Psyllid ID: psy10284

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100---
Protein Sequence
MLPLDLIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEEEEcHHHHHHcccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEcccccccccEEEEEccccccHHHHHHHHHccccccccccccccHHHccccccccEEEEHHccccccHHHHHHHHcccccEEEEEEEEccccccc
Coil and Loop (DISEMBL)
mlpldliwtctplppdkkLFVGMLSkqqneddnlSHCFHLLfphlqcfpwdliwtctplppdkkLFVGMLskqqneddvrkifapfgtieectvlkgpdgtsk
Flexible Loop (DISEMBL)
MLPLDLIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFApfgtieectvlkgpdgtsk
Low Complexity Region (SEG)
MLPLDLIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK
Disordered region (IsUnstruct)
***LDLIWTCTPLPPDKKLFVGMLSK****DDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL********
Disordered Region (DISOPRED)
*LPLDLIWTCTPLPPDKKLFVGMLSK**************************************LFVGMLSKQQNEDDVRKIFAPFGTIEECTV**GP*****
Disordered Region (DISEMBL)
MLPLDLIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK
Disordered Region (DISPRO)
*LPLDLIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLPLDLIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK
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	103	2.2.26 [Sep-21-2011]
Q5SZQ8	465	CUGBP Elav-like family me	no	N/A	0.407	0.090	0.785	4e-14
Q8CIN6	465	CUGBP Elav-like family me	no	N/A	0.407	0.090	0.785	4e-14
Q5NVC8	486	CUGBP Elav-like family me	no	N/A	0.475	0.100	0.666	4e-14
Q9BZC1	486	CUGBP Elav-like family me	no	N/A	0.475	0.100	0.666	4e-14
Q08E07	461	CUGBP Elav-like family me	yes	N/A	0.407	0.091	0.785	5e-14
Q7TSY6	486	CUGBP Elav-like family me	no	N/A	0.475	0.100	0.666	5e-14
Q91579	462	CUGBP Elav-like family me	N/A	N/A	0.407	0.090	0.738	1e-13
Q7TN33	460	CUGBP Elav-like family me	no	N/A	0.407	0.091	0.761	2e-13
Q4R535	474	CUGBP Elav-like family me	N/A	N/A	0.407	0.088	0.738	2e-13
Q6DGV1	520	CUGBP Elav-like family me	no	N/A	0.407	0.080	0.738	2e-13

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 94  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

RNA-binding protein involved in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.
Homo sapiens (taxid: 9606)

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 93  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 134

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

Mus musculus (taxid: 10090)

>sp|Q5NVC8|CELF4_PONAB CUGBP Elav-like family member 4 OS=Pongo abelii GN=CELF4 PE=2 SV=2

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 55  TCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +C   PP  D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct: 142 SCLRQPPSQDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 192

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

Pongo abelii (taxid: 9601)

>sp|Q9BZC1|CELF4_HUMAN CUGBP Elav-like family member 4 OS=Homo sapiens GN=CELF4 PE=1 SV=1

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 55  TCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +C   PP  D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct: 142 SCLRQPPSQDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 192

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

Homo sapiens (taxid: 9606)

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

 Score = 76.6 bits (187), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 94  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

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

Bos taurus (taxid: 9913)

>sp|Q7TSY6|CELF4_MOUSE CUGBP Elav-like family member 4 OS=Mus musculus GN=Celf4 PE=1 SV=2

 Score = 76.6 bits (187), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 55  TCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +C   PP  D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct: 142 SCLRQPPSQDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 192

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

Mus musculus (taxid: 10090)

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

 Score = 75.5 bits (184), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML KQQ ++DVR++F PFG I+ECTVL+GPDGTSK
Sbjct: 94  DRKLFVGMLGKQQTDEDVRRMFEPFGNIDECTVLRGPDGTSK 135

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

Xenopus laevis (taxid: 8355)

>sp|Q7TN33|CELF6_MOUSE CUGBP Elav-like family member 6 OS=Mus musculus GN=Celf6 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/42 (76%), Positives = 37/42 (88%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML KQQ E+DVR++F PFG IEECTVL+ PDGTSK
Sbjct: 133 DRKLFVGMLGKQQGEEDVRRLFQPFGHIEECTVLRSPDGTSK 174

RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of TNNT2 in a muscle-specific splicing enhancer (MSE)-dependent manner. Promotes also exon exclusion of INSR pre-mRNA.

