SCCEEEEEEC
T ss_pred             EEEEEee--CCCCC-eeeEEEEEEC
Confidence            4466666  46774 9999999993

>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=93.21  E-value=0.018  Score=37.92  Aligned_cols=26  Identities=19%  Similarity=0.156  Sum_probs=21.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+ ++. ++|||||+|...+
T Consensus        56 i~~v~i~~~~-~g~-~~g~afV~f~~~~   81 (107)
T 3ulh_A           56 LKKAAVHYDR-SGR-SLGTADVHFERKA   81 (107)
T ss_dssp             EEEEEEEECT-TSC-EEEEEEEEESSHH
T ss_pred             eEEEEEEECC-CCC-cceEEEEEECCHH
Confidence            5689999999 784 9999999994443

>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=93.15  E-value=0.0098  Score=38.52  Aligned_cols=26  Identities=15%  Similarity=0.092  Sum_probs=20.7

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .++.+++|+.+++ ++||+||+|...+
T Consensus        43 ~~~~~~~~~~~g~-~~g~afV~f~~~~   68 (98)
T 2cqp_A           43 PGSVCLKYNEKGM-PTGEAMVAFESRD   68 (98)
T ss_dssp             TTTCEEEECSSSC-EEEEEEEEESCHH
T ss_pred             cceEEEEECCCCC-eeeEEEEEECCHH
Confidence            3567888999995 9999999994444

>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=93.05  E-value=0.02  Score=40.99  Aligned_cols=28  Identities=11%  Similarity=0.182  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.++. ++|||||+|....
T Consensus        98 ~i~~v~i~~~~~~g~-~~g~afV~f~~~~  125 (165)
T 1rk8_A           98 EIKNIHLNLDRRTGF-SKGYALVEYETHK  125 (165)
T ss_dssp             CEEEEEEEECTTTSS-EEEEEEEEESSHH
T ss_pred             CEEEEEEEecCCCCc-EeeEEEEEECCHH
Confidence            357899999999995 9999999994433

>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=92.97  E-value=0.01  Score=38.17  Aligned_cols=27  Identities=15%  Similarity=0.123  Sum_probs=21.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +..+.+++|+.+++ +|||+||+|...+
T Consensus        42 i~~~~~~~~~~~g~-~~g~afV~f~~~~   68 (95)
T 2ek1_A           42 IPGSVCLKYNEKGM-PTGEAMVAFESRD   68 (95)
T ss_dssp             CTTCCEEEECTTSC-EEEEEEEEESSHH
T ss_pred             ccceEEEEeCCCCC-EeeEEEEEECCHH
Confidence            34577888999985 9999999994444

>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=92.88  E-value=0.017  Score=39.24  Aligned_cols=25  Identities=12%  Similarity=0.011  Sum_probs=19.2

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      ++.++.|..+++ ++|||||+|...+
T Consensus        54 ~~~~~~~~~~g~-~~G~afV~F~~~~   78 (124)
T 1wel_A           54 DSIYIAYGPNGK-ATGEGFVEFRNEA   78 (124)
T ss_dssp             TTCEEEECTTSS-EEEEEEEEBSSSH
T ss_pred             ceEEEEECCCCC-CCeEEEEEECCHH
Confidence            456777888885 9999999994333

>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=92.57  E-value=0.033  Score=35.60  Aligned_cols=24  Identities=17%  Similarity=0.117  Sum_probs=16.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIR   36 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~   36 (192)
                      +.++.+++|      +||||||+|...+.+
T Consensus        38 i~~v~i~~~------srGfaFV~F~~~~~A   61 (89)
T 3d2w_A           38 VVDVFIPKP------FRAFAFVTFADDKVA   61 (89)
T ss_dssp             EEEEECCSS------CCSEEEEEESCHHHH
T ss_pred             EEEEEEeeC------CCCEEEEEECCHHHH
Confidence            456666652      899999999554443

>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=92.47  E-value=0.4  Score=40.72  Aligned_cols=56  Identities=23%  Similarity=0.295  Sum_probs=46.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNG  122 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~  122 (192)
                      ...++|+ +|..+...+|.+.|+.||.+ +|+++.+.       .|||.|.+.+.|..++..+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHHh
Confidence            3566665 88899999999999999954 77776663       699999999999999998854

>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=92.31  E-value=0.044  Score=35.37  Aligned_cols=24  Identities=4%  Similarity=-0.110  Sum_probs=18.9

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+    ||||||+|...+
T Consensus        40 v~~v~i~~~~~~----rg~afV~f~~~~   63 (96)
T 2dgx_A           40 VKSVELSPHTDY----QLKAVVQMENLQ   63 (96)
T ss_dssp             EEEEEECSCCST----TCCEEEEESSHH
T ss_pred             EEEEEEEeCCCC----CeEEEEEECCHH
Confidence            568889988876    789999994433

>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=91.80  E-value=0.07  Score=44.52  Aligned_cols=28  Identities=21%  Similarity=0.242  Sum_probs=23.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+..|.++.|+.++. ++|||||+|....
T Consensus       128 ~I~~v~i~~d~~tg~-~kG~aFV~F~~~e  155 (437)
T 3pgw_S          128 PIKRIHMVYSKRSGK-PRGYAFIEYEHER  155 (437)
T ss_pred             CeeEEEeeccCCCCC-ccceEEEeeccHH
Confidence            366899999999995 9999999994433

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.58  E-value=0.037  Score=36.76  Aligned_cols=27  Identities=30%  Similarity=0.319  Sum_probs=20.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+ ++ +++||+||+|...+
T Consensus        41 ~i~~~~i~~~~-~g-~~~g~afV~f~~~~   67 (114)
T 2do0_A           41 VVVRADILEDK-DG-KSRGIGTVTFEQSI   67 (114)
T ss_dssp             CEEEEEEEECT-TC-SEEEEEEEEESSHH
T ss_pred             CeEEEEEEECC-CC-CeeeEEEEEECCHH
Confidence            35688899998 46 49999999994433

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.55  E-value=0.037  Score=36.07  Aligned_cols=25  Identities=20%  Similarity=0.343  Sum_probs=19.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|  ++. ++||+||+|...+
T Consensus        42 i~~v~i~~~--~g~-~~g~afV~f~~~~   66 (103)
T 2d9p_A           42 ITSAKVMME--GGR-SKGFGFVCFSSPE   66 (103)
T ss_dssp             EEEEEEEEC--SSS-EEEEEEEEESSHH
T ss_pred             EEEEEEEcC--CCC-cCEEEEEEECCHH
Confidence            568888888  774 9999999994433

>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=91.35  E-value=0.029  Score=38.13  Aligned_cols=35  Identities=6%  Similarity=-0.095  Sum_probs=23.6

Q ss_pred             eeeeEEeeccCc----CCCCCCccCCCCChhH--HHhhhccc
Q psy15152          7 LKGIARLKEKAR----KKKGRGFGTETSTRNE--IREYESME   42 (192)
Q Consensus         7 ~~~v~~~~d~~~----~~k~rG~gfv~f~~~~--~~~~~~~~   42 (192)
                      +.+|.+++|+.+    ++ ++||+||+|...+  ..++..++
T Consensus        52 V~~v~I~~~~~~~~~~~~-~~G~~FV~F~~~e~A~~Ai~~Ln   92 (118)
T 3ue2_A           52 VNRVIIYQEKQGEEEDAE-IIVKIFVEFSIASETHKAIQALN   92 (118)
T ss_dssp             EEEEEEEEEEESSSTTCE-EEEEEEEEESSHHHHHHHHHHHT
T ss_pred             EeEEEEeecCCCcccCCc-ceEEEEEEECCHHHHHHHHHHHC
Confidence            568888988763    43 8899999994444  33444443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=91.27  E-value=0.12  Score=35.41  Aligned_cols=17  Identities=12%  Similarity=0.008  Sum_probs=12.6

Q ss_pred             cCCCCCCccCCCCChhHH
Q psy15152         18 RKKKGRGFGTETSTRNEI   35 (192)
Q Consensus        18 ~~~k~rG~gfv~f~~~~~   35 (192)
                      ++ ++||||||+|...+.
T Consensus        68 ~~-~~rG~aFV~F~~~~~   84 (127)
T 2a3j_A           68 SD-DNSGKAYIVFATQES   84 (127)
T ss_dssp             CC-SSCCCEEEEESSHHH
T ss_pred             CC-CcCCEEEEEECCHHH
Confidence            56 499999999954443

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=91.26  E-value=0.07  Score=38.78  Aligned_cols=27  Identities=19%  Similarity=0.072  Sum_probs=21.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+..|+ +++ ++|||||+|...+.
T Consensus       115 I~~v~i~~d~-~g~-~kG~afV~F~~~~~  141 (177)
T 2f3j_A          115 LKKAAVDYDR-SGR-SLGTADVHFERRAD  141 (177)
T ss_dssp             CSEEEECCCT-TSS-CSCCEEEEESCHHH
T ss_pred             eEEEEEEECC-CCC-EeeEEEEEeCCHHH
Confidence            4688899999 885 99999999954443

>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=91.20  E-value=0.086  Score=35.59  Aligned_cols=22  Identities=9%  Similarity=0.238  Sum_probs=14.3

Q ss_pred             CCCccCCCCChh--HHHhhhcccC
Q psy15152         22 GRGFGTETSTRN--EIREYESMET   43 (192)
Q Consensus        22 ~rG~gfv~f~~~--~~~~~~~~~~   43 (192)
                      +||||||+|...  +..++..++.
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG   85 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNG   85 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCC
Confidence            589999999443  3445554444

>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=91.09  E-value=0.073  Score=34.60  Aligned_cols=25  Identities=8%  Similarity=0.017  Sum_probs=18.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.+   +||||||+|...+
T Consensus        42 i~~v~i~~~~~~---~~g~afV~f~~~~   66 (103)
T 2cqi_A           42 CKSCKMITEHTS---NDPYCFVEFYEHR   66 (103)
T ss_dssp             EEEEEEECCCCS---SCCEEEEEESSHH
T ss_pred             EeEEEEEecCCC---CCCEEEEEECCHH
Confidence            567888888543   6899999994443

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.74  E-value=0.079  Score=34.29  Aligned_cols=24  Identities=17%  Similarity=0.101  Sum_probs=17.4

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .|.++++ .+++ ++||+||+|...+
T Consensus        41 ~v~~~~~-~~g~-~~g~afV~f~~~~   64 (101)
T 2fc9_A           41 FIKVPQN-QNGK-SKGYAFIEFASFE   64 (101)
T ss_dssp             EEECCBC-SSSC-BCSEEEEECSSHH
T ss_pred             EEEEEEC-CCCC-EeeEEEEEECCHH
Confidence            4566666 6674 9999999994443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=90.37  E-value=0.039  Score=35.81  Aligned_cols=21  Identities=14%  Similarity=0.132  Sum_probs=16.9

Q ss_pred             EEeeccCcCCCCCCccCCCCCh
Q psy15152         11 ARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus        11 ~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      .++.|+.+++ +||||||+|..
T Consensus        47 ~~~~~~~~g~-~~g~afV~f~~   67 (101)
T 1fj7_A           47 LAVVDVRTGT-NRKFGYVDFES   67 (101)
T ss_dssp             CCCCEEEEET-TTTEEEEEESS
T ss_pred             EEEecCCCCC-cCcEEEEEECC
Confidence            4567888885 99999999943

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.36  E-value=0.11  Score=34.41  Aligned_cols=23  Identities=17%  Similarity=0.346  Sum_probs=17.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCCh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      +.++.+++|+  +. +||||||+|..
T Consensus        56 i~~v~i~~~~--~~-~kg~afV~f~~   78 (109)
T 2err_A           56 ILDVEIIFNE--RG-SKGFGFVTFEN   78 (109)
T ss_dssp             CSCEEECCBT--TB-CTTEEEEECCC
T ss_pred             EEEEEEEECC--CC-CceEEEEEECC
Confidence            4578888885  33 89999999933

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=89.83  E-value=0.064  Score=34.01  Aligned_cols=25  Identities=20%  Similarity=0.109  Sum_probs=18.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|  ++ ++|||+||+|...+
T Consensus        35 v~~~~i~~~--~g-~~~g~afV~f~~~~   59 (92)
T 2dgv_A           35 VLYADIKME--NG-KSKGCGVVKFESPE   59 (92)
T ss_dssp             EEEEEEEES--SS-CEEEEEEEEESSHH
T ss_pred             EEEEEEEcc--CC-CcceEEEEEECCHH
Confidence            456777774  66 49999999994433

>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=89.73  E-value=0.12  Score=33.61  Aligned_cols=25  Identities=16%  Similarity=0.287  Sum_probs=18.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.   .++||+||+|...+
T Consensus        42 v~~v~i~~~~~---~~~g~afV~f~~~~   66 (103)
T 2cq3_A           42 ILDVEIIFNER---GSKGFGFVTFENSA   66 (103)
T ss_dssp             EEEEEEECCTT---TTCCEEEEEESCHH
T ss_pred             eEEEEEEecCC---CCcEEEEEEECCHH
Confidence            56788888864   28999999994433

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.64  E-value=0.14  Score=33.55  Aligned_cols=22  Identities=9%  Similarity=-0.005  Sum_probs=15.2

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.++     + ++||||||+|...+
T Consensus        44 V~~v~i~-----~-~~rGfaFVeF~~~~   65 (100)
T 2d9o_A           44 VLNLVLS-----S-KKPGTAVVEFATVK   65 (100)
T ss_dssp             EEEEEEE-----S-SSSSEEEEEESCHH
T ss_pred             EEEEEEc-----c-CCCCEEEEEECCHH
Confidence            4456665     2 59999999994433

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.47  E-value=0.16  Score=33.75  Aligned_cols=19  Identities=11%  Similarity=0.064  Sum_probs=14.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCCh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      +.+|.+++|       ||||||+|..
T Consensus        43 V~~v~i~~~-------kGfaFVeF~~   61 (105)
T 1sjq_A           43 VTNLLMLKG-------KNQAFIEMNT   61 (105)
T ss_dssp             EEEEEEETT-------TTEEEEEESS
T ss_pred             EEEEEEEcC-------CCEEEEEECC
Confidence            456777653       7999999943

>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=88.38  E-value=0.088  Score=34.92  Aligned_cols=19  Identities=21%  Similarity=0.090  Sum_probs=13.7

Q ss_pred             ccCcCCCCCCccCCCCChhH
Q psy15152         15 EKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus        15 d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +..+++ +||||||+|...+
T Consensus        60 ~~~~g~-~~g~afV~f~~~~   78 (115)
T 2cpx_A           60 RMMTGR-MRGQAFITFPNKE   78 (115)
T ss_dssp             EEECSS-SCSEEEEECSSHH
T ss_pred             EcCCCc-cceEEEEEECCHH
Confidence            333774 9999999994444

>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=87.84  E-value=0.14  Score=37.63  Aligned_cols=26  Identities=15%  Similarity=-0.087  Sum_probs=20.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|.. + ++||||||+|...+
T Consensus       136 v~~v~i~~~~~-~-~~kG~aFVeF~~~e  161 (193)
T 2voo_A          136 VLNIQMRRTLH-K-AFKGSIFVVFDSIE  161 (193)
T ss_dssp             EEEEEEEECTT-C-CEEEEEEEEESSHH
T ss_pred             EEEEEEEECCC-C-CcccEEEEEECCHH
Confidence            56788888875 6 49999999994444

>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=87.63  E-value=0.19  Score=31.50  Aligned_cols=23  Identities=22%  Similarity=0.156  Sum_probs=15.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|      +||||||+|...+.
T Consensus        32 i~~v~i~~~------~~g~afV~f~~~~~   54 (88)
T 1wf0_A           32 VMDVFIPKP------FRAFAFVTFADDQI   54 (88)
T ss_dssp             CCEEECCSS------CCSCCEEECSCHHH
T ss_pred             eeEEEEecC------CCCEEEEEECCHHH
Confidence            345555542      89999999954443

>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=84.43  E-value=0.3  Score=32.78  Aligned_cols=31  Identities=13%  Similarity=0.019  Sum_probs=18.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhccc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESME   42 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~   42 (192)
                      +.+|.+.++.     +|||+||+|...+  ..++..++
T Consensus        44 V~~v~i~~~~-----~~G~~fV~f~~~e~A~~Ai~~ln   76 (114)
T 3s6e_A           44 VIHIYVDKNS-----AQGNVYVKCPSIAAAIAAVNALH   76 (114)
T ss_dssp             CSEEEECTTC-----TTCCEEEECSSHHHHHHHHHHHT
T ss_pred             EEEEEEecCC-----CcEEEEEEECCHHHHHHHHHHhC
Confidence            3466665542     6899999994444  33444443