Mus musculus (taxid: 10090)

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

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct: 140 DRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 181

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

Macaca fascicularis (taxid: 9541)

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

 Score = 73.9 bits (180), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/42 (73%), Positives = 38/42 (90%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML+KQQ EDDVR++F  FG+IEECT+L+GPDG SK
Sbjct: 134 DRKLFVGMLNKQQCEDDVRRLFESFGSIEECTILRGPDGNSK 175

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

Danio rerio (taxid: 7955)

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	103
270016805	214	hypothetical protein TcasGA2_TC001521 [T	0.407	0.196	0.809	1e-13
189241911	569	PREDICTED: similar to bruno-3 CG12478-PA	0.407	0.073	0.809	2e-13
195171586	458	GL21647 [Drosophila persimilis] gi|19411	0.407	0.091	0.833	2e-13
269868259	154	Bruno-3 transcript variant 32 [Drosophil	0.407	0.272	0.833	3e-13
296222551	479	PREDICTED: CUGBP Elav-like family member	0.446	0.096	0.717	3e-13
449279762	165	CUG-BP- and ETR-3-like factor 3, partial	0.407	0.254	0.809	3e-13
195590112	616	GD12651 [Drosophila simulans] gi|1941968	0.407	0.068	0.833	3e-13
363742941	401	PREDICTED: CUGBP Elav-like family member	0.407	0.104	0.809	4e-13
269868210	370	Bruno-3 transcript variant 9, partial [D	0.407	0.113	0.833	4e-13
269868303	407	Bruno-3 transcript variant 4 [Drosophila	0.407	0.103	0.833	4e-13

>gi|270016805|gb|EFA13251.1| hypothetical protein TcasGA2_TC001521 [Tribolium castaneum]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/42 (80%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ E+DVR++FAPFGTIEECT+L+GPDG SK
Sbjct: 96  DRKLFVGMLSKQQTEEDVRQLFAPFGTIEECTILRGPDGASK 137

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189241911|ref|XP_971057.2| PREDICTED: similar to bruno-3 CG12478-PA [Tribolium castaneum]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 34/42 (80%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ E+DVR++FAPFGTIEECT+L+GPDG SK
Sbjct: 212 DRKLFVGMLSKQQTEEDVRQLFAPFGTIEECTILRGPDGASK 253

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195171586|ref|XP_002026586.1| GL21647 [Drosophila persimilis] gi|194111502|gb|EDW33545.1| GL21647 [Drosophila persimilis]

 Score = 79.3 bits (194), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/42 (83%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ EDDVR+IF PFG+IEECT+L+GPDGTSK
Sbjct: 54  DRKLFVGMLSKQQTEDDVRQIFHPFGSIEECTILRGPDGTSK 95

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|269868259|gb|ACZ52434.1| Bruno-3 transcript variant 32 [Drosophila melanogaster]

 Score = 79.3 bits (194), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/42 (83%), Positives = 39/42 (92%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ EDDVR+IF PFGTIEECT+L+GPDG SK
Sbjct: 23  DRKLFVGMLSKQQTEDDVRQIFHPFGTIEECTILRGPDGASK 64

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|296222551|ref|XP_002757237.1| PREDICTED: CUGBP Elav-like family member 4-like [Callithrix jacchus]

 Score = 79.3 bits (194), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 33/46 (71%), Positives = 41/46 (89%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           P+P D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct: 141 PVPKDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 186

Source: Callithrix jacchus

Species: Callithrix jacchus

Genus: Callithrix

Family: Cebidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449279762|gb|EMC87248.1| CUG-BP- and ETR-3-like factor 3, partial [Columba livia]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/42 (80%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 2   DRKLFVGMLSKQQADEDVRKMFEPFGTIDECTVLRGPDGTSK 43

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|195590112|ref|XP_002084791.1| GD12651 [Drosophila simulans] gi|194196800|gb|EDX10376.1| GD12651 [Drosophila simulans]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/42 (83%), Positives = 39/42 (92%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ EDDVR+IF PFGTIEECT+L+GPDG SK
Sbjct: 248 DRKLFVGMLSKQQTEDDVRQIFHPFGTIEECTILRGPDGASK 289

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|363742941|ref|XP_428898.3| PREDICTED: CUGBP Elav-like family member 3 isoform 3 [Gallus gallus]

 Score = 79.0 bits (193), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 34/42 (80%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 94  DRKLFVGMLSKQQADEDVRKMFEPFGTIDECTVLRGPDGTSK 135

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|269868210|gb|ACZ52411.1| Bruno-3 transcript variant 9, partial [Drosophila pseudoobscura]

 Score = 79.0 bits (193), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/42 (83%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ EDDVR+IF PFG+IEECT+L+GPDGTSK
Sbjct: 40  DRKLFVGMLSKQQTEDDVRQIFHPFGSIEECTILRGPDGTSK 81

Source: Drosophila pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|269868303|gb|ACZ52456.1| Bruno-3 transcript variant 4 [Drosophila persimilis]

 Score = 79.0 bits (193), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/42 (83%), Positives = 40/42 (95%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ EDDVR+IF PFG+IEECT+L+GPDGTSK
Sbjct: 40  DRKLFVGMLSKQQTEDDVRQIFHPFGSIEECTILRGPDGTSK 81

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	103
UNIPROTKB|A1L544	139	TNRC4 "Trinucleotide repeat co	0.407	0.302	0.785	3.7e-17
UNIPROTKB|F1NXF6	476	BRUNOL6 "Uncharacterized prote	0.436	0.094	0.760	5.7e-16
UNIPROTKB|Q5SZQ7	415	CELF3 "CUGBP Elav-like family	0.407	0.101	0.785	8.5e-16
UNIPROTKB|Q08E07	461	CELF3 "CUGBP Elav-like family	0.407	0.091	0.785	1.4e-15
UNIPROTKB|Q5SZQ8	465	CELF3 "CUGBP Elav-like family	0.407	0.090	0.785	1.4e-15
MGI|MGI:1926034	465	Celf3 "CUGBP, Elav-like family	0.407	0.090	0.785	1.4e-15
RGD|1563168	494	Celf3 "CUGBP, Elav-like family	0.407	0.085	0.785	1.8e-15
ZFIN|ZDB-GENE-110408-50	442	celf3b "cugbp, Elav-like famil	0.407	0.095	0.785	3.1e-15
UNIPROTKB|Q9BZC1	486	CELF4 "CUGBP Elav-like family	0.475	0.100	0.666	4.5e-15
UNIPROTKB|Q5NVC8	486	CELF4 "CUGBP Elav-like family	0.475	0.100	0.666	4.5e-15

UNIPROTKB|A1L544 TNRC4 "Trinucleotide repeat containing 4" [Bos taurus (taxid:9913)]

 Score = 185 (70.2 bits), Expect = 3.7e-17, Sum P(2) = 3.7e-17
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    94 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1NXF6 BRUNOL6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 191 (72.3 bits), Expect = 5.7e-16, Sum P(2) = 5.7e-16
 Identities = 35/46 (76%), Positives = 41/46 (89%)

Query:    59 LPP-DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             LPP D+KLFVGML KQQ+EDDVR++F PFG IEECT+L+GPDG SK
Sbjct:   138 LPPEDRKLFVGMLGKQQSEDDVRRLFEPFGQIEECTILRGPDGASK 183