>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=83.95  E-value=0.37  Score=31.47  Aligned_cols=20  Identities=20%  Similarity=0.207  Sum_probs=13.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      +.+|.+++       .||||||+|...
T Consensus        42 v~~v~i~~-------~kg~aFVef~~~   61 (101)
T 2cq1_A           42 VTNILMLK-------GKNQAFLELATE   61 (101)
T ss_dssp             EEEEEEET-------TTTEEEEEESSH
T ss_pred             EEEEEEEC-------CCCEEEEEECCH
Confidence            34565554       389999999433

>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=83.64  E-value=0.34  Score=32.81  Aligned_cols=19  Identities=11%  Similarity=0.064  Sum_probs=13.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCCh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      +.+|.+++|       ||||||+|..
T Consensus        58 V~~v~i~~~-------kG~AFVeF~~   76 (119)
T 2ad9_A           58 VTNLLMLKG-------KNQAFIEMNT   76 (119)
T ss_dssp             CCEEEEEGG-------GTEEEEECSC
T ss_pred             EEEEEEeCC-------CCEEEEEECC
Confidence            456667654       7999999943

>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=82.51  E-value=0.45  Score=31.03  Aligned_cols=24  Identities=17%  Similarity=0.221  Sum_probs=15.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+..   ++ ++|||+||+|...+
T Consensus        49 v~~~~i~~---~~-~~~g~afV~f~~~~   72 (109)
T 1x4a_A           49 IRDIDLKN---RR-GGPPFAFVEFEDPR   72 (109)
T ss_dssp             EEEEEECC---SS-SSSCCEEEEESCHH
T ss_pred             eEEEEEEE---CC-CCCcEEEEEECCHH
Confidence            34555544   34 38999999994433

>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=81.79  E-value=0.54  Score=30.98  Aligned_cols=13  Identities=15%  Similarity=0.151  Sum_probs=10.5

Q ss_pred             CCCccCCCCChhH
Q psy15152         22 GRGFGTETSTRNE   34 (192)
Q Consensus        22 ~rG~gfv~f~~~~   34 (192)
                      +|||+||+|...+
T Consensus        63 ~~G~afV~f~~~~   75 (112)
T 2dit_A           63 PDGVASVSFRDPE   75 (112)
T ss_dssp             TTCEEEEECSCHH
T ss_pred             CCEEEEEEECCHH
Confidence            8999999994444

>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=80.95  E-value=0.55  Score=31.40  Aligned_cols=21  Identities=0%  Similarity=-0.176  Sum_probs=13.4

Q ss_pred             CCCccCCCCChh--HHHhhhccc
Q psy15152         22 GRGFGTETSTRN--EIREYESME   42 (192)
Q Consensus        22 ~rG~gfv~f~~~--~~~~~~~~~   42 (192)
                      +||||||+|...  +..++..++
T Consensus        61 ~kg~aFVef~~~~~A~~Ai~~l~   83 (112)
T 1x4f_A           61 MKSQAFIEMETREDAMAMVDHCL   83 (112)
T ss_dssp             TTTEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHhc
Confidence            789999999433  344444443

>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=80.87  E-value=0.34  Score=36.02  Aligned_cols=37  Identities=5%  Similarity=-0.205  Sum_probs=22.6

Q ss_pred             eeeeEEeeccCc----CCCCCCccCCCCChhHHHhhhcccCC
Q psy15152          7 LKGIARLKEKAR----KKKGRGFGTETSTRNEIREYESMETD   44 (192)
Q Consensus         7 ~~~v~~~~d~~~----~~k~rG~gfv~f~~~~~~~~~~~~~~   44 (192)
                      +.++.++++..+    ++ ++|++||+|...+.+..+...++
T Consensus       156 v~~~~v~~~~~~~~~~~~-~~G~~fv~f~~~~~a~~a~~~l~  196 (222)
T 3dxb_A          156 VNRVIIYQEKQGEEEDAE-IIVKIFVEFSIASETHKAIQALN  196 (222)
T ss_dssp             EEEEEEEEEECCSSTTCC-EEEEEEEEESSHHHHHHHHHHHT
T ss_pred             eEEEEEecCCCCcccCcC-ceeEEEEEECCHHHHHHHHHHhc
Confidence            456777755544    45 99999999955443333333333

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=80.37  E-value=0.36  Score=32.17  Aligned_cols=14  Identities=21%  Similarity=0.128  Sum_probs=10.9

Q ss_pred             CCCCccCCCCChhH
Q psy15152         21 KGRGFGTETSTRNE   34 (192)
Q Consensus        21 k~rG~gfv~f~~~~   34 (192)
                      ++||||||+|...+
T Consensus        65 ~~rGfaFV~F~~~e   78 (111)
T 2jvr_A           65 DFDGTGALEFPSEE   78 (111)
T ss_dssp             SSSCCEEEEESSHH
T ss_pred             CCCCEEEEEECCHH
Confidence            38999999994444

---

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	192
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	6e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	6e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.001
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.002
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.002
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.003
d1ufwa_	95	d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens)	0.003

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 80.1 bits (197), Expect = 9e-21
 Identities = 67/88 (76%), Positives = 80/88 (90%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           PQRSVEGWILFVT +HEEAQED++ EKF +YGEIKN+HLNLDRRTGF KGYALVEY+++K
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 112 EASAARDALNGTTILGQTVTVDWCFVKG 139
           +A AA++ALNG  I+GQT+ VDWCFVKG
Sbjct: 61  QALAAKEALNGAEIMGQTIQVDWCFVKG 88

>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 = 64.2 bits (156), Expect = 1e-14
 Identities = 24/74 (32%), Positives = 37/74 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +H +  E  ++EKFS  G I ++ +  D  T    GYA V +    +A  A D +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 121 NGTTILGQTVTVDW 134
           N   I G+ V + W
Sbjct: 63  NFDVIKGKPVRIMW 76

>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 = 61.5 bits (149), Expect = 2e-13
 Identities = 20/77 (25%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAARDA 119
           + V  +  +A + ++ E FS +GE+K + L      TG  +G+  V++ + ++A  A +A
Sbjct: 11  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 70

Query: 120 L-NGTTILGQTVTVDWC 135
           L + T + G+ + ++W 
Sbjct: 71  LCHSTHLYGRRLVLEWA 87

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-13
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           IL++  +  +   ++M++ F +YG I+ +       T   +G A V Y+   +A  A D 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 120 LNGTTILGQTVTVDWCFVKGPKKVAGEQK 148
           L+G  +  + + V +       +    +K
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKK 94

>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 = 60.4 bits (146), Expect = 3e-13
 Identities = 23/74 (31%), Positives = 39/74 (52%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+V  +     E+ ++E FS+ G+IK + + LD+      G+  VEY S  +A  A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 121 NGTTILGQTVTVDW 134
           NGT +  + +  DW
Sbjct: 70  NGTRLDDRIIRTDW 83

>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 = 60.0 bits (145), Expect = 4e-13
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           S++   L+VT +     +D +   F +YG I   ++  D+ TG  +G A V Y+  +EA 
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 115 AARDALNGTTILG--QTVTVDW 134
            A  ALN     G  Q ++V  
Sbjct: 63  EAISALNNVIPEGGSQPLSVRL 84

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-12
 Identities = 25/83 (30%), Positives = 49/83 (59%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +L+V G+ EE  +  +H  F  +G+I ++ + LD  T   +G+A VE++  ++A+AA D 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 120 LNGTTILGQTVTVDWCFVKGPKK 142
           +N + + G+T+ V+       K+
Sbjct: 67  MNESELFGRTIRVNLAKPMRIKE 89

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 2e-12
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           S+    L+V+G+ +   + ++ + FS+YG I    + +D+ TG  +G   + +D   EA 
Sbjct: 3   SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 62

Query: 115 AARDALNGTTILGQT--VTVDW 134
            A   LNG    G T  +TV +
Sbjct: 63  EAIKGLNGQKPSGATEPITVKF 84

>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 = 58.1 bits (140), Expect = 2e-12
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR---TGFLKGYALVEYDSYKEASAAR 117
           LF+  ++    E+ +   FS+ G IK+  ++  +         G+  VEY   ++A  A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 118 DALNGTTILGQTVTVDW 134
             L G T+ G  + V  
Sbjct: 61  KQLQGHTVDGHKLEVRI 77

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.7 bits (139), Expect = 2e-12
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+ G+  +  ++ + E F ++GE+K   +  D  T   +G+  V +           A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 121 NGTTILGQTVTVDWCF 136
           +   +  +T+     F
Sbjct: 62  SRHELDSKTIDPKVAF 77

>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 = 57.7 bits (139), Expect = 3e-12
 Identities = 19/74 (25%), Positives = 37/74 (50%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + ++  + +++  F   G I    +  D +TG+  GYA V++ S  ++  A   L
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 121 NGTTILGQTVTVDW 134
           NG T+  + + V +
Sbjct: 65  NGITVRNKRLKVSY 78

>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 = 57.0 bits (137), Expect = 5e-12
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
             P P        L V G+     E D+ E FS+YG I ++ +  D+++   +G+A V +
Sbjct: 4   ANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58

Query: 108 DSYKEASAARDALNGTTILGQTVTV 132
           ++  +A  A++  NG  + G+ + V
Sbjct: 59  ENVDDAKEAKERANGMELDGRRIRV 83

>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 = 57.0 bits (137), Expect = 5e-12
 Identities = 22/74 (29%), Positives = 36/74 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V  + +   +++    F   GEI++  L  D+ TG   GY  V Y   K+A  A + L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 121 NGTTILGQTVTVDW 134
           NG  +  +T+ V +
Sbjct: 65  NGLRLQTKTIKVSY 78

>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 = 57.3 bits (138), Expect = 6e-12
 Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 6/87 (6%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           E+   Q S +   ++  G+     +  M + FS +G+I  + +  ++       Y+ V +
Sbjct: 8   EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRF 61

Query: 108 DSYKEASAARDALNGTTILGQTVTVDW 134
            +++ A+ A  ++NGTTI G  V   W
Sbjct: 62  STHESAAHAIVSVNGTTIEGHVVKCYW 88

>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 = 56.9 bits (137), Expect = 7e-12
 Identities = 22/74 (29%), Positives = 33/74 (44%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+     +D + E  + +G +K  +L  D  TG  KGYA  EY        A   L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 121 NGTTILGQTVTVDW 134
           NG  +  + + V  
Sbjct: 64  NGMQLGDKKLLVQR 77

>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 = 56.7 bits (136), Expect = 1e-11
 Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHL--------NLDRRTGFLKGYA 103
           P    +   ++V G+++    DD+ + F + G +K             LD+ TG  KG A
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 104 LVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK 141
            V Y+    A AA +  +G    G  + V     K P 
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 56.2 bits (135), Expect = 1e-11
 Identities = 22/82 (26%), Positives = 44/82 (53%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
           +R+ +   + VT + E+ +E D+ E F  +G I  ++L  D+ TG  KG+A + +   ++
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 113 ASAARDALNGTTILGQTVTVDW 134
           A+ A   ++G       + V+W
Sbjct: 63  AARAIAGVSGFGYDHLILNVEW 84

>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 = 55.8 bits (134), Expect = 2e-11
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 48  EEPGPQRSV-EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVE 106
           E+P   + V     L    +     ED++ E F +        + L  + G  KG A +E
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIE 59

Query: 107 YDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           + S  +A    +   G  I G++V++ +   KG  +
Sbjct: 60  FKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 55.8 bits (134), Expect = 2e-11
 Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 7/95 (7%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           E+ G  R+     L+V  +  +  E  + + FS+ G  K+  +  +  +     +  VE+
Sbjct: 3   EDDGQPRT-----LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF--VEF 55

Query: 108 DSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
             +++A+AA  A+NG  ILG+ V V+W      +K
Sbjct: 56  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 55.4 bits (133), Expect = 3e-11
 Identities = 22/74 (29%), Positives = 40/74 (54%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V G+ E+  E  + E F + G + N H+  DR TG  +GY  VE+ S ++A  A   +
Sbjct: 12  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 71

Query: 121 NGTTILGQTVTVDW 134
           +   + G+ + V+ 
Sbjct: 72  DMIKLYGKPIRVNK 85

>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 = 5e-11
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLH-LNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +F+  +  E  E  +++ FS +G I     +  D  TG  KGYA + + S+  + AA +A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 120 LNGTTILGQTVTVDWCFVKGPK 141
           +NG  +  + +TV + F K  K
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 1e-10
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 36  REYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR 95
           +  E++  +    E    R      LF+ G+  E  E+ +   + ++G++ +  +  D  
Sbjct: 3   KTLETVPLERKKREKEQFRK-----LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 57

Query: 96  TGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK 138
           +   +G+  V + S  E  AA  A    +I G+ V       +
Sbjct: 58  SKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAR 99

>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 = 53.7 bits (129), Expect = 2e-10
 Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 13/98 (13%)

Query: 46  GDEEPGPQRSVEGWILFVTGVH-EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYAL 104
           G  +P    S     +F+  ++    ++ D+   FS+YG+I    ++        KG+A 
Sbjct: 7   GKTDPRSMNSR----VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAF 54

Query: 105 VEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           V+Y + + A AA    +G  I GQ + ++        +
Sbjct: 55  VQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 53.2 bits (127), Expect = 2e-10
 Identities = 24/85 (28%), Positives = 40/85 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +   + E+D+ + FS YG +  LH  +D  T   KG+A V +   + A  A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAG 145
           +G    G+ + V    +K     +G
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQSG 95

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 2e-10
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F   +    +  D+ + FS  G+++++ +  DR +   KG A VE+    ++      L
Sbjct: 21  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE-IQSVPLAIGL 79

Query: 121 NGTTILGQTVTVDW 134
            G  +LG  + V  
Sbjct: 80  TGQRLLGVPIIVQA 93

>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 = 52.2 bits (125), Expect = 3e-10
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V+ +     + D+ E F+E+G +K   ++   R+G   G A V ++   +A  A    
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQY 61

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ + +  
Sbjct: 62  NGVPLDGRPMNIQL 75

>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 = 52.7 bits (126), Expect = 3e-10
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           + +   ++E  E+   E   +YGE++ +++  D     L G   V++   ++A  A   L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 121 NGTTILGQTVTVDWC 135
           N     GQ +  +  
Sbjct: 89  NNRWFNGQPIHAELS 103

>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 = 9e-10
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +F+ G+  +  + D+ + FS++GE+ +  L LD  TG  +G+  V +   +      D  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 121 NGTTILGQTVTV 132
               + G+ +  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 51.2 bits (122), Expect = 1e-09
 Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V+ +    ++ D+ + F ++G+I ++ +  + R    KG+  V +++  +A  AR+ L
Sbjct: 14  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 71

Query: 121 NGTTILGQTVTVDW 134
           +GT + G+ + V+ 
Sbjct: 72  HGTVVEGRKIEVNN 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.1 bits (122), Expect = 1e-09
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L V G+  +  E D+ E FS +GE+  + +  D +TG  KG+  V +  Y+         
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 121 NGTTILGQTVTVDW 134
           +   I G+      
Sbjct: 71  H--MIDGRWCDCKL 82

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 1e-09
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV G+  +  E  + + FS+YG+I  + +  DR T   +G+  V +++  +A  A  A+
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 121 NGTTILGQTVTVDW 134
           NG ++ G+ + VD 
Sbjct: 68  NGKSVDGRQIRVDQ 81

>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 = 50.8 bits (121), Expect = 1e-09
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNL--HLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           LF+ G+ +  + +++ E+ ++  E                 +G+A VEY+S++ A+ AR 
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 119 ALNGTTIL--GQTVTVDW 134
            L    I   G  + VDW
Sbjct: 64  KLMPGRIQLWGHQIAVDW 81

>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 = 1e-09
 Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 50  PGPQRSV-EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYD 108
            G Q+   EG  LF+  + +E  + D+ + F  +G + +  + +D++T   K +  V YD
Sbjct: 9   AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYD 68

Query: 109 SYKEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           +   A AA  ++NG  I  + + V     K   K
Sbjct: 69  NPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 50.5 bits (120), Expect = 2e-09
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLN-----LDRRTGFLKGYALVEYDSYKEASA 115
           L+V  +     E+ M + F+    +  L        L  +    K +A +E+ S  E + 
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 116 ARDALNGTTILGQTVTV 132
           A    +G    GQ++ +
Sbjct: 64  AMA-FDGIIFQGQSLKI 79

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 2e-09
 Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           ++V  +  + +  D+ + F +YG I+++     +       +A VE++  ++A  A    
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 121 NGTTILGQTVTVDW 134
           +G    G  + V++
Sbjct: 74  DGYDYDGYRLRVEF 87