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

UNIPROTKB|Q5SZQ7 CELF3 "CUGBP Elav-like family member 3" [Homo sapiens (taxid:9606)]

 Score = 185 (70.2 bits), Expect = 8.5e-16, Sum P(2) = 8.5e-16
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    94 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q08E07 CELF3 "CUGBP Elav-like family member 3" [Bos taurus (taxid:9913)]

 Score = 185 (70.2 bits), Expect = 1.4e-15, Sum P(2) = 1.4e-15
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    94 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030317 "sperm motility" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q5SZQ8 CELF3 "CUGBP Elav-like family member 3" [Homo sapiens (taxid:9606)]

 Score = 185 (70.2 bits), Expect = 1.4e-15, Sum P(2) = 1.4e-15
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    94 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0030317 "sperm motility" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0003723 "RNA binding" evidence=IMP

GO:0008380 "RNA splicing" evidence=IMP

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

GO:0005737 "cytoplasm" evidence=IDA

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

MGI|MGI:1926034 Celf3 "CUGBP, Elav-like family member 3" [Mus musculus (taxid:10090)]

 Score = 185 (70.2 bits), Expect = 1.4e-15, Sum P(2) = 1.4e-15
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    93 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 134

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IMP

GO:0008380 "RNA splicing" evidence=ISO

GO:0030317 "sperm motility" evidence=IMP

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

RGD|1563168 Celf3 "CUGBP, Elav-like family member 3" [Rattus norvegicus (taxid:10116)]

 Score = 185 (70.2 bits), Expect = 1.8e-15, Sum P(2) = 1.8e-15
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct:    94 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 135

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0007283 "spermatogenesis" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=ISO

GO:0030317 "sperm motility" evidence=ISO

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

ZFIN|ZDB-GENE-110408-50 celf3b "cugbp, Elav-like family member 3b" [Danio rerio (taxid:7955)]

 Score = 182 (69.1 bits), Expect = 3.1e-15, Sum P(2) = 3.1e-15
 Identities = 33/42 (78%), Positives = 39/42 (92%)

Query:    62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML KQQ+++DVRKIF PFG I+ECTVL+GPDGTSK
Sbjct:    94 DRKLFVGMLGKQQSDEDVRKIFEPFGGIDECTVLRGPDGTSK 135

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9BZC1 CELF4 "CUGBP Elav-like family member 4" [Homo sapiens (taxid:9606)]

 Score = 184 (69.8 bits), Expect = 4.5e-15, Sum P(2) = 4.5e-15
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query:    55 TCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             +C   PP  D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct:   142 SCLRQPPSQDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 192

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0006376 "mRNA splice site selection" evidence=IEA

GO:0090394 "negative regulation of excitatory postsynaptic membrane potential" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0042835 "BRE binding" evidence=ISS

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

GO:0007281 "germ cell development" evidence=NAS

GO:0009790 "embryo development" evidence=NAS

GO:0000900 "translation repressor activity, nucleic acid binding" evidence=NAS

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

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q5NVC8 CELF4 "CUGBP Elav-like family member 4" [Pongo abelii (taxid:9601)]

 Score = 184 (69.8 bits), Expect = 4.5e-15, Sum P(2) = 4.5e-15
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query:    55 TCTPLPP--DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             +C   PP  D+KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct:   142 SCLRQPPSQDRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 192

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

---

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)
Q08E07	CELF3_BOVIN	No assigned EC number	0.7857	0.4077	0.0911	yes	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	103
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-27
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	3e-19
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	8e-17
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	9e-17
smart00360	73	smart00360, RRM, RNA recognition motif	4e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-06
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	3e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	7e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	3e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	4e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	6e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-04
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	3e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.001
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.001
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.002
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.002
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.002
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.003
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.003
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.003
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.004

>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 = 95.6 bits (238), Expect = 2e-27
 Identities = 34/42 (80%), Positives = 39/42 (92%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGMLSKQQ EDDVR++F PFGTIEECT+L+GPDG SK
Sbjct: 1   DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSK 42

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 74.5 bits (183), Expect = 3e-19
 Identities = 28/42 (66%), Positives = 37/42 (88%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           ++KLFVGMLSK+ NE+DVR +FAPFG+IEECTVL+  +G S+
Sbjct: 1   ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSR 42

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 68.5 bits (167), Expect = 8e-17
 Identities = 26/42 (61%), Positives = 37/42 (88%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLF+GM+SK+ NE+D+R +F+PFG IEEC +L+GPDG S+
Sbjct: 1   DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSR 42

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|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 = 68.0 bits (167), Expect = 9e-17
 Identities = 21/41 (51%), Positives = 27/41 (65%), Gaps = 1/41 (2%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           KLFVG L K   E+DVR +F  +G IEE T+++  D G SK
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSK 41

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|214636 smart00360, RRM, RNA recognition motif

 Score = 46.0 bits (110), Expect = 4e-08
 Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            LFVG L     E+++R++F+ FG +E   +++  + G SK
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSK 41

Length = 73

>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 = 45.7 bits (109), Expect = 7e-08
 Identities = 14/35 (40%), Positives = 22/35 (62%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          KLFV  LS +  E ++  +F+ FG +EE  ++K P
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDP 37

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

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

 Score = 44.9 bits (107), Expect = 7e-08
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KLFVG L      +++R +F  +GT+ EC V+K
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVK 33

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

 Score = 43.4 bits (103), Expect = 3e-07
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           LFVG L     E+D+R++F+ FG IE   +++  DG SK
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSK 39

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

 Score = 43.1 bits (102), Expect = 5e-07
 Identities = 17/37 (45%), Positives = 26/37 (70%), Gaps = 1/37 (2%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          PP+ +LF+ +  K   EDD+R+ FAPFG I++  V+K
Sbjct: 1  PPNSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVK 36

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 41.4 bits (98), Expect = 2e-06
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           LFVG L     E+D++ +F+ FG IE   +++   G SK
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSK 39

(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|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 = 41.6 bits (98), Expect = 3e-06
 Identities = 17/33 (51%), Positives = 21/33 (63%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KLFVG + +   E D+R +F  FG I E TVLK
Sbjct: 7  KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLK 39

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 41.5 bits (98), Expect = 3e-06
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 102
           ++VG +       ++R+ F PFG IEE T+    DG +
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN 42

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 40.3 bits (95), Expect = 6e-06
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +L V  L  +  E D++K+F+PFG + E T+ + PDG  K
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKK 40

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

 Score = 40.3 bits (95), Expect = 7e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            L+VG L     E+D++ +F  FG +    V+   + G S+
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSR 41

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

 Score = 40.1 bits (94), Expect = 1e-05
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT 101
           LFVG L     E+++R+ F  +G +E+  + + P G 
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQ 41

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG-PDGTSK 103
            K+FVG L     +D +RK F+ FG IEE  V+     G S+
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSR 42

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           L+VG L     EDD+R IF PFG IE   + + P+ G SK
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSK 40

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

 Score = 39.9 bits (94), Expect = 1e-05
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          P   LFVG LS Q  E+ +R++F+ +G I   
Sbjct: 2  PYLTLFVGRLSLQTTEETLREVFSRYGDIRRL 33

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

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           +FVG LS + + + +R  FAPFG I +  V+K    G SK
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSK 41

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

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          LF+G LS    E+ +R+ F+ +G + +C ++K P
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDP 34

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

 Score = 38.9 bits (91), Expect = 3e-05
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          KLF+G LS +  +D ++  F+ +G I +C V+K P
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDP 35

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

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

 Score = 38.6 bits (90), Expect = 3e-05
 Identities = 9/33 (27%), Positives = 22/33 (66%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          K+FVG + +  +++++R +F  +G +  C V++
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMR 34

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

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

 Score = 38.3 bits (89), Expect = 3e-05
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          K+FVG +S     D++R +F  FG + EC  +K 
Sbjct: 2  KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD 35