>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 = 50.0 bits (119), Expect = 2e-09
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           IL+V  +     E+ + ++F+              R   ++ YA V + + ++A  A  A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 120 LNGTTILGQTVTVDW 134
           LNG  + G  + V  
Sbjct: 64  LNGKVLDGSPIEVTL 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 = 50.0 bits (119), Expect = 2e-09
 Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LFV  +  +  E++M + F +YG+   + ++ D+       +  +  ++   A  A+  L
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVEL 64

Query: 121 NGTTILGQTVTVDW 134
           +   + G+ + V +
Sbjct: 65  DNMPLRGKQLRVRF 78

>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 = 50.0 bits (119), Expect = 3e-09
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 48  EEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEY 107
           +EP   R      LF+ G+  E  ++ +   F ++G + +  +  D  T   +G+  V Y
Sbjct: 1   KEPEQLRK-----LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 55

Query: 108 DSYKEASAARDALNGTTILGQTVTVDW 134
            + +E  AA +A     + G+ V    
Sbjct: 56  ATVEEVDAAMNA-RPHKVDGRVVEPKR 81

>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 = 50.0 bits (119), Expect = 3e-09
 Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 50  PGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDS 109
           P  ++S  G  +F+  + +      +++ FS +G I +  +  D       G+  V +++
Sbjct: 1   PSLRKSGVGN-IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF--VHFET 57

Query: 110 YKEASAARDALNGTTILGQTVTVDW 134
            + A  A + +NG  +  + V V  
Sbjct: 58  QEAAERAIEKMNGMLLNDRKVFVGR 82

>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 = 50.1 bits (119), Expect = 3e-09
 Identities = 35/114 (30%), Positives = 50/114 (43%), Gaps = 10/114 (8%)

Query: 49  EPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYD 108
           +P   RS+    +FV  +  EA E+ + + FSE G + +  L  DR TG  KGY   EY 
Sbjct: 1   DPAVDRSLR--SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQ 58

Query: 109 SYKEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGVKVLFPVI 162
             + A +A   LNG    G+ + VD    +  K+       G         PVI
Sbjct: 59  DQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGA--------PVI 104

>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 = 49.3 bits (117), Expect = 3e-09
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++  +      DD+ + F +          L  +     GYA V+Y     A  A + L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 121 NGTTIL-GQTVTVDWCFVKGPK 141
           +G   L G+ + VD+   K  +
Sbjct: 58  SGKVELHGKIMEVDYSVSKKLR 79

>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 = 49.7 bits (118), Expect = 4e-09
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ++   G+      + +     + G +  L +  ++   F        Y + +E+  A   
Sbjct: 22  VVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSF------ARYRTTEESKRAYVT 75

Query: 120 LNGTTIL---GQTVTVDWCFVKG 139
           LNG  ++   GQ +T+   FV+ 
Sbjct: 76  LNGKEVVDDLGQKITLYLNFVEK 98

>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 = 48.4 bits (115), Expect = 8e-09
 Identities = 12/72 (16%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+  +  E+ + E F  +GE++++ L +D +T   +G+  + +   +      +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 121 NGTTILGQTVTV 132
               +      +
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 48.7 bits (115), Expect = 1e-08
 Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 6/89 (6%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
           P    EG  +F+  +  +++E+ + E   ++G++K + + L   T   KG A  ++ + +
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 112 EASAARDALN------GTTILGQTVTVDW 134
            A     A +      G  + G+ + VD 
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDL 90

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 7/94 (7%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
            F+  +  +  E+ + E F                   LKG+   E++      +A  +L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
           N  ++  + + VD        +   ++  GP  G
Sbjct: 77  NEESLGNKRIRVDVAD---QAQ---DKDSGPSSG 104

>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 = 47.7 bits (113), Expect = 2e-08
 Identities = 19/75 (25%), Positives = 30/75 (40%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           I+ V  +      D++ + F  Y  I           G   G A+V ++S  EA+AA   
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 120 LNGTTILGQTVTVDW 134
           LN   I  + V +  
Sbjct: 71  LNDRPIGSRKVKLVL 85

>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 = 47.7 bits (113), Expect = 2e-08
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           + V  +      D +H+ FS++G +  +           +  AL++Y     A  A+ +L
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLSL 65

Query: 121 NGTTILGQTVTVDWCFVK 138
           +G  I     T+   F K
Sbjct: 66  DGQNIYNACCTLRIDFSK 83

>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 = 47.0 bits (111), Expect = 3e-08
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+      +D+   F ++G++ +  L  D+ T   +G+  V ++S          +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 121 NGTTILGQTVTVDW 134
           +   I  + V    
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 47.1 bits (111), Expect = 3e-08
 Identities = 12/74 (16%), Positives = 28/74 (37%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++T       + ++ +   +   +         R    + +A ++  S ++A    + L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 121 NGTTILGQTVTVDW 134
           NG  I G T+    
Sbjct: 64  NGLKIEGYTLVTKV 77

>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 = 48.8 bits (115), Expect = 3e-08
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +D +          
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 158

Query: 121 NGTTILGQTVTVDW 134
              T+ G    V  
Sbjct: 159 KYHTVNGHNCEVRK 172

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (104), Expect = 1e-06
 Identities = 15/62 (24%), Positives = 30/62 (48%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           LF+ G+  E  ++ +   F ++G + +  +  D  T   +G+  V Y + +E  AA +A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 121 NG 122
             
Sbjct: 69  PH 70

>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 = 48.0 bits (113), Expect = 4e-08
 Identities = 26/115 (22%), Positives = 47/115 (40%), Gaps = 5/115 (4%)

Query: 27  TETSTRNEIREYESMETDVGDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK 86
           T    + + ++ + +     + EP   R+     L V  +     E  + + F  YG I+
Sbjct: 16  TAQLQQLQQQQQQHIPPTQMNPEPDVLRN-----LMVNYIPTTVDEVQLRQLFERYGPIE 70

Query: 87  NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKGPK 141
           ++ +  DR T   +GY  V++ S   A  A   LNG  IL + + V        +
Sbjct: 71  SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125

>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 = 47.0 bits (111), Expect = 5e-08
 Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 4/105 (3%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           G Q+      +FV G+     +  + + F  +G+I+   +  DR+TG  +GY  V     
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 111 KEASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGGV 155
             A  A    N   I G+   V+  ++    +     + G   GV
Sbjct: 63  AAAERACKDPNP-IIDGRKANVNLAYLGAKPR---SLQTGFAIGV 103

>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 = 46.0 bits (108), Expect = 7e-08
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 54  RSVEGWILFVTGVHEEAQEDDM---HEKFSEYGEIKNLHLNLDRRTG---FLKGYALVEY 107
           R V+  ++FV G+ +   + ++    E F ++G+I  + +N              A V Y
Sbjct: 4   RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTY 63

Query: 108 DSYKEASAARDALNGTTILGQTVTV 132
              ++A  A   +N   + G+T+  
Sbjct: 64  IRSEDALRAIQCVNNVVVDGRTLKA 88

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 8e-08
 Identities = 10/75 (13%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEY-GEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           +++  ++E+ ++D++ +           +   L  R+  ++G A V +     A+ A  +
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 120 LNGTTILGQTVTVDW 134
           + G     + + + +
Sbjct: 66  MQGFPFYDKPMRIQY 80

>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 = 46.1 bits (109), Expect = 1e-07
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 4/63 (6%)

Query: 72  EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT 131
            +D+  + S++G+I+ L L          G A V +   +EA      L+G    G+ +T
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 132 VDW 134
              
Sbjct: 89  AQA 91

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 2e-07
 Identities = 13/84 (15%), Positives = 32/84 (38%), Gaps = 1/84 (1%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
              +T +     + D+ +        +N    L    G   G ALV++ +  +A  +   
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-R 68

Query: 120 LNGTTILGQTVTVDWCFVKGPKKV 143
           L+   + G+   V    ++  +++
Sbjct: 69  LHRKKLNGREAFVHVVTLEDMREI 92

>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 = 44.6 bits (105), Expect = 2e-07
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 57  EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAA 116
           +G  L+V G   +     +   FS +G I +L ++  R        A V Y+  + A  A
Sbjct: 4   KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQA 55

Query: 117 RDALNGTTILGQTVTVDW 134
              LNGT +    + V+ 
Sbjct: 56  VAELNGTQVESVQLKVNI 73

>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 = 43.6 bits (102), Expect = 4e-07
 Identities = 20/70 (28%), Positives = 33/70 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++ G+     + D+ +    YG+I +    LD+ T   KGY  V++DS   A  A  AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 121 NGTTILGQTV 130
             + +  Q  
Sbjct: 61  KASGVQAQMA 70

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (104), Expect = 6e-07
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 66  VHEEAQEDDMHEKFSEYGEIKNLHL--NLDRRTGFLKGYALVEYDSYKEASAARDALNGT 123
              E   +D+ ++ S+YG +K++ +   +D       G   VE+ S  +   A   L G 
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 124 TILGQTVTVDWC 135
               + V   +C
Sbjct: 82  KFANRVVVTKYC 93

>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 = 44.0 bits (103), Expect = 6e-07
 Identities = 10/87 (11%), Positives = 24/87 (27%), Gaps = 11/87 (12%)

Query: 61  LFVTGVHEEAQED-----DMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASA 115
           L     +++   +          F  Y +                    + + +   A+ 
Sbjct: 8   LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAAD 61

Query: 116 ARDALNGTTILGQTVTVDWCFVKGPKK 142
           AR  L+ T  LG+ + + +        
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQTLHIGS 88

>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 = 43.6 bits (102), Expect = 6e-07
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV G+ E+ +E  + + F +YG+I+ + +  DR +G  +G+A V +D   ++       
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 63

Query: 121 NGTTILGQTVTVD 133
              T+ G    V 
Sbjct: 64  KYHTVNGHNCEVR 76

>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 = 44.0 bits (103), Expect = 7e-07
 Identities = 15/74 (20%), Positives = 35/74 (47%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L++  +     E D+   F+ + E K   +     TG ++G A + + + + A  A   +
Sbjct: 21  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 80

Query: 121 NGTTILGQTVTVDW 134
           NG  + G+ + +++
Sbjct: 81  NGYKLYGKILVIEF 94

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 14/82 (17%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 55  SVEGWILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKE 112
           ++EG  + +  +  E   E+ + E F  +G I+ +++   ++   F    A + +++   
Sbjct: 1   TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 113 ASAARDALNGTTILGQTVTVDW 134
           A  A   +N + +  + ++V  
Sbjct: 61  AERAL-QMNRSLLGNREISVSL 81

>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 = 42.1 bits (98), Expect = 3e-06
 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 5/90 (5%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           + F   + ++   +D+H  FS +GEIK +      + G +        +  KEA      
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEKAKEALGKAKD 67

Query: 120 LNGTTILGQTVTVDWCFVKGPKKVAGEQKV 149
            N   +  +   V W  ++G  +    +K+
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKI 97

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 41.1 bits (95), Expect = 6e-06
 Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 46  GDEEPGPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALV 105
           G        S   + LF+  ++      ++    SE     +    +D RTG  + +  V
Sbjct: 1   GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYV 59

Query: 106 EYDSYKEASAARDALNGTTILGQTVTVDW 134
           +++S ++   A + L G  + G  + ++ 
Sbjct: 60  DFESAEDLEKALE-LTGLKVFGNEIKLEK 87

>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 = 9e-06
 Identities = 10/74 (13%), Positives = 26/74 (35%), Gaps = 7/74 (9%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           + V  + +++   ++H+   +Y                 K  A V   + ++A  A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 121 NGTTILGQTVTVDW 134
           +  +  G+ + V  
Sbjct: 61  HQYSFRGKDLIVQL 74

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 19/94 (20%), Positives = 34/94 (36%), Gaps = 13/94 (13%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +FV     +  ED++ E FS+YG++ +            + +A V +   + A +     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQIAQSL--CG 60

Query: 121 NGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
               I G +V +     K           GP  G
Sbjct: 61  EDLIIKGISVHISNAEPK------HNSNSGPSSG 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (92), Expect = 2e-05
 Identities = 15/92 (16%), Positives = 30/92 (32%), Gaps = 7/92 (7%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           GP      + + V+G+       D+ +   E G++    +  D          +VEY   
Sbjct: 8   GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRK 60

Query: 111 KEASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           ++   A   L+ T          +  V   + 
Sbjct: 61  EDMEYALRKLDDTKFRSHEGETSYIRVYPERS 92

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 52  PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYK 111
             +S  G  + + G+   A E+D++  FS    ++          G + G A VE+ +++
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHE 66

Query: 112 EASAARDALNGTTILGQTVTVDWCFVKGPKK 142
           +A AA  A +   +  + V +      G   
Sbjct: 67  DAVAAM-AKDKANMQHRYVELFLNSTAGTSG 96

>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 = 39.7 bits (92), Expect = 2e-05
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 51  GPQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY 110
           G  ++     L+V G+        +  +F  +G I+ +             +A ++Y+S 
Sbjct: 10  GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESL 63

Query: 111 KEASAARDALNGTTILGQT--VTVDW 134
             A AA   + G  + G    + VD+
Sbjct: 64  DAAQAACAKMRGFPLGGPDRRLRVDF 89

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 7e-05
 Identities = 16/102 (15%), Positives = 34/102 (33%), Gaps = 7/102 (6%)

Query: 53  QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKE 112
            +     ++ V G+ E   E D+ E   ++G I  + +   +R         VE+++   
Sbjct: 10  HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQAL------VEFENIDS 63

Query: 113 ASAARDALNGTTILGQTVTVDWCFVKGPKKVAGEQKVGPEGG 154
           A           +        + +    K++      GP  G
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYST-SKRITRPGNSGPSSG 104

>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 = 34.3 bits (78), Expect = 0.001
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           +++ G   +A  DD+ E   + G++ N            KG   V +DS + A       
Sbjct: 9   VYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 121 NGTTILGQTVTVDW 134
            G       + + +
Sbjct: 67  PGQKYKETDLLILF 80

>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 = 34.7 bits (79), Expect = 0.001
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 60  ILFVTGVHEEA-QEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD 118
           +L V+ ++ E      +   F  YG+++ + +  +++       ALV+     +A  A  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 58

Query: 119 ALNGTTILGQTVTVDW 134
            LNG  + G+ + +  
Sbjct: 59  HLNGHKLHGKPIRITL 74

>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 = 34.5 bits (78), Expect = 0.002
 Identities = 15/93 (16%), Positives = 31/93 (33%), Gaps = 10/93 (10%)

Query: 60  ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDA 119
           ++    +       ++ E FS +G +                 A+VE+    EA  A   
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLG------RVLLPEGGITAIVEFLEPLEARKAFRH 65

Query: 120 LNGTTILGQTVTVDW----CFVKGPKKVAGEQK 148
           L  +      + ++W     F   P+K   + +
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHE 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 = 34.1 bits (77), Expect = 0.002
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 7/78 (8%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           + V+G+       D+ +   E G++    +  D            E+   ++ + A   L
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVV-------EFVRKEDMTYAVRKL 55

Query: 121 NGTTILGQTVTVDWCFVK 138
           + T          +  VK
Sbjct: 56  DNTKFRSHEGETAYIRVK 73

>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 = 33.6 bits (76), Expect = 0.003
 Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 1/74 (1%)

Query: 61  LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL 120
           L+++ +     E ++      +G++ +    L   +G  +G      +S ++  A     
Sbjct: 21  LYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 121 NGTTILGQTVTVDW 134
           NG  I         
Sbjct: 80  NGKFIKTPPGVSAP 93

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {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: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.3 bits (76), Expect = 0.003
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 9/78 (11%)

Query: 55  SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEAS 114
           +++   L       E    ++ +    YG I  +           +G  LV +     A 
Sbjct: 21  NLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVR--------INQGQMLVTFADSHSAL 72

Query: 115 AARDALNGTTILGQTVTV 132
           +  D ++G  + G+ V +
Sbjct: 73  SVLD-VDGMKVKGRAVKI 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	192
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.93
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.92
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.92
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.92
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.91
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.91
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.91
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.9
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.9
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.9
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.89
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.89
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.89
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.88
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.88
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.88
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.87
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.87
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.86
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.86
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.85
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.85
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.85
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.85
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.85
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.84
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.84
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.84
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.83
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.83
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.83
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.82
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.82
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.82
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.81
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.8
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.79
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.78
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.76
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
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	99.69
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.61
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.6
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.55
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.87
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.78
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	97.13
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	96.98
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	96.95
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.9
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	96.87
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	96.79
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	96.67
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	96.51
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	96.48
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	96.47
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	96.43
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	96.41
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	96.4
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	96.37
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	96.35
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	96.32
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	96.15
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	96.02
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	96.01
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	96.0
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	96.0
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	95.99
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	95.9
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	95.62
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	95.52
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	95.48
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	95.4
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	95.3
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.24
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	95.08
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	95.07
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	95.01
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	94.97
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	94.66
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	94.39
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	94.16
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	94.15
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	94.05
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	93.91
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	93.9
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	93.46
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	93.15
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	92.62
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	91.55
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	91.31
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	91.3
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	90.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	90.26
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	89.82
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	88.63
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	88.26
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	87.94
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	87.86
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	86.57
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	86.14
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	84.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	83.72
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	82.4
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	82.02
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	80.03

>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=99.93  E-value=8.5e-26  Score=148.49  Aligned_cols=88  Identities=76%  Similarity=1.308  Sum_probs=82.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      |+++.++++|||+|||.++++++|.++|++||.|.+++++.|+.+|+++|||||+|.+.++|++|+..|||..++|+.|+
T Consensus         1 P~~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~   80 (88)
T d1rk8a_           1 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   80 (88)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            46677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |+||.+++
T Consensus        81 V~~a~~kG   88 (88)
T d1rk8a_          81 VDWCFVKG   88 (88)
T ss_dssp             EEESEECC
T ss_pred             EEEecCCC
Confidence            99998763

>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=99.92  E-value=8.8e-25  Score=147.42  Aligned_cols=86  Identities=26%  Similarity=0.372  Sum_probs=81.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|+.|++.|||..|.|+.|+|+||
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy15152        136 FVKGPK  141 (192)
Q Consensus       136 ~~~~~~  141 (192)
                      .++..+
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            877543

>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=99.92  E-value=6.8e-25  Score=142.20  Aligned_cols=80  Identities=24%  Similarity=0.393  Sum_probs=77.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +++|||+|||+++++++|+++|++||.|.++++..++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|+||.|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.92  E-value=2e-24  Score=143.30  Aligned_cols=83  Identities=28%  Similarity=0.408  Sum_probs=79.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..+++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|+.|++.|||..++|+.|+|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      .+.
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.92  E-value=5e-25  Score=145.05  Aligned_cols=84  Identities=29%  Similarity=0.539  Sum_probs=79.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|++||+|.++.++.|+.+|.++|||||+|.+.++|++|++.||+..++|+.|.|+||.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy15152        137 VKGP  140 (192)
Q Consensus       137 ~~~~  140 (192)
                      ++..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.91  E-value=2.1e-24  Score=142.32  Aligned_cols=85  Identities=25%  Similarity=0.436  Sum_probs=80.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.++.|+.+|.++|||||+|.+.++|++|++.|||..++|+.|.|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      |.|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98653

>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=99.91  E-value=3.3e-24  Score=143.82  Aligned_cols=85  Identities=28%  Similarity=0.384  Sum_probs=80.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      +...++|||+|||+++++++|+++|++||.|.+++++.|+.+|+++|||||+|.+.++|++|++.||+..++|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      |.++.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98764

>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=99.91  E-value=3.4e-24  Score=138.86  Aligned_cols=80  Identities=28%  Similarity=0.392  Sum_probs=77.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|.||.|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            35799999999999999999999999999999999998999999999999999999999999999999999999999975

>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=99.91  E-value=2.1e-24  Score=143.16  Aligned_cols=83  Identities=27%  Similarity=0.408  Sum_probs=79.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||.++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+||.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            764

>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=99.91  E-value=1.8e-24  Score=141.13  Aligned_cols=81  Identities=28%  Similarity=0.459  Sum_probs=77.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|||+|||+++++++|+++|++||+|.+++++.|+.||.++|||||+|.+.++|+.|++.|||..+.|++|.|.||.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             C
Q psy15152        139 G  139 (192)
Q Consensus       139 ~  139 (192)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.91  E-value=3.7e-24  Score=138.10  Aligned_cols=77  Identities=31%  Similarity=0.431  Sum_probs=75.2

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .|||+|||+.+|+++|+++|++||+|.+++|+.|+.+|+++|||||+|.++++|+.|++.|+|..+.|++|+|.||.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.90  E-value=8.9e-24  Score=137.80  Aligned_cols=80  Identities=28%  Similarity=0.523  Sum_probs=75.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~  133 (192)
                      ..+++|||+|||+++++++|+++|++||+|.+++++.|+.+|.++|||||+|.+.++|++|++.|||..+.|  ++|.|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            346789999999999999999999999999999999999899999999999999999999999999999997  569999


Q ss_pred             ec
Q psy15152        134 WC  135 (192)
Q Consensus       134 ~a  135 (192)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.90  E-value=1.5e-23  Score=136.76  Aligned_cols=80  Identities=30%  Similarity=0.449  Sum_probs=75.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~v~  133 (192)
                      ...++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..+.|  ++|.|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            345779999999999999999999999999999999999999999999999999999999999999999976  889999


Q ss_pred             ec
Q psy15152        134 WC  135 (192)
Q Consensus       134 ~a  135 (192)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>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=99.90  E-value=5.5e-24  Score=140.24  Aligned_cols=86  Identities=27%  Similarity=0.457  Sum_probs=80.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+..+|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|+|..+.|+.|+|++|
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34577999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy15152        136 FVKGPK  141 (192)
Q Consensus       136 ~~~~~~  141 (192)
                      .++...
T Consensus        83 ~~~~~~   88 (90)
T d1x5sa1          83 GKSSDN   88 (90)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.90  E-value=1.4e-23  Score=141.60  Aligned_cols=86  Identities=23%  Similarity=0.377  Sum_probs=78.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      +.....++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.+++ .|.|+.|.|
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V   83 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   83 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEE
Confidence            3444457899999999999999999999999999999999999999999999999999999999998875 799999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      ++|..+.
T Consensus        84 ~~a~~~~   90 (103)
T d2cqda1          84 NLAYLGA   90 (103)
T ss_dssp             EESTTTC
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.90  E-value=9.6e-24  Score=140.18  Aligned_cols=84  Identities=24%  Similarity=0.459  Sum_probs=78.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCeEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRR-TGFLKGYALVEYDSYKEASAARDAL-NGTTILGQTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~-tg~~~g~afV~f~~~~~a~~al~~l-~~~~~~g~~l~v~  133 (192)
                      ...++|||+|||+++++++|+++|+.||.|.+++|+.++. +|.++|||||+|.+.++|++|++.| |+..+.|++|.|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            4557799999999999999999999999999999988854 8999999999999999999999998 8999999999999


Q ss_pred             ecccCC
Q psy15152        134 WCFVKG  139 (192)
Q Consensus       134 ~a~~~~  139 (192)
                      ||.+..
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998764

>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=99.90  E-value=1.7e-23  Score=137.83  Aligned_cols=81  Identities=25%  Similarity=0.363  Sum_probs=75.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++|+++|+++|+.||.|.++.++.|+.+|.++|||||+|.+.++|++||+.  ...|+|+.|.|++|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            456799999999999999999999999999999999999999999999999999999999984  458999999999998


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ++.
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            764

>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=99.90  E-value=3.3e-23  Score=147.13  Aligned_cols=85  Identities=26%  Similarity=0.366  Sum_probs=79.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.||+++|||||+|.+.++|++|++.|||..|+|+.|+|++|.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy15152        137 VKGPK  141 (192)
Q Consensus       137 ~~~~~  141 (192)
                      ++..+
T Consensus       121 ~~~~~  125 (139)
T d1u6fa1         121 SGHQR  125 (139)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            66433

>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=99.89  E-value=2.9e-23  Score=153.40  Aligned_cols=130  Identities=22%  Similarity=0.390  Sum_probs=104.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHh--hhcccCC------------CCCCCCCCCCCCCCcEEEEcCCCCCCcH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIRE--YESMETD------------VGDEEPGPQRSVEGWILFVTGVHEEAQE   72 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~--~~~~~~~------------~~~~~~~~~~~~~~~~l~V~nLp~~~t~   72 (192)
                      +.++.+++|+.++. +|||+||+|...+.+.  +......            ..............++|||+|||+.+++
T Consensus        33 v~~~~~~~~~~~~~-~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te  111 (183)
T d1u1qa_          33 LTDCVVMRDPNTKR-SRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE  111 (183)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCH
T ss_pred             EEEEEeeecccCCC-ccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcccccccccccccceeEEccCCCcCCH
Confidence            46889999999996 9999999994444322  2221110            0111112233455689999999999999


Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         73 DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        73 ~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++..+.|+.|.|.+|.++
T Consensus       112 ~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             HHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            9999999999999999999999899999999999999999999997 7999999999999999765

>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=99.89  E-value=1e-23  Score=136.30  Aligned_cols=79  Identities=15%  Similarity=0.159  Sum_probs=69.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..+.|++|.|++|.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6899999999999999999999999999888888888999999999999999999999999999999999999999976

>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=99.89  E-value=1e-23  Score=136.86  Aligned_cols=80  Identities=30%  Similarity=0.556  Sum_probs=75.3

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccCC
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNL-HLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~-~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~~  139 (192)
                      |||+|||+++++++|+++|++||.|..+ .++.++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|+||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999999764 789999999999999999999999999999999999999999999998765


Q ss_pred             C
Q psy15152        140 P  140 (192)
Q Consensus       140 ~  140 (192)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.89  E-value=2.9e-23  Score=134.75  Aligned_cols=76  Identities=28%  Similarity=0.488  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ++++|||+|||+++|+++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.|||..++|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            3567999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.89  E-value=3.2e-23  Score=132.98  Aligned_cols=76  Identities=25%  Similarity=0.426  Sum_probs=73.7

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +|||+|||+++++++|+++|++||.|.++++..++ +|+++|||||+|.+.++|++|++.|||..+.|++|+|++|.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999999999999996 89999999999999999999999999999999999999985

>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=99.89  E-value=6.6e-24  Score=135.85  Aligned_cols=76  Identities=16%  Similarity=0.291  Sum_probs=73.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ++|||+|||+++++++|+++|++||.|.+++++.|+.||+++|||||+|.+.++|++|++ ++++.++|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999997 7999999999999987

>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=99.89  E-value=9.3e-24  Score=142.81  Aligned_cols=81  Identities=33%  Similarity=0.487  Sum_probs=77.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|+||.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q psy15152        138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            5

>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=99.89  E-value=6.5e-23  Score=133.32  Aligned_cols=78  Identities=21%  Similarity=0.371  Sum_probs=74.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..+|||+|||+++++++|+++|+.||.|.++.++.|+.+|+++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            3689999999999999999999999999999999999999999999999999999999997 69999999999999875

>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=99.89  E-value=1e-22  Score=134.11  Aligned_cols=82  Identities=27%  Similarity=0.466  Sum_probs=75.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +.++|||+|||.++++++|+++|+.||.|.++.++.++.++  +|||||+|.+.++|+.|++.|+|..+.|+.|+|.||.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999987544  7899999999999999999999999999999999997


Q ss_pred             cCCC
Q psy15152        137 VKGP  140 (192)
Q Consensus       137 ~~~~  140 (192)
                      ++..
T Consensus        85 ~~~~   88 (90)
T d2cqia1          85 TPSS   88 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.88  E-value=6.9e-23  Score=133.48  Aligned_cols=78  Identities=24%  Similarity=0.418  Sum_probs=73.0

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTG---FLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg---~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      |||+|||+++++++|+++|++||.|.++.++.++.++   .++|||||+|.+.++|++|++.|||..++|+.|.|+||..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999987665   4789999999999999999999999999999999999864


Q ss_pred             C
Q psy15152        138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.88  E-value=3.1e-22  Score=132.51  Aligned_cols=83  Identities=20%  Similarity=0.405  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ....++|||+|||+++++++|+++|++||.|.++.++.++  +.++|||||+|.+.++|++|++.||+..++|+.|+|+|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3445689999999999999999999999999999999986  34689999999999999999999999999999999999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      |.++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98764

>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=99.88  E-value=8.5e-23  Score=137.20  Aligned_cols=88  Identities=28%  Similarity=0.465  Sum_probs=79.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIK--------NLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--------~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      .....++|||+|||+.+++++|+++|+.||.|.        .+.+..++.+|+++|||||+|.+.++|.+|++.|||..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            344567999999999999999999999999873        567788888999999999999999999999999999999


Q ss_pred             CCeEEEEEecccCCCC
Q psy15152        126 LGQTVTVDWCFVKGPK  141 (192)
Q Consensus       126 ~g~~l~v~~a~~~~~~  141 (192)
                      .|+.|+|++|.++.+.
T Consensus        84 ~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          84 QGSKLKVSLARKKPPM   99 (101)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCEEEEEEEcCCCCCC
Confidence            9999999999876544

>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=99.88  E-value=1.4e-22  Score=135.39  Aligned_cols=86  Identities=21%  Similarity=0.400  Sum_probs=78.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC------CCeeCC
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN------GTTILG  127 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~------~~~~~g  127 (192)
                      ...++++|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++.|+      |..+.|
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            34456789999999999999999999999999999999999999999999999999999999999886      567899


Q ss_pred             eEEEEEecccCC
Q psy15152        128 QTVTVDWCFVKG  139 (192)
Q Consensus       128 ~~l~v~~a~~~~  139 (192)
                      +.|+|.||.++.
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            999999998754

>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=99.88  E-value=9.5e-23  Score=137.41  Aligned_cols=82  Identities=20%  Similarity=0.333  Sum_probs=77.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|++||.|..+.|+.|+.++.++|||||+|.+.++|++|++ +++..|.|+.|.|++|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3689999999999999999999999999999999999999999999999999999999996 799999999999999987


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            643

>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=99.88  E-value=4.3e-23  Score=131.40  Aligned_cols=75  Identities=21%  Similarity=0.453  Sum_probs=71.6

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++ +++..|+|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            49999999999999999999999999999999999999999999999999999999997 7999999999999754

>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=99.88  E-value=5.5e-23  Score=138.15  Aligned_cols=80  Identities=23%  Similarity=0.373  Sum_probs=76.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|++|++ |||..|.|+.|.|.+|.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999999999999999999999999995 999999999999999865


Q ss_pred             C
Q psy15152        138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.88  E-value=6.1e-23  Score=134.06  Aligned_cols=83  Identities=18%  Similarity=0.344  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCCCCc-HHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         56 VEGWILFVTGVHEEAQ-EDDMHEKFSEYGEIKNLHLNLD-RRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t-~~~L~~~F~~~G~i~~~~i~~~-~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      .++++|||+|||++++ +++|+++|++||.|.++++..+ ..+|+++|||||+|.+.++|++|++ ||+..++|+.|+|+
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            4578999999999976 5669999999999999998764 4689999999999999999999996 99999999999999


Q ss_pred             ecccCC
Q psy15152        134 WCFVKG  139 (192)
Q Consensus       134 ~a~~~~  139 (192)
                      +|.+++
T Consensus        81 ~a~~kP   86 (86)
T d2ghpa3          81 LADKKP   86 (86)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998763

>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=99.87  E-value=4e-22  Score=128.06  Aligned_cols=77  Identities=25%  Similarity=0.442  Sum_probs=73.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .++|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|++ |++..|+|+.|.|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999996 8999999999999876

>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=99.87  E-value=1.1e-22  Score=133.59  Aligned_cols=80  Identities=20%  Similarity=0.338  Sum_probs=74.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..+|||+|||+++++++|+++|++||.|..++++.++  +.++|||||+|.+.++|++|++.|||..++|+.|.|.+|.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3579999999999999999999999999999999986  44789999999999999999999999999999999999986


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.87  E-value=4.8e-23  Score=131.04  Aligned_cols=75  Identities=16%  Similarity=0.393  Sum_probs=71.4

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +|||+|||+++|+++|+++|++||.|.++.|+.|+.+|+++|||||+|.+.++|++|++ +++..|+|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 4778999999999875

>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=99.87  E-value=3.2e-22  Score=134.45  Aligned_cols=85  Identities=14%  Similarity=0.210  Sum_probs=77.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      .+...+.++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|++|++.|||..|.|+++.
T Consensus        12 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~   90 (101)
T d1x5oa1          12 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   90 (101)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCc
Confidence            3445556889999999999999999999999999999998885 899999999999999999999999999999999998


Q ss_pred             EEeccc
Q psy15152        132 VDWCFV  137 (192)
Q Consensus       132 v~~a~~  137 (192)
                      |.++.|
T Consensus        91 v~~~~P   96 (101)
T d1x5oa1          91 SAPTEP   96 (101)
T ss_dssp             CCCSSC
T ss_pred             cCCCCC
Confidence            877654

>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=99.86  E-value=2.5e-22  Score=127.69  Aligned_cols=75  Identities=19%  Similarity=0.379  Sum_probs=72.3