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

 Score = 40.6 bits (95), Expect = 3e-05
 Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           P   KL+VG L     E ++R+IF PFG IE+  + + P+ G SK
Sbjct: 184 PNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSK 228

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

 Score = 38.3 bits (89), Expect = 3e-05
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KLFVG L  +  E ++R +F  +G + EC ++K
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIK 34

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

>gnl|CDD|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 = 38.6 bits (90), Expect = 4e-05
 Identities = 11/33 (33%), Positives = 22/33 (66%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          K+FVG + +  +E D+R++F  +G + +  VL+
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLR 35

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

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 14/40 (35%), Positives = 22/40 (55%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
            L+V  L    +++ +R+ F+PFGTI    V+    G SK
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSK 42

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

>gnl|CDD|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 = 38.3 bits (89), Expect = 5e-05
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KLF+G LS   NE  + ++F+ +G I E  V+K
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVK 34

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

 Score = 38.3 bits (89), Expect = 5e-05
 Identities = 14/33 (42%), Positives = 25/33 (75%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KLFVG L+KQ  E +V ++F+P+G +E+  +++
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMR 33

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

 Score = 37.7 bits (88), Expect = 6e-05
 Identities = 16/33 (48%), Positives = 21/33 (63%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 95
          KK+FVG L     E D+RK F+ FGT+ E  V+
Sbjct: 3  KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVM 35

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

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

 Score = 37.6 bits (88), Expect = 6e-05
 Identities = 12/32 (37%), Positives = 21/32 (65%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL 95
          KLFVG L +   E+D+R+ F+ +G +E   ++
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIV 32

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

 Score = 37.8 bits (87), Expect = 7e-05
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          +FVG LS +   +D++  FAPFG I +  V+K
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVK 35

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 37.4 bits (86), Expect = 1e-04
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          K+F+G LS Q + D +R  F+ FG I EC V++ P
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDP 35

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 13/35 (37%), Positives = 22/35 (62%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          KLFVG L+ + ++  +R+ F  +G + EC V+  P
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDP 38

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

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

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           LFVG LS    +DD+ + F   G + +  + +  DG SK
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSK 40

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

 Score = 36.5 bits (85), Expect = 2e-04
 Identities = 10/34 (29%), Positives = 20/34 (58%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          +LFVG L     E++ +++F+ +G + E  + K 
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE 36

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 15/40 (37%), Positives = 27/40 (67%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           ++FVG +  + NE+D+RK F+ +GT++E  ++    G SK
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSK 43

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 37.0 bits (85), Expect = 2e-04
 Identities = 14/36 (38%), Positives = 25/36 (69%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          +KLF+G LS +  +D +R+ F  +GT+ +C V++ P
Sbjct: 3  RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDP 38

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 38.0 bits (87), Expect = 2e-04
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             +  LFVG L     E+D+R++F  FG ++   +++  + G S+
Sbjct: 113 EENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157

Length = 306

>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 = 36.1 bits (84), Expect = 2e-04
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTI 89
          +FVG L     ED++R +F PFG I
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEI 28

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

 Score = 36.2 bits (84), Expect = 2e-04
 Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 1/33 (3%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          +LFV ++ K   E+D+R+ F  FG IE  +++K
Sbjct: 3  RLFV-VIPKSYTEEDLREKFKEFGDIEYVSIVK 34

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 36.2 bits (83), Expect = 3e-04
 Identities = 12/36 (33%), Positives = 23/36 (63%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          +KLF+G LS +  E+ +R  +  +G + +C V++ P
Sbjct: 3  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP 38

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          K+FVG LS    EDDV+K F+ FG +E+ 
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDA 29

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 36.2 bits (83), Expect = 3e-04
 Identities = 13/37 (35%), Positives = 25/37 (67%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
          +KLF+G LS +  ++ +R  F  +GT+ +C V++ P+
Sbjct: 3  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN 39