Q ss_pred             EEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         60 ILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        60 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      +|||+|||+++|+++|+++|+.||.|..+.+..++.+|.++|||||+|.+.++|++|++ |||..|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            49999999999999999999999999999999999999999999999999999999997 9999999999999986

>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=99.86  E-value=2e-22  Score=135.64  Aligned_cols=84  Identities=19%  Similarity=0.334  Sum_probs=79.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .++++|||+|||.++++++|+++|+.||.|..+.+..+..+|+++|||||+|.+.++|++|++.|||..+.|++|+|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            35678999999999999999999999999999988888889999999999999999999999999999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .++.
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
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=99.85  E-value=1.1e-21  Score=130.56  Aligned_cols=77  Identities=26%  Similarity=0.483  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+      +|||||+|.+.++|++|+..|+|..|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999999876      6899999999999999999999999999999999997


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      +++
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.85  E-value=1.9e-21  Score=129.36  Aligned_cols=82  Identities=24%  Similarity=0.326  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ..+.++|||+|||+++++++|+++|+.||.|..+..     +|.++|||||+|.+.++|++|++.|||..|+|+.|+|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999998876542     788999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      +.++...
T Consensus        88 a~~k~~~   94 (96)
T d1fjca_          88 TGEKGGT   94 (96)
T ss_dssp             CSSSCCC
T ss_pred             eCCCCCC
Confidence            9887654

>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=99.85  E-value=2.8e-21  Score=128.35  Aligned_cols=80  Identities=19%  Similarity=0.315  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      .+.++|||+|||+++++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|+.|++.||+..|.|++|+|+||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            44578999999999999999999999999999887544   456899999999999999999999999999999999998


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=99.85  E-value=4.8e-21  Score=129.23  Aligned_cols=84  Identities=19%  Similarity=0.294  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDR-RTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~-~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      .+.++|||+|||+++++++|+++|+.|| +..+.++.+. .+|+++|||||+|.+.++|++|+ .||+..|+|+.|+|++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3458999999999999999999999998 7787777765 47899999999999999998777 5999999999999999


Q ss_pred             cccCCCC
Q psy15152        135 CFVKGPK  141 (192)
Q Consensus       135 a~~~~~~  141 (192)
                      |.++...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876443

>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=99.85  E-value=3.1e-21  Score=132.27  Aligned_cols=79  Identities=22%  Similarity=0.368  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+++|||+|||.++++++|+++|+.||.|.+|++..+   +.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999998754   5678999999999999999999999999999999999986


Q ss_pred             cC
Q psy15152        137 VK  138 (192)
Q Consensus       137 ~~  138 (192)
                      +.
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.85  E-value=1.6e-22  Score=133.34  Aligned_cols=81  Identities=17%  Similarity=0.290  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.+ .+|+++|||||+|.+.++|++|++ |||..++|+.|+|.+|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34678999999999999999999999999998888765 589999999999999999999996 9999999999999998


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      .++
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            753

>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=99.85  E-value=5.6e-21  Score=127.51  Aligned_cols=75  Identities=25%  Similarity=0.409  Sum_probs=68.1

Q ss_pred             CCCcEEEEcCCC-CCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEe
Q psy15152         56 VEGWILFVTGVH-EEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDW  134 (192)
Q Consensus        56 ~~~~~l~V~nLp-~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~  134 (192)
                      ...++|||+||| ..+++++|+++|++||.|.++.+        ++|||||+|.+.++|++|++.|||..+.|+.|+|+|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999997 56888999999999999999988        378999999999999999999999999999999999


Q ss_pred             cccC
Q psy15152        135 CFVK  138 (192)
Q Consensus       135 a~~~  138 (192)
                      +.++
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9754

>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=99.85  E-value=5.1e-21  Score=128.68  Aligned_cols=86  Identities=22%  Similarity=0.279  Sum_probs=76.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      ......+++|||+|||+++|+++|+++|..|| +..+.++.+. +|.++|||||+|.+.++|++|++ ||+..|+|+.|+
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~   85 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEE
Confidence            34556678999999999999999999999997 5578888885 79999999999999999999986 899999999999


Q ss_pred             EEecccCCC
Q psy15152        132 VDWCFVKGP  140 (192)
Q Consensus       132 v~~a~~~~~  140 (192)
                      |.++.+.+.
T Consensus        86 V~~s~~~~~   94 (102)
T d1weza_          86 LFLNSTAGT   94 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EEEcCCCCC
Confidence            999876643

>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=99.85  E-value=4.2e-21  Score=130.54  Aligned_cols=77  Identities=19%  Similarity=0.382  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         58 GWILFVTGVHE-EAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        58 ~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +++|||+|||+ .+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|++|++.|||..|.|+.|+|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999965 59999999999999999999998874     7899999999999999999999999999999999986


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.85  E-value=6.9e-21  Score=123.86  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=72.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .++|||+|||.++|+++|+++|+.||.|..+.+..++ +|.++|||||+|.+.++|++|++ +++..+.|+.|.|.|+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999999999998885 89999999999999999999996 79999999999999864

>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=99.84  E-value=3.9e-21  Score=125.31  Aligned_cols=76  Identities=21%  Similarity=0.437  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||.++++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|++.|||..++|+.|+|+||.+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            467999999999999999999999999999999766      57999999999999999999999999999999999976


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>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=99.84  E-value=5.9e-21  Score=123.65  Aligned_cols=77  Identities=26%  Similarity=0.406  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee-CCeEEEEE
Q psy15152         55 SVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI-LGQTVTVD  133 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~-~g~~l~v~  133 (192)
                      .+++++|||+|||.++++++|.++|+.||.|.+++++.++     +|||||+|.+.++|++|++.|||..+ +|+.|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            4457899999999999999999999999999999997653     68999999999999999999999988 46899999


Q ss_pred             ecc
Q psy15152        134 WCF  136 (192)
Q Consensus       134 ~a~  136 (192)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            985

>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=99.84  E-value=3.6e-21  Score=126.29  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHH---HHhhccCCCeeEEEEeecCCCCCc---ceEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy15152         56 VEGWILFVTGVHEEAQEDDM---HEKFSEYGEIKNLHLNLDRRTGFL---KGYALVEYDSYKEASAARDALNGTTILGQT  129 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L---~~~F~~~G~i~~~~i~~~~~tg~~---~g~afV~f~~~~~a~~al~~l~~~~~~g~~  129 (192)
                      ...++|||+|||+++++++|   .++|++||.|.++.++.++.++.+   +|||||+|.+.++|++|++.|||..++|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34567999999999999999   778999999999999999866654   499999999999999999999999999999


Q ss_pred             EEEE
Q psy15152        130 VTVD  133 (192)
Q Consensus       130 l~v~  133 (192)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9984

>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=99.84  E-value=5e-21  Score=124.78  Aligned_cols=79  Identities=24%  Similarity=0.195  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..++|||+|||+++++++|+++|+.||.+....++.+..+|.++|+|||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3467999999999999999999999999876433344458999999999999999999999999999999999999875

>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=99.84  E-value=3.6e-21  Score=128.01  Aligned_cols=82  Identities=23%  Similarity=0.409  Sum_probs=73.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCC-eeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCC--eeCCeEEEEEe
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGE-IKNLHLNLDR-RTGFLKGYALVEYDSYKEASAARDALNGT--TILGQTVTVDW  134 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~-i~~~~i~~~~-~tg~~~g~afV~f~~~~~a~~al~~l~~~--~~~g~~l~v~~  134 (192)
                      ++|||+|||.++++++|+++|+.||. |..+.++.+. .+|+++|||||+|.+.++|..|++.|++.  .+.|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 8999998885 46899999999999999999999999654  56799999999


Q ss_pred             cccCCC
Q psy15152        135 CFVKGP  140 (192)
Q Consensus       135 a~~~~~  140 (192)
                      |.++..
T Consensus        82 A~p~~~   87 (96)
T d2disa1          82 AEPEID   87 (96)
T ss_dssp             SCSSCS
T ss_pred             cCCCCC
Confidence            987543

>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=99.83  E-value=2.7e-21  Score=124.42  Aligned_cols=76  Identities=24%  Similarity=0.362  Sum_probs=68.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCC-eeCCeEEEEEeccc
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGT-TILGQTVTVDWCFV  137 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~-~~~g~~l~v~~a~~  137 (192)
                      ++|||+|||.++++++|+++|++||.|..+.+...      +|||||+|.+.++|++|++.|||. .+.|++|+|+||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            46999999999999999999999999887666544      689999999999999999999996 69999999999987


Q ss_pred             CCC
Q psy15152        138 KGP  140 (192)
Q Consensus       138 ~~~  140 (192)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            643

>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=99.83  E-value=1.7e-21  Score=122.83  Aligned_cols=71  Identities=28%  Similarity=0.478  Sum_probs=68.5

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      |||+|||+++++++|+++|++||.|..+++..++.++.++|||||+|.+.++|++|++.|||..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999999999999998764

>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=99.83  E-value=9.3e-21  Score=121.56  Aligned_cols=75  Identities=25%  Similarity=0.400  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      .+++|||+||+  +|+++|+++|++||.|.++.+..+      +|||||+|.+.++|..|++.|||..++|++|+|.||.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            46789999996  899999999999999999998654      5799999999999999999999999999999999997


Q ss_pred             cCC
Q psy15152        137 VKG  139 (192)
Q Consensus       137 ~~~  139 (192)
                      +++
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.83  E-value=4.2e-20  Score=124.56  Aligned_cols=83  Identities=14%  Similarity=0.038  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ....+|||+|||+++|+++|+++|..+|.+....++.+..++.++|||||+|.++++|++|++ +|+..|+|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            345679999999999999999999999999887677777799999999999999999999996 8999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7664

>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=99.83  E-value=4e-20  Score=120.42  Aligned_cols=76  Identities=21%  Similarity=0.308  Sum_probs=69.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      .++|||+|||+++++++|+++|++||.|..+.+..      ++|||||+|.+.++|.+|+..|||..|.|+.|.|.||.|
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            46899999999999999999999999988776643      478999999999999999999999999999999999986


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpda1          82 VD   83 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.83  E-value=1.7e-20  Score=122.70  Aligned_cols=78  Identities=18%  Similarity=0.194  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee-CCeEEEEEec
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI-LGQTVTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~-~g~~l~v~~a  135 (192)
                      ++++|||+|||+++++++|+++|++||.|..+.+...    +.+|||||+|.+.++|.+|+..|||..+ +|+.|+|.|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            4678999999999999999999999999988776543    4578999999999999999999999988 5899999998


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.82  E-value=9.3e-21  Score=129.15  Aligned_cols=78  Identities=17%  Similarity=0.198  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++++++|+++|+.||.|..+.|..      ++|||||+|.+.++|++|++.|||..|.|++|.|+|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3457899999999999999999999999999998743      4789999999999999999999999999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      ....
T Consensus        82 ~~~~   85 (111)
T d1whxa_          82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            6553

>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=99.82  E-value=3e-20  Score=123.92  Aligned_cols=82  Identities=17%  Similarity=0.271  Sum_probs=73.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy15152         52 PQRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVT  131 (192)
Q Consensus        52 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~  131 (192)
                      |......++|||+|||+++++++|+++|++||.|..+.+..       +|||||+|.+.++|++|++.|||..+.|+.|+
T Consensus         9 p~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_           9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             CCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            34445678899999999999999999999999999998753       47999999999999999999999999999999


Q ss_pred             EEecccCCC
Q psy15152        132 VDWCFVKGP  140 (192)
Q Consensus       132 v~~a~~~~~  140 (192)
                      |.++.....
T Consensus        82 v~~~~~~~~   90 (98)
T d1wg4a_          82 TSYIRVYPE   90 (98)
T ss_dssp             EEEEEEECC
T ss_pred             EEEEecCCC
Confidence            999977653

>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=99.82  E-value=1.1e-20  Score=124.37  Aligned_cols=80  Identities=15%  Similarity=0.395  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy15152         57 EGWILFVTGVHEEAQEDDMH----EKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTV  132 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~----~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v  132 (192)
                      ++++|||+|||+++++++|+    ++|++||+|.++.+..   ++.++|||||+|.+.++|.+|++.|||..+.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            46789999999999999886    4689999999988743   5778999999999999999999999999999999999


Q ss_pred             EecccCC
Q psy15152        133 DWCFVKG  139 (192)
Q Consensus       133 ~~a~~~~  139 (192)
                      .||.++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9997653

>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=99.82  E-value=4e-21  Score=125.55  Aligned_cols=74  Identities=19%  Similarity=0.248  Sum_probs=68.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|||+|||+++++++|+++|++||.|.++.+..+       |||||+|.+.++|++|++.|||..|.|+.|.|.++.+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999988644       79999999999999999999999999999999988765


Q ss_pred             C
Q psy15152        139 G  139 (192)
Q Consensus       139 ~  139 (192)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            4

>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=99.82  E-value=6.2e-20  Score=122.18  Aligned_cols=80  Identities=20%  Similarity=0.368  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC--eEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILG--QTVT  131 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g--~~l~  131 (192)
                      ...+.++|||+|||+++++++|+++|++||.|..+++..+      ++||||+|.+.++|++|++.||+..|.|  ++|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEE
Confidence            4456788999999999999999999999999999998755      5799999999999999999999999986  5899


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |+||++.+
T Consensus        87 v~~ak~~~   94 (97)
T d1whya_          87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99997653

>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=99.82  E-value=1.4e-20  Score=123.21  Aligned_cols=77  Identities=21%  Similarity=0.320  Sum_probs=68.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..+++|||+|||+++++++|+++|++||.|.++++.     ..++|||||+|.+.++|++|+.  ++..|+|+.|.|++|
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            346789999999999999999999999999998764     3458999999999999999995  788999999999999


Q ss_pred             ccCC
Q psy15152        136 FVKG  139 (192)
Q Consensus       136 ~~~~  139 (192)
                      .++.
T Consensus        76 ~~k~   79 (88)
T d1wf0a_          76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.81  E-value=5.9e-20  Score=120.15  Aligned_cols=75  Identities=15%  Similarity=0.184  Sum_probs=65.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      +++|||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|++|++.||+..+.|++|.|+|+..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46799999999999999999999999 323332      44589999999999999999999999999999999999965


Q ss_pred             CC
Q psy15152        138 KG  139 (192)
Q Consensus       138 ~~  139 (192)
                      +.
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.81  E-value=6.5e-20  Score=116.38  Aligned_cols=74  Identities=15%  Similarity=0.181  Sum_probs=67.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ++|||+|||+++++++|+++|+.||.|..+++..++.  ..++||||+|.+.++|++|+. +++..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999999864  345799999999999999995 8999999999999865

>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=99.80  E-value=3.6e-19  Score=116.32  Aligned_cols=80  Identities=14%  Similarity=0.178  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCeEEE
Q psy15152         54 RSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL--NGTTILGQTVT  131 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l--~~~~~~g~~l~  131 (192)
                      ...++++|||+|||.++++++|+++|++||.|.++.+..+      +|||||+|.+.++|++|++.+  ++..+.|++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3456789999999999999999999999999999988755      479999999999999999865  56789999999


Q ss_pred             EEecccCC
Q psy15152        132 VDWCFVKG  139 (192)
Q Consensus       132 v~~a~~~~  139 (192)
                      |.|+..+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997553

>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=99.80  E-value=1.9e-19  Score=122.06  Aligned_cols=79  Identities=20%  Similarity=0.260  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee--CCeEEEEEe
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI--LGQTVTVDW  134 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~--~g~~l~v~~  134 (192)
                      +..+|||+|||+.+|+++|+++|++||.|.++.+..++    ++|||||+|.+.++|+.|+..|||..|  .|+.|.|.|
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34679999999999999999999999999999998774    479999999999999999999999998  578899999


Q ss_pred             cccCC
Q psy15152        135 CFVKG  139 (192)
Q Consensus       135 a~~~~  139 (192)
                      +.+..
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87654

>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=99.79  E-value=2.5e-19  Score=113.59  Aligned_cols=71  Identities=18%  Similarity=0.331  Sum_probs=63.9

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         61 LFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        61 l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|++.|||..+.|++|.|+|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444443      456899999999999999999999999999999999999654

>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=99.79  E-value=6.1e-20  Score=123.51  Aligned_cols=79  Identities=16%  Similarity=0.111  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         58 GWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        58 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      ..+|||+|||+++++++|+++|+.||.+..+.++.+..+|+++|||||+|.+.++|++|++ ||+..|.|+.|.|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            4579999999999999999999999998765444444699999999999999999999996 899999999999998754

>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=99.79  E-value=1.4e-18  Score=116.89  Aligned_cols=81  Identities=22%  Similarity=0.265  Sum_probs=71.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCeEE
Q psy15152         53 QRSVEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL--NGTTILGQTV  130 (192)
Q Consensus        53 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l--~~~~~~g~~l  130 (192)
                      ....++.+|||+|||..+++++|.++|++||.|..+.+..+      +|+|||+|.+.++|++|++.|  ++..+.|++|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            34456789999999999999999999999999999988654      689999999999999999987  5567899999


Q ss_pred             EEEecccCC
Q psy15152        131 TVDWCFVKG  139 (192)
Q Consensus       131 ~v~~a~~~~  139 (192)
                      +|.|+..+.
T Consensus        84 ~v~~s~~~~   92 (104)
T d1wexa_          84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEcCCCc
Confidence            999997553

>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=99.78  E-value=2e-19  Score=122.72  Aligned_cols=82  Identities=16%  Similarity=0.163  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         56 VEGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ...++|||+|||+++|+++|.++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|++ ||+..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            356789999999999999999999999999776566666699999999999999999999996 8999999999999987


Q ss_pred             ccC
Q psy15152        136 FVK  138 (192)
Q Consensus       136 ~~~  138 (192)
                      .+.
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            543

>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=99.77  E-value=1.1e-18  Score=116.45  Aligned_cols=79  Identities=22%  Similarity=0.255  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH--HhCCCeeCCeEE
Q psy15152         54 RSVEGWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARD--ALNGTTILGQTV  130 (192)
Q Consensus        54 ~~~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~--~l~~~~~~g~~l  130 (192)
                      ....+++|||+|||.+ +|+++|.++|++||.|.++.++.+      +|+|||+|.+.++|.+|++  .+++..++|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3455689999999985 899999999999999999998765      5899999999999999998  568889999999


Q ss_pred             EEEecccC
Q psy15152        131 TVDWCFVK  138 (192)
Q Consensus       131 ~v~~a~~~  138 (192)
                      .|.||..+
T Consensus        88 ~V~~s~~~   95 (99)
T d1x4fa1          88 KVDLSEKY   95 (99)
T ss_dssp             EEEEECSC
T ss_pred             EEEEcCCc
Confidence            99999644

>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=99.76  E-value=1e-18  Score=117.53  Aligned_cols=79  Identities=13%  Similarity=0.114  Sum_probs=69.2

Q ss_pred             CCCcEEEEcCCCCCCc-----HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy15152         56 VEGWILFVTGVHEEAQ-----EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTV  130 (192)
Q Consensus        56 ~~~~~l~V~nLp~~~t-----~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l  130 (192)
                      ...++|||+||+.++.     +++|+++|+.||.|.+++++..      +|||||+|.+.++|.+|++.|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            3457899999999753     3569999999999999998744      6799999999999999999999999999999


Q ss_pred             EEEecccCCC
Q psy15152        131 TVDWCFVKGP  140 (192)
Q Consensus       131 ~v~~a~~~~~  140 (192)
                      +|.||.+...
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999976643

>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=99.75  E-value=3e-18  Score=112.10  Aligned_cols=78  Identities=15%  Similarity=0.173  Sum_probs=69.3

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCeEEE
Q psy15152         55 SVEGWILFVTGVHEE-AQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL--NGTTILGQTVT  131 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~-~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l--~~~~~~g~~l~  131 (192)
                      ..++.+|||+|||.. +|+++|.++|++||.|.++.++.+      +++|||+|++.++|..|++.|  ++..+.|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            345678999999996 889999999999999999999766      468999999999999999966  67789999999


Q ss_pred             EEecccC
Q psy15152        132 VDWCFVK  138 (192)
Q Consensus       132 v~~a~~~  138 (192)
                      |.||...
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999643

>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=99.71  E-value=6.6e-20  Score=120.39  Aligned_cols=76  Identities=21%  Similarity=0.286  Sum_probs=66.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEE-----eecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHL-----NLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVD  133 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i-----~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~  133 (192)
                      ++|||+|||+++++++|+++|+.||.+..+.+     ..+..+++++|||||+|.+.++|++|++ |||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            57999999999999999999999998766544     3445678899999999999999999995 99999999999996


Q ss_pred             ec
Q psy15152        134 WC  135 (192)
Q Consensus       134 ~a  135 (192)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.69  E-value=2.9e-18  Score=115.28  Aligned_cols=76  Identities=20%  Similarity=0.215  Sum_probs=71.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEec
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWC  135 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a  135 (192)
                      ..++|.+++..+++++|+++|++||+|.++.|+.+. +|.++|+|||+|.+.++|.+|++.|||..++|++|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            358888999999999999999999999999998774 8999999999999999999999999999999999999985

>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=99.63  E-value=4.3e-16  Score=106.08  Aligned_cols=74  Identities=20%  Similarity=0.322  Sum_probs=65.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCH-HHHHHHHHHhCCCeeCCeEEEEEeccc
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSY-KEASAARDALNGTTILGQTVTVDWCFV  137 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~-~~a~~al~~l~~~~~~g~~l~v~~a~~  137 (192)
                      -.+||||||+++|+++|+++|++||+|.+|.++.+      +|||||.|.++ ++|..|+..|++..+.++.+.|.|+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34599999999999999999999999999999755      68999999985 789999999999998888877877654


Q ss_pred             C
Q psy15152        138 K  138 (192)
Q Consensus       138 ~  138 (192)
                      .
T Consensus        86 ~   86 (113)
T d1owxa_          86 E   86 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.61  E-value=2.3e-15  Score=110.29  Aligned_cols=80  Identities=21%  Similarity=0.399  Sum_probs=73.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecccC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCFVK  138 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~~~  138 (192)
                      ++|||+|||+++|+++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|+.. ++..+.++.+.+.+..+.
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhhc
Confidence            6899999999999999999999999999999999999999999999999999999999984 777888999888876544


Q ss_pred             C
Q psy15152        139 G  139 (192)
Q Consensus       139 ~  139 (192)
                      .
T Consensus        86 ~   86 (183)
T d1u1qa_          86 E   86 (183)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.61  E-value=6.4e-16  Score=103.07  Aligned_cols=64  Identities=20%  Similarity=0.346  Sum_probs=57.5

Q ss_pred             CCCcEEEEc--CCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         56 VEGWILFVT--GVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        56 ~~~~~l~V~--nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      .+..+|||.  |||.++|+++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345678895  59999999999999999999999988755      57999999999999999999999987

>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=99.60  E-value=2.8e-15  Score=99.54  Aligned_cols=84  Identities=20%  Similarity=0.286  Sum_probs=71.0

Q ss_pred             CCCCCCCcEEEEcCC--CCCCc---------HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy15152         52 PQRSVEGWILFVTGV--HEEAQ---------EDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDAL  120 (192)
Q Consensus        52 ~~~~~~~~~l~V~nL--p~~~t---------~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l  120 (192)
                      |.+...+.+|+|.||  |.++.         +++|++.|++||.|..+.+..+    ..+|+|||+|.+.++|.+|+..|
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHh
Confidence            455667789999999  54322         3678999999999999988654    45799999999999999999999


Q ss_pred             CCCeeCCeEEEEEecccCC
Q psy15152        121 NGTTILGQTVTVDWCFVKG  139 (192)
Q Consensus       121 ~~~~~~g~~l~v~~a~~~~  139 (192)
                      ||..++|++|.|.++.++.
T Consensus        78 ng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          78 DGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TTCEETTEECEEEECCSCC
T ss_pred             CCcEECCEEEEEEEeCCcC
Confidence            9999999999999987653

>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=99.55  E-value=6.2e-15  Score=94.16  Aligned_cols=73  Identities=18%  Similarity=0.238  Sum_probs=61.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeE-EEEEec
Q psy15152         57 EGWILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQT-VTVDWC  135 (192)
Q Consensus        57 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~-l~v~~a  135 (192)
                      +.+.|+|+++|++.+++.| ++|++||.|.++++.      ..+|||||+|.++++|++||+ +||..++|+. |.|..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3466999999999987655 579999999999864      346899999999999999996 8999999984 678776


Q ss_pred             cc
Q psy15152        136 FV  137 (192)
Q Consensus       136 ~~  137 (192)
                      ..
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.4e-14  Score=95.03  Aligned_cols=82  Identities=21%  Similarity=0.282  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCC--CCCCc--------HHHHHHhhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCC
Q psy15152         56 VEGWILFVTGV--HEEAQ--------EDDMHEKFSEYGEIKNLHLNLDRRTG--FLKGYALVEYDSYKEASAARDALNGT  123 (192)
Q Consensus        56 ~~~~~l~V~nL--p~~~t--------~~~L~~~F~~~G~i~~~~i~~~~~tg--~~~g~afV~f~~~~~a~~al~~l~~~  123 (192)
                      .++..|.+.|+  |..+.        .++|++.|++||.|.++.|+++..+.  ...|++||+|.+.++|.+|+..|||.
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            35678999999  44432        35789999999999999998876443  35689999999999999999999999


Q ss_pred             eeCCeEEEEEeccc
Q psy15152        124 TILGQTVTVDWCFV  137 (192)
Q Consensus       124 ~~~g~~l~v~~a~~  137 (192)
                      .++||.|.+.|+..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>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=97.87  E-value=4.5e-05  Score=45.37  Aligned_cols=61  Identities=21%  Similarity=0.300  Sum_probs=52.2

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEecc
Q psy15152         73 DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTILGQTVTVDWCF  136 (192)
Q Consensus        73 ~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~~g~~l~v~~a~  136 (192)
                      +.|...|+++|.|.++.+.... .|..  .|-|...+.++|.-|+..||...|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3466789999999999886653 3443  69999999999999999999999999999999875

>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=97.78  E-value=0.00011  Score=46.26  Aligned_cols=77  Identities=10%  Similarity=0.232  Sum_probs=60.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHHHhCCCeeCC-----eEEE
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGF--LKGYALVEYDSYKEASAARDALNGTTILG-----QTVT  131 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~--~~g~afV~f~~~~~a~~al~~l~~~~~~g-----~~l~  131 (192)
                      ++|.|+.||+.+|++++.+.++..|++..........+-+  .-.-|||.|.+.++.....+..+|..+.+     .+-.
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            4799999999999999999999999888776655543322  22579999999999999999999998642     2345


Q ss_pred             EEec
Q psy15152        132 VDWC  135 (192)
Q Consensus       132 v~~a  135 (192)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5555

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.77  E-value=5e-05  Score=47.46  Aligned_cols=72  Identities=18%  Similarity=0.268  Sum_probs=56.5

Q ss_pred             CCCCcEEEEcCCCCCCcH---------HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q psy15152         55 SVEGWILFVTGVHEEAQE---------DDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALNGTTI  125 (192)
Q Consensus        55 ~~~~~~l~V~nLp~~~t~---------~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~~~~~  125 (192)
                      .++..+|.|.=...+..+         .+|.+.|+.||+|.-+++..+        -..|+|.+-++|.+|+. ++|.++
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEE
Confidence            344456777544433222         367888999999999999877        58999999999999997 799999


Q ss_pred             CCeEEEEEec
Q psy15152        126 LGQTVTVDWC  135 (192)
Q Consensus       126 ~g~~l~v~~a  135 (192)
                      .|+.|.|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999999743

>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=97.13  E-value=0.00011  Score=44.91  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.5

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETST   31 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~   31 (192)
                      +.++.+++|+.+++ +||||||+|.
T Consensus        27 i~~v~i~~d~~tg~-~kG~aFV~f~   50 (77)
T d1uawa_          27 VKECLVMRDPLTKR-SRGFGFVTFM   50 (77)
T ss_dssp             CCCEEEECCCCSSS-CSSEEEECCC
T ss_pred             cceeeeecccCCCC-ccceEEEEEC
Confidence            56889999999995 9999999993

>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=96.98  E-value=0.00011  Score=44.75  Aligned_cols=28  Identities=25%  Similarity=0.286  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        25 ~I~~v~i~~d~~t~~-~rG~~FV~f~~~~   52 (75)
T d1x0fa1          25 EVESIELPMDNKTNK-RRGFCFITFKEEE   52 (75)
T ss_dssp             CEEEEECCCCTTTCC-TTCCEEEEESSSH
T ss_pred             Ccccccccccccccc-cccEEEEEECCHH
Confidence            367899999999995 9999999994333

>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=96.95  E-value=9.5e-05  Score=46.64  Aligned_cols=28  Identities=21%  Similarity=0.233  Sum_probs=23.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ +||||||+|...+
T Consensus        34 ~i~~v~i~~d~~tg~-srG~aFV~f~~~~   61 (90)
T d2cqga1          34 EVLMVQVKKDLKTGH-SKGFGFVRFTEYE   61 (90)
T ss_dssp             CEEEEEEEECSSSCS-EEEEEEEEESSHH
T ss_pred             ccceeeeccCCCCcc-cCCEEEEEECCHH
Confidence            367899999999996 9999999994444

>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=96.90  E-value=0.00027  Score=43.85  Aligned_cols=28  Identities=18%  Similarity=0.264  Sum_probs=23.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|+.|++ +||||||+|...+.
T Consensus        28 v~~v~i~~d~~tg~-~rg~aFV~f~~~~~   55 (85)
T d2u2fa_          28 LKAFNLVKDSATGL-SKGYAFCEYVDINV   55 (85)
T ss_dssp             EEEEEEECCCSSSC-CCCEEEEEESSSHH
T ss_pred             cceEEeeccccccc-cceeEEEEECCHHH
Confidence            56899999999996 99999999944443

>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=96.87  E-value=0.00022  Score=45.90  Aligned_cols=26  Identities=4%  Similarity=0.322  Sum_probs=22.6

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCCh
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTR   32 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~   32 (192)
                      .+.+|.+++|+.+++ +||||||+|..
T Consensus        44 ~V~~v~i~~d~~tg~-~kG~afV~F~~   69 (101)
T d2cq4a1          44 KVRDVRIISDRNSRR-SKGIAYVEFCE   69 (101)
T ss_dssp             CEEEEEECCSCCSSS-CCCCEEEEESC
T ss_pred             eEEEEEeeecCCCcc-ccceEEEEECC
Confidence            456899999999996 99999999933

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.85  E-value=0.0039  Score=39.26  Aligned_cols=55  Identities=18%  Similarity=0.210  Sum_probs=45.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy15152         59 WILFVTGVHEEAQEDDMHEKFSEYGEIKNLHLNLDRRTGFLKGYALVEYDSYKEASAARDALN  121 (192)
Q Consensus        59 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~~~i~~~~~tg~~~g~afV~f~~~~~a~~al~~l~  121 (192)
                      .-||.-..|..+...+|.++|++||.| .|.++-|.       -|||...+.++|+.++..+.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            347888999999999999999999988 44555552       69999999999999987654

>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=96.79  E-value=0.00018  Score=44.09  Aligned_cols=32  Identities=9%  Similarity=0.115  Sum_probs=25.4

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHHHhh
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEIREY   38 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~~   38 (192)
                      .+.+|.+++|+.+++ +||||||+|...+.+..
T Consensus        26 ~i~~v~i~~d~~tg~-~~g~aFV~f~~~~~a~~   57 (80)
T d1cvja1          26 PILSIRVCRDMITRR-SLGYAYVNFQQPADAER   57 (80)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHHHHH
T ss_pred             CEeEEEEEecccccC-CCCceEEEECCHHHHHH
Confidence            367899999999995 99999999955544333

>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=96.67  E-value=0.00028  Score=42.68  Aligned_cols=28  Identities=18%  Similarity=0.222  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ +||||||+|...+
T Consensus        25 ~i~~~~i~~d~~t~~-~kg~afV~f~~~~   52 (75)
T d1hd0a_          25 EVVDCTLKLDPITGR-SRGFGFVLFKESE   52 (75)
T ss_dssp             CEEEEECCCBTTTTB-CCSEEEEEESSHH
T ss_pred             cccccccccCCCCCC-cCceEEEEECCHH
Confidence            356889999999995 9999999994444

>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=96.51  E-value=0.00038  Score=43.90  Aligned_cols=27  Identities=15%  Similarity=0.229  Sum_probs=22.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ +||||||+|...+
T Consensus        36 v~~v~~~~d~~tg~-~kg~afV~f~~~~   62 (93)
T d1x5ua1          36 VVNTHMPKDRVTGQ-HQGYGFVEFLSEE   62 (93)
T ss_dssp             EEEEECCBCSSSCS-BCSCEEEEESSHH
T ss_pred             ccccceeecccccc-cccceEEEECCHH
Confidence            56889999999996 9999999994443

>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=96.48  E-value=0.00035  Score=43.68  Aligned_cols=27  Identities=22%  Similarity=0.202  Sum_probs=22.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ +||||||+|...+
T Consensus        32 i~~v~i~~d~~~~~-~kg~afV~f~~~~   58 (89)
T d2cqba1          32 ITDIQIPLDYETEK-HRGFAFVEFELAE   58 (89)
T ss_dssp             CCCEECCCCSSSCC-CSSEEEECCSSHH
T ss_pred             EEeccccccccccc-ccceeEEEECCHH
Confidence            56889999999996 9999999994444

>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=96.47  E-value=0.00066  Score=43.59  Aligned_cols=29  Identities=17%  Similarity=0.351  Sum_probs=24.0

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.+++ +||||||+|...+.
T Consensus        36 ~i~~v~i~~d~~tg~-~kg~afV~f~~~~~   64 (103)
T d2cqda1          36 DIEEAVVITDRQTGK-SRGYGFVTMADRAA   64 (103)
T ss_dssp             CEEEEEESCCSSSCC-CCSEEEEEESSHHH
T ss_pred             cccceeccccccccc-cCCeEEEEECCHHH
Confidence            467899999999996 99999999944443

>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=96.43  E-value=0.00036  Score=43.19  Aligned_cols=28  Identities=29%  Similarity=0.449  Sum_probs=23.3

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.++. +||||||+|...+
T Consensus        32 ~i~~v~i~~d~~tg~-~kG~afV~f~~~~   59 (84)
T d1l3ka1          32 TLTDCVVMRDPNTKR-SRGFGFVTYATVE   59 (84)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHH
T ss_pred             cccceeecccccCCC-cccEEEEEEcCHH
Confidence            356889999999995 9999999994444

>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=96.41  E-value=0.00029  Score=43.97  Aligned_cols=28  Identities=11%  Similarity=0.182  Sum_probs=23.3

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        33 ~i~~v~i~~d~~tg~-~~g~afV~f~~~~   60 (88)
T d1rk8a_          33 EIKNIHLNLDRRTGF-SKGYALVEYETHK   60 (88)
T ss_dssp             CEEEEEEEECTTTSS-EEEEEEEEESSHH
T ss_pred             Ccccccccccccccc-cccceeEEECCHH
Confidence            356899999999995 9999999994444

>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=96.40  E-value=0.00044  Score=44.04  Aligned_cols=27  Identities=26%  Similarity=0.207  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|+.+++ +||||||+|...+
T Consensus        35 v~~v~i~~d~~tg~-~~g~afV~f~~~~   61 (99)
T d1whwa_          35 LSELHYPIDSLTKK-PKGFAFVTFMFPE   61 (99)
T ss_dssp             EEEEECCCCTTTCC-CCSEEEEEESSHH
T ss_pred             ceeeeecccccccc-cCcceEEEECCHH
Confidence            56899999999996 9999999994433

>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=96.37  E-value=0.00031  Score=43.49  Aligned_cols=29  Identities=17%  Similarity=0.190  Sum_probs=23.6

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.++.+++|+.++. +||||||+|...+.
T Consensus        32 ~i~~~~~~~d~~~g~-~~g~afV~f~~~~~   60 (85)
T d1b7fa2          32 SIVQKNILRDKLTGR-PRGVAFVRYNKREE   60 (85)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHH
T ss_pred             CEeeeeeeccccccc-CceeEEEEECCHHH
Confidence            356899999999995 99999999944443

>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=96.35  E-value=0.00038  Score=43.60  Aligned_cols=28  Identities=25%  Similarity=0.350  Sum_probs=23.1

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.++. +||||||+|...+
T Consensus        34 ~v~~v~i~~d~~t~~-~rg~afV~f~~~~   61 (90)
T d2cq0a1          34 SISRIYLAKDKTTGQ-SKGFAFISFHRRE   61 (90)
T ss_dssp             CEEEEEEEECSSSCS-EEEEEEEEESSHH
T ss_pred             ccccccccccccccc-cccceeEEECCHH
Confidence            356899999999996 9999999994333

>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=96.32  E-value=0.00095  Score=42.88  Aligned_cols=28  Identities=29%  Similarity=0.472  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.++. +||||||+|....
T Consensus        46 ~i~~~~i~~d~~~~~-~kg~aFV~f~~~~   73 (103)
T d1x4ba1          46 KLTDCVVMRDPASKR-SRGFGFVTFSSMA   73 (103)
T ss_dssp             CCSEEEEECCTTTSS-CCSEEEEECSSHH
T ss_pred             cccceeecccccCCC-ccCeEEEEECCHH
Confidence            356899999999995 9999999994443

>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=96.15  E-value=0.00081  Score=41.52  Aligned_cols=28  Identities=18%  Similarity=0.167  Sum_probs=23.3

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ +||||||+|...+
T Consensus        32 ~v~~v~i~~d~~~g~-~kg~afV~f~~~~   59 (85)
T d1fxla2          32 RIITSRILVDQVTGV-SRGVGFIRFDKRI   59 (85)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHH
T ss_pred             Ccccccccccccccc-CCCeeEEEEcCHH
Confidence            367899999999996 9999999994444

>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=96.02  E-value=0.0011  Score=40.66  Aligned_cols=26  Identities=4%  Similarity=0.100  Sum_probs=20.8

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+++|+.+++ +||||||+|...+.
T Consensus        28 ~~~i~~~~~~g~-~~g~afV~f~~~~~   53 (83)
T d1x5ta1          28 TPKIMRDPDTGN-SKGYAFINFASFDA   53 (83)
T ss_dssp             CCEECCCTTTCS-CCSEEEEEBSSHHH
T ss_pred             eEEEEeeccccc-cCceEEEEECCHHH
Confidence            457889999996 99999999944443

>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=96.01  E-value=0.00058  Score=41.77  Aligned_cols=29  Identities=7%  Similarity=0.015  Sum_probs=23.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.++.+++|+.+++ +||||||+|...+.
T Consensus        28 ~v~~~~i~~~~~~g~-~~g~afV~f~~~~~   56 (82)
T d1b7fa1          28 PINTCRIMRDYKTGY-SYGYAFVDFTSEMD   56 (82)
T ss_dssp             CEEEEECCEETTTTE-ECSEEEEEESSHHH
T ss_pred             CcceeeeeeecccCC-ccccceEEECCHHH
Confidence            356889999999995 99999999944443

>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=96.00  E-value=0.00056  Score=43.90  Aligned_cols=29  Identities=14%  Similarity=0.236  Sum_probs=23.7

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.+++ +||||||+|...+.
T Consensus        34 ~i~~v~i~~~~~tg~-~~g~afV~f~~~~~   62 (104)
T d1p1ta_          34 PVVSFRLVYDRETGK-PKGYGFCEYQDQET   62 (104)
T ss_dssp             CCSEEEEEEETTTTE-EEEEEEEECSCHHH
T ss_pred             cccccccccccceec-cCCceEEEECCHHH
Confidence            356899999999996 99999999944443

>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=96.00  E-value=0.00063  Score=41.76  Aligned_cols=28  Identities=11%  Similarity=0.280  Sum_probs=23.2

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+++|+.+++ +||||||+|...+
T Consensus        35 ~i~~v~i~~~~~~~~-~~g~afV~f~~~~   62 (83)
T d2cqca1          35 PIADVSIVYDQQSRR-SRGFAFVYFENVD   62 (83)
T ss_dssp             CEEEEEEEECSSSSS-EEEEEEEEESSHH
T ss_pred             CCccccccccccccc-cccceEEEECCHH
Confidence            357899999999995 9999999994444

>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=95.99  E-value=0.00075  Score=42.45  Aligned_cols=29  Identities=21%  Similarity=0.106  Sum_probs=23.9

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++|+.+++ +||||||+|...+.
T Consensus        33 ~i~~v~i~~~~~~~~-~kg~afV~f~~~~~   61 (93)
T d1h2vz_          33 DIKKIIMGLDKMKKT-ACGFCFVEYYSRAD   61 (93)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHH
T ss_pred             Ccceecccccccccc-ccceEEEEECCHHH
Confidence            357899999999996 99999999944443

>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=95.90  E-value=0.00072  Score=45.74  Aligned_cols=28  Identities=11%  Similarity=0.349  Sum_probs=23.6

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.+++ +||||||+|...+
T Consensus        68 ~i~~v~i~~d~~t~~-~rg~afV~f~~~~   95 (139)
T d1u6fa1          68 PIESVKIVCDRETRQ-SRGYGFVKFQSGS   95 (139)
T ss_dssp             CEEEEEEEEETTTTE-EEEEEEEEESSHH
T ss_pred             ccccccccccccccc-ccceeeEEECCHH
Confidence            467899999999996 9999999994444

>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=95.62  E-value=0.002  Score=40.54  Aligned_cols=31  Identities=19%  Similarity=0.213  Sum_probs=22.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIRE   37 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~   37 (192)
                      +.+|.+++|.....++||||||+|.....+.
T Consensus        29 i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~   59 (96)
T d2disa1          29 VLDVIVYASAADKMKNRGFAFVEYESHRAAA   59 (96)
T ss_dssp             EEEEECCSSSCTTTTTCCEEEEEESSHHHHH
T ss_pred             ceEEEEeeeccccccCCCeEEEEEcCHHHHH
Confidence            5688899987643359999999995554433

>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=95.52  E-value=0.0012  Score=40.18  Aligned_cols=29  Identities=10%  Similarity=0.203  Sum_probs=23.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.++.+++|..+++ +||||||+|...+.
T Consensus        28 ~v~~v~i~~~~~~~~-~~g~afv~f~~~~~   56 (82)
T d1fxla1          28 EIESCKLVRDKITGQ-SLGYGFVNYIDPKD   56 (82)
T ss_dssp             CEEEEEEEECTTTCC-EEEEEEEEESSHHH
T ss_pred             CcccccceeeccCCC-ceeeEEEEECCHHH
Confidence            356889999999995 99999999954443

>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=95.48  E-value=0.0034  Score=39.37  Aligned_cols=27  Identities=15%  Similarity=0.155  Sum_probs=22.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.++.++.++. +||||||+|...+
T Consensus        35 v~~~~~~~~~~~~~-~~g~afV~F~~~~   61 (98)
T d1x4ha1          35 LKYVRVVLHPDTEH-SKGCAFAQFMTQE   61 (98)
T ss_dssp             EEEEECCBCSSSCC-BCSEEEEEESSHH
T ss_pred             ceeeeecccccccc-ccceEEEEEcCHH
Confidence            56788899999995 9999999994444

>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=95.40  E-value=0.0014  Score=41.87  Aligned_cols=29  Identities=10%  Similarity=0.090  Sum_probs=23.6

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.++.++.|+.+++ +||||||+|...+.
T Consensus        44 ~i~~~~~~~~~~~g~-~kG~afV~f~~~~~   72 (102)
T d2cpza1          44 NVVSAKVFIDKQTNL-SKCFGFVSYDNPVS   72 (102)
T ss_dssp             CCSEEEEEECSSSCS-EEEEEEEECSSHHH
T ss_pred             cccccceeeecccCC-CccceEEEeCCHHH
Confidence            356889999999996 99999999944443

>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=95.30  E-value=0.0027  Score=38.28  Aligned_cols=26  Identities=23%  Similarity=0.350  Sum_probs=21.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      +..+.+..|+.++. ++|||||+|...
T Consensus        29 i~~~~~~~~~~~~~-~~g~afV~f~~~   54 (79)
T d1l3ka2          29 IEVIEIMTDRGSGK-KRGFAFVTFDDH   54 (79)
T ss_dssp             EEEEEEEECTTTCC-EEEEEEEEESSH
T ss_pred             ccccccccCCCCcc-cccEEEEEEcCH
Confidence            56788999999995 999999999433

>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=95.24  E-value=0.0033  Score=39.42  Aligned_cols=27  Identities=26%  Similarity=0.301  Sum_probs=20.9

Q ss_pred             eeeeEEeeccC-cCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKA-RKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~-~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++|.. ++ ++||||||+|...+
T Consensus        35 i~~v~i~~~~~~~g-~~rg~afV~f~~~~   62 (94)
T d2cpha1          35 LKTVRLPKKMTGTG-AHRGFGFVDFITKQ   62 (94)
T ss_dssp             EEEEECCCCCSSSC-SSCSEEEEEESSHH
T ss_pred             ceEEEEEeccccCC-CcccEEEEEECCHH
Confidence            56888888865 66 49999999994433

>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=95.08  E-value=0.0031  Score=38.02  Aligned_cols=26  Identities=19%  Similarity=0.156  Sum_probs=20.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+..|+ +++ +||||||+|...+
T Consensus        27 v~~~~i~~~~-~g~-~~g~afV~f~~~~   52 (78)
T d1no8a_          27 LKKAAVHYDR-SGR-SLGTADVHFERKA   52 (78)
T ss_dssp             EEEEEESCSS-CCC-SCCEEEEEESCHH
T ss_pred             CeEEEEEEee-ccc-cceeEEEEECCHH
Confidence            5678888886 664 9999999994433

>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=95.07  E-value=0.0035  Score=38.77  Aligned_cols=30  Identities=20%  Similarity=0.396  Sum_probs=23.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIRE   37 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~   37 (192)
                      +.++.+++++.++. +||||||+|...+.+.
T Consensus        32 i~~~~~~~~~~~~~-~~g~afV~f~~~~~a~   61 (90)
T d1x5sa1          32 ISEVVVVKDRETQR-SRGFGFVTFENIDDAK   61 (90)
T ss_dssp             CCEEEECCCSSSCS-CCSEEEEECSSHHHHH
T ss_pred             ccceeecccccccc-ccceEEEEECCHHHHH
Confidence            56788899999996 9999999995554433

>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=95.01  E-value=0.0057  Score=36.05  Aligned_cols=26  Identities=15%  Similarity=0.282  Sum_probs=21.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRN   33 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~   33 (192)
                      +..+.+.+++.++. ++|||||+|...
T Consensus        25 v~~~~~~~~~~~~~-~~g~afV~f~~~   50 (72)
T d1x4ea1          25 IVSTKAILDKTTNK-CKGYGFVDFDSP   50 (72)
T ss_dssp             EEEEEEECCSSSCS-CCSEEEEEESCH
T ss_pred             cccccccccccccc-ccceeEEEECCH
Confidence            45788999999995 999999999433

>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=94.97  E-value=0.0021  Score=39.37  Aligned_cols=29  Identities=24%  Similarity=0.280  Sum_probs=21.6

Q ss_pred             eeeeEEeeccCcCC--CCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKK--KGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~--k~rG~gfv~f~~~~~   35 (192)
                      +.++.+++|+.++.  ++||||||+|...+.
T Consensus        25 v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~   55 (85)
T d2cpfa1          25 IKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ   55 (85)
T ss_dssp             EEEEEEEEEECTTCCEEEEEEEEEEESSHHH
T ss_pred             ccccceecccccccccccceEEEEEECCHHH
Confidence            56788888887763  368999999954443

>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=94.66  E-value=0.0081  Score=38.08  Aligned_cols=30  Identities=13%  Similarity=0.303  Sum_probs=21.0

Q ss_pred             ceeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          5 FRLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         5 ~~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+.++.+++++....++||||||+|...+
T Consensus        39 ~g~~~~~~~~~~~~~g~~~g~afV~f~~~e   68 (104)
T d1wi8a_          39 LNISAVRLPREPSNPERLKGFGYAEFEDLD   68 (104)
T ss_dssp             SCEEEEECCBCSSCTTSBCSCEEEEESSHH
T ss_pred             hccccceeeeeeccCCCcceeeeEEECCHH
Confidence            345677777777644359999999994333

>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=94.39  E-value=0.0071  Score=37.07  Aligned_cols=28  Identities=7%  Similarity=-0.042  Sum_probs=18.2

Q ss_pred             eeeeeEEeec-cCcCCCCCCccCCCCChhH
Q psy15152          6 RLKGIARLKE-KARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d-~~~~~k~rG~gfv~f~~~~   34 (192)
                      .+.++.+.++ ..++ ++||||||+|...+
T Consensus        31 ~i~~v~i~~~~~~~~-~~kg~afV~f~~~~   59 (86)
T d2ghpa3          31 SIEKINIPAGQKEHS-FNNCCAFMVFENKD   59 (86)
T ss_dssp             CEEEEECCSCCC----CCCEEEEEEESSHH
T ss_pred             hccceeeecccCCcc-ccceeeeEEECCHH
Confidence            3567777665 4566 59999999994444

>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=94.16  E-value=0.007  Score=37.40  Aligned_cols=29  Identities=10%  Similarity=0.030  Sum_probs=21.3

Q ss_pred             eeeeeEEeeccCcCC--CCCCccCCCCChhH
Q psy15152          6 RLKGIARLKEKARKK--KGRGFGTETSTRNE   34 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~--k~rG~gfv~f~~~~   34 (192)
                      .+.+|.+++|+.++.  ..+||+||+|...+
T Consensus        37 ~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~   67 (89)
T d2cpia1          37 KIHKVVINNSTSYAGSQGPSASAYVTYIRSE   67 (89)
T ss_dssp             CEEEEEEECCSSCCSSSCCCEEEEEEESSHH
T ss_pred             CceEEEEeeccCcCCCCCcceEEEEecccch
Confidence            456899999988764  23489999994444

>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=94.15  E-value=0.0072  Score=36.99  Aligned_cols=27  Identities=15%  Similarity=-0.089  Sum_probs=19.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.++.+.++. +++ +||||||+|...+.
T Consensus        33 v~~v~l~~~~-~~~-~kG~afV~f~~~e~   59 (85)
T d1zh5a2          33 VLNIQMRRTL-HKA-FKGSIFVVFDSIES   59 (85)
T ss_dssp             EEEEEEEECT-TCC-EEEEEEEEESCHHH
T ss_pred             cccceeeeec-cCC-cceEEEEEEcCHHH
Confidence            5677777765 674 99999999944443

>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=94.05  E-value=0.0056  Score=39.12  Aligned_cols=28  Identities=11%  Similarity=-0.067  Sum_probs=20.5

Q ss_pred             eeeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          6 RLKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         6 ~~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .+.+|.+++| .+++ +|||+||+|...+.
T Consensus        53 ~I~~v~I~~~-~~~~-~~G~~fV~f~~~~~   80 (104)
T d1jmta_          53 EVEEMNVCDN-LGDH-LVGNVYVKFRREED   80 (104)
T ss_dssp             CEEEEEECCS-SSSS-SEEEEEEEESCHHH
T ss_pred             CEEEEEeecC-CCCC-EeeEEEEEEechhH
Confidence            3568888766 5674 99999999944443

>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=93.91  E-value=0.0059  Score=36.87  Aligned_cols=27  Identities=22%  Similarity=0.062  Sum_probs=14.8

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      ..+.++.+..++. +||||||+|...+.
T Consensus        29 ~~~~~~~~~~~~~-~~g~afV~f~~~e~   55 (81)
T d2ghpa1          29 ALSIRLPSLRFNT-SRRFAYIDVTSKED   55 (81)
T ss_dssp             CCEEECC--------CCEEEEECSSHHH
T ss_pred             Eeeeeeccccccc-ccceeEEEECCHHH
Confidence            3566778888885 99999999954443

>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=93.90  E-value=0.013  Score=35.98  Aligned_cols=28  Identities=14%  Similarity=0.235  Sum_probs=20.1

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHHh
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIRE   37 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~~   37 (192)
                      +.++.++.|+.+   +||||||+|...+.+.
T Consensus        35 v~~~~i~~~~~~---~kg~afV~f~~~~~A~   62 (89)
T d1cvja2          35 ILSCKVVCDENG---SKGYGFVHFETQEAAE   62 (89)
T ss_dssp             EEEEEECCBTTB---CCSCEEEEESCHHHHH
T ss_pred             ceEEEEEeecCC---CcceeEEEECCHHHHH
Confidence            567888888642   7899999995555433

>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=93.46  E-value=0.013  Score=34.55  Aligned_cols=27  Identities=22%  Similarity=0.377  Sum_probs=21.8

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.++.+++++.++. ++|||||+|...+
T Consensus        26 i~~~~~~~~~~~~~-~~~~afV~F~~~~   52 (75)
T d2msta_          26 VDDAMLMFDKTTNR-HRGFGFVTFESED   52 (75)
T ss_dssp             CSEECCBCCTTCTT-SCCEEEEECSCHH
T ss_pred             cceeeeeeeccccc-cCceeEEEECCHH
Confidence            45778889999995 9999999994444

>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=93.15  E-value=0.02  Score=36.06  Aligned_cols=35  Identities=14%  Similarity=0.171  Sum_probs=22.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhcccC
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESMET   43 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~~   43 (192)
                      +.++.+..|. ++ +++|||||+|...+  ..++..+++
T Consensus        45 i~~~~~~~~~-~~-~~~g~afV~f~~~~~A~~Ai~~lng   81 (101)
T d1x5oa1          45 VISTRILRDS-SG-TSRGVGFARMESTEKCEAVIGHFNG   81 (101)
T ss_dssp             EEEEEEEECS-SS-CEEEEEEEEESCHHHHHHHHHHHBT
T ss_pred             ccceeeeccc-cc-ccccceeEEeCCHHHHHHHHHHhCC
Confidence            4566677764 66 49999999994433  334444443

>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=92.62  E-value=0.014  Score=36.66  Aligned_cols=26  Identities=19%  Similarity=0.060  Sum_probs=20.9

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      ..+...+|+.+++ ++|||||+|...+
T Consensus        44 ~~~~~~~d~~~~~-~~g~afV~f~~~~   69 (101)
T d2cpea1          44 PMIHIYLDKETGK-PKGDATVSYEDPP   69 (101)
T ss_dssp             BSEECCBCTTTCS-BCSEEEEEBSSHH
T ss_pred             ceeEEeecccccc-ccceeeEEecCHH
Confidence            4677888999995 9999999994444

>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=91.55  E-value=0.016  Score=36.43  Aligned_cols=27  Identities=26%  Similarity=0.116  Sum_probs=20.6

Q ss_pred             eeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          8 KGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         8 ~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      .++.++.|..++. ++|||||+|...+.
T Consensus        46 ~~~~~~~~~~~g~-~~g~~fV~f~~~~~   72 (102)
T d2cpxa1          46 KGPPIQFRMMTGR-MRGQAFITFPNKEI   72 (102)
T ss_dssp             SSSCCEEEEECSS-SCSEEEEECSSHHH
T ss_pred             eeEEeeccccccc-ccccceEEeccHHH
Confidence            4567778888885 99999999944443

>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=91.31  E-value=0.052  Score=34.12  Aligned_cols=29  Identities=14%  Similarity=0.044  Sum_probs=20.2

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEIR   36 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~~   36 (192)
                      +..+.++.+..+++ ++|||||+|..++.+
T Consensus        42 v~~~v~~~~~~~~~-~kG~afV~F~~~e~a   70 (104)
T d1wg5a_          42 VPNGMTLPVDFQGR-STGEAFVQFASQEIA   70 (104)
T ss_dssp             EEEEEECCBCSSSC-BCSEEEEEESSHHHH
T ss_pred             ceEEEEEEeCCCCC-cceEEEEEeCCHHHH
Confidence            34455667777774 999999999544443

>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=91.30  E-value=0.032  Score=34.46  Aligned_cols=26  Identities=15%  Similarity=0.229  Sum_probs=19.0

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.++.|+.+   +||||||+|...+.
T Consensus        38 v~~v~~~~~~~~---~kg~afV~f~~~~~   63 (93)
T d2cq3a1          38 ILDVEIIFNERG---SKGFGFVTFENSAD   63 (93)
T ss_dssp             EEEEEEECCTTT---TCCEEEEEESCHHH
T ss_pred             eeeccccccccC---CcceeEEEECCHHH
Confidence            567888888643   78999999944443

>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=90.79  E-value=0.058  Score=33.79  Aligned_cols=27  Identities=7%  Similarity=0.021  Sum_probs=18.9

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhHHH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNEIR   36 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~~~   36 (192)
                      ...++.+..+++ ++|||||+|...+.+
T Consensus        37 ~~~~~~~~~~g~-~~G~afV~F~s~~~a   63 (103)
T d2cpya1          37 NAVHVLVDNNGQ-GLGQALVQFKNEDDA   63 (103)
T ss_dssp             TTEEECCCTTSS-CSSCEEEECSSHHHH
T ss_pred             EEEEEEeCCCCC-cCccEEEEECCHHHH
Confidence            344556667885 999999999554443

>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=90.26  E-value=0.047  Score=33.39  Aligned_cols=25  Identities=8%  Similarity=0.023  Sum_probs=18.6

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|+.++   +|||||+|...+
T Consensus        35 i~~v~i~~d~~~~---~~~afV~f~~~~   59 (90)
T d2cqia1          35 CKSCKMITEHTSN---DPYCFVEFYEHR   59 (90)
T ss_dssp             EEEEEEECCCCSS---CCEEEEEESSHH
T ss_pred             ceeeeeecccCcc---ceeeEEEECCHH
Confidence            5678888887654   699999994433

>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=89.82  E-value=0.055  Score=33.90  Aligned_cols=28  Identities=7%  Similarity=-0.085  Sum_probs=19.7

Q ss_pred             ceeeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          5 FRLKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         5 ~~~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+..|.+++|.. ++ ++|||||+|...+
T Consensus        39 ~~~~~v~~~~~~~-g~-~~G~afVeF~~~~   66 (102)
T d1weza_          39 LNPMRVHIEIGPD-GR-VTGEADVEFATHE   66 (102)
T ss_dssp             CCCSEEEEEESSS-SC-EEEEEEEECSSSH
T ss_pred             cCcceeeeEEecC-Cc-ceEEEEEEECCHH
Confidence            3455777887765 53 8999999994333

>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=88.63  E-value=0.03  Score=34.24  Aligned_cols=23  Identities=4%  Similarity=-0.006  Sum_probs=16.7

Q ss_pred             EEeeccCcCCCCCCccCCCCChhH
Q psy15152         11 ARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus        11 ~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      ....+..+++ ++|||||+|...+
T Consensus        37 ~~~~~~~~~~-~kg~afV~f~~~e   59 (90)
T d1u2fa_          37 NPVLAVQINQ-DKNFAFLEFRSVD   59 (90)
T ss_dssp             CSEEECCEET-TTTEEEEEESSCT
T ss_pred             ceeeecccCC-CceEEEEEeCCHH
Confidence            3456777785 9999999994433

>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=88.26  E-value=0.062  Score=34.25  Aligned_cols=25  Identities=12%  Similarity=-0.069  Sum_probs=16.3

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+..   ++ ++||||||+|...+.
T Consensus        34 v~~i~~~~---~~-~~kG~afV~f~~~~~   58 (114)
T d2f9da1          34 IRQIRVGN---TP-ETRGTAYVVYEDIFD   58 (114)
T ss_dssp             EEEEEEEC---ST-TTTTEEEEEESSHHH
T ss_pred             eEeecccc---cC-CcCCeEEEEECCHHH
Confidence            34566554   34 378999999944443

>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=87.94  E-value=0.042  Score=33.81  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=16.8

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      ++.++ +..+++ +||||||+|...+
T Consensus        42 ~~~v~-~~~~g~-~kg~afv~F~~~e   65 (91)
T d1fjeb1          42 DLAVV-DVRTGT-NRKFGYVDFESAE   65 (91)
T ss_dssp             TCCCC-EEEEET-TTTEEEEEESSHH
T ss_pred             Eeeee-ecCCCC-ccEEeEEeeCCHH
Confidence            44444 556785 9999999994443

>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=87.86  E-value=0.028  Score=34.07  Aligned_cols=26  Identities=12%  Similarity=-0.035  Sum_probs=17.4

Q ss_pred             EeeccCcCCCCCCccCCCCChhHHHhh
Q psy15152         12 RLKEKARKKKGRGFGTETSTRNEIREY   38 (192)
Q Consensus        12 ~~~d~~~~~k~rG~gfv~f~~~~~~~~   38 (192)
                      ++.+..+++ ++||+||+|...+.+..
T Consensus        41 ~~~~~~~g~-~~G~afV~f~~~e~a~~   66 (86)
T d2cqpa1          41 CLKYNEKGM-PTGEAMVAFESRDEATA   66 (86)
T ss_dssp             EEEECSSSC-EEEEEEEEESCHHHHHH
T ss_pred             EEEeCCCCC-cceEEEEEEcCcHHHHH
Confidence            344456774 99999999955444333

>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=86.57  E-value=0.056  Score=34.53  Aligned_cols=26  Identities=12%  Similarity=-0.038  Sum_probs=18.9

Q ss_pred             eeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          9 GIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         9 ~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      ++.++.+..+++ ++|||||+|...+.
T Consensus        47 ~~~~~~~~~~g~-~~G~afVeF~~~e~   72 (112)
T d1wela1          47 DSIYIAYGPNGK-ATGEGFVEFRNEAD   72 (112)
T ss_dssp             TTCEEEECTTSS-EEEEEEEEBSSSHH
T ss_pred             cceeeecCcccc-eeeEEEEEECCHHH
Confidence            445667777885 99999999944443

>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=86.14  E-value=0.1  Score=32.81  Aligned_cols=22  Identities=5%  Similarity=-0.006  Sum_probs=15.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +.+|.+++|      .||||||+|...+
T Consensus        30 I~~v~i~~~------~kg~afV~f~~~~   51 (109)
T d2adca1          30 VQRVKILFN------KKENALVQMADGN   51 (109)
T ss_dssp             EEEEEECCT------TSCCEEEEESCHH
T ss_pred             cceEEEEec------ccceEEEEECCHH
Confidence            557777765      3799999994444

>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=84.73  E-value=0.25  Score=28.79  Aligned_cols=26  Identities=8%  Similarity=0.000  Sum_probs=18.7

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+..|+..   ++|||||+|..++.
T Consensus        27 I~~v~~~~~~~~---~~~~afV~F~~~~~   52 (75)
T d2ghpa2          27 IIHVDVADSLKK---NFRFARIEFARYDG   52 (75)
T ss_dssp             EEEEEEEECTTS---SSEEEEEEESSHHH
T ss_pred             eEEEEEEeeccc---cceEEEEEEcchHH
Confidence            467888888764   45799999954443

>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=83.72  E-value=0.14  Score=31.64  Aligned_cols=22  Identities=14%  Similarity=0.223  Sum_probs=15.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhHH
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNEI   35 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~~   35 (192)
                      +.+|.+++       +||||||+|...+.
T Consensus        45 i~~v~i~~-------~kg~afV~f~~~~~   66 (96)
T d1x4ga1          45 IMEIRVFP-------EKGYSFVRFSTHES   66 (96)
T ss_dssp             EEEEEEET-------TTTEEEEEESSHHH
T ss_pred             ceEEEEEe-------cceEEEEEECCHHH
Confidence            45677765       48999999944443

>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=82.40  E-value=0.072  Score=32.56  Aligned_cols=20  Identities=15%  Similarity=-0.112  Sum_probs=14.0

Q ss_pred             eccCcCCCCCCccCCCCChhH
Q psy15152         14 KEKARKKKGRGFGTETSTRNE   34 (192)
Q Consensus        14 ~d~~~~~k~rG~gfv~f~~~~   34 (192)
                      +...++. +||||||+|...+
T Consensus        38 ~~~~~~~-~~g~afV~F~~~~   57 (91)
T d1nu4a_          38 LVSRSLK-MRGQAFVIFKEVS   57 (91)
T ss_dssp             ECCHHHH-HTTCEEEEESSHH
T ss_pred             EEeeecc-CCCceEEEECCHH
Confidence            3444664 8999999994444

>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=82.02  E-value=0.14  Score=32.24  Aligned_cols=31  Identities=6%  Similarity=-0.069  Sum_probs=18.4

Q ss_pred             eeeeEEeeccCcCCCCCCccCCCCChhH--HHhhhccc
Q psy15152          7 LKGIARLKEKARKKKGRGFGTETSTRNE--IREYESME   42 (192)
Q Consensus         7 ~~~v~~~~d~~~~~k~rG~gfv~f~~~~--~~~~~~~~   42 (192)
                      +..+.+.++     +++|||||+|...+  ..++..++
T Consensus        34 i~~~~i~~~-----~~~g~aFV~f~~~e~A~~Ai~~ln   66 (108)
T d2adba1          34 VLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLD   66 (108)
T ss_dssp             EEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHH
T ss_pred             EEEEEEEee-----CCCCeEEEEECCHHHHHHHHHHHC
Confidence            345666654     36899999994333  33444443

>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=80.03  E-value=0.25  Score=30.69  Aligned_cols=24  Identities=4%  Similarity=0.004  Sum_probs=14.1

Q ss_pred             CCCccCCCCChhHHHhhhcccCCC
Q psy15152         22 GRGFGTETSTRNEIREYESMETDV   45 (192)
Q Consensus        22 ~rG~gfv~f~~~~~~~~~~~~~~~   45 (192)
                      +||||||+|...+.+..+-..+++
T Consensus        55 ~k~~aFV~f~~~e~A~~A~~~lng   78 (101)
T d2cq2a1          55 NKPYSFARYRTTEESKRAYVTLNG   78 (101)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTT
T ss_pred             CccEEEEEECCHHHHHHHHHHhCC
Confidence            689999999444433333333343