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

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

 Score = 35.7 bits (83), Expect = 4e-04
 Identities = 14/37 (37%), Positives = 23/37 (62%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          PP+  LFV  L+    ++D+  IF+ FG I+ C V++
Sbjct: 1  PPENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIR 37

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 35.6 bits (83), Expect = 4e-04
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
          L+V  L     E+D+R+ F+P+G +E   +++  D
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD 35

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

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 35.8 bits (82), Expect = 4e-04
 Identities = 14/35 (40%), Positives = 24/35 (68%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          K+F+G LS Q  ++ +R+ F  FG ++EC V++ P
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 36

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 35.5 bits (82), Expect = 5e-04
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          +F+G LS Q   + +R+ F+ FG I+EC V++ P
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDP 34

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 11/34 (32%), Positives = 22/34 (64%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          +F+G L+ +  +D +R+ F  FG + +CTV++  
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDS 34

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 10/39 (25%), Positives = 23/39 (58%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           ++V  L +  +++ ++++F  +G I    V+K  +G SK
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSK 42

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 14/30 (46%), Positives = 20/30 (66%)

Query: 61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIE 90
          P KK+FVG L+ +  E+ +R+ F  FG IE
Sbjct: 3  PVKKIFVGGLNPEATEEKIREYFGEFGEIE 32

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIE 90
          +FVG L     + D++K+F  FG IE
Sbjct: 3  VFVGNLPLTTKKKDLKKLFKQFGPIE 28

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS 102
           + LF+G L K     D+R+ F  FG I +  + K     +
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPA 42

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 33.9 bits (77), Expect = 0.002
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          +FVG LS +   DD++  FAPFG I +  V+K
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVK 35

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

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 11/40 (27%), Positives = 24/40 (60%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           ++FVG +     E+++R  F+ FG++++  ++    G SK
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSK 43

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

 Score = 33.6 bits (77), Expect = 0.003
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
           KLFVG LS +  ++ +R+ F+ +G + +C ++K    
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTT 37

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

>gnl|CDD|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 = 33.4 bits (77), Expect = 0.003
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          ++VG L     E+++++ F+PFG IEE  V K 
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD 35

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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 1/36 (2%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
           L++G LSK+  E+D++ +F  +G I+   ++  P G
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI-PPRG 39

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 33.1 bits (76), Expect = 0.004
 Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            +LFV  L     EDD+ K+F+ FG + E  V      G SK
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSK 44

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	103
KOG0149|consensus	247		99.13
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.96
KOG0148|consensus	321		98.92
KOG0126|consensus	219		98.89
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.75
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.71
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.71
KOG0144|consensus	510		98.7
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.69
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.69
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.67
KOG0144|consensus	510		98.62
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.6
KOG4205|consensus	311		98.6
PLN03120	260	nucleic acid binding protein; Provisional	98.54
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.54
KOG0148|consensus	321		98.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.53
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.51
PLN03121	243	nucleic acid binding protein; Provisional	98.49
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.47
KOG0145|consensus	360		98.47
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.38
KOG0113|consensus	335		98.36
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.36
KOG0117|consensus	506		98.36
KOG0109|consensus	346		98.35
KOG0121|consensus	153		98.34
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.33
PLN03213	759	repressor of silencing 3; Provisional	98.32
KOG0122|consensus	270		98.24
KOG0125|consensus	376		98.23
KOG0107|consensus	195		98.23
KOG4205|consensus	311		98.21
KOG0147|consensus	549		98.19
smart00362	72	RRM_2 RNA recognition motif.	98.17
KOG0146|consensus	371		98.16
KOG0127|consensus	678		98.16
KOG0124|consensus	544		98.1
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.08
KOG0109|consensus	346		98.07
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.06
KOG0114|consensus	124		98.03
KOG0123|consensus	369		98.02
KOG0145|consensus	360		97.98
smart00360	71	RRM RNA recognition motif.	97.95
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.93
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	97.92
KOG0123|consensus	369		97.81
KOG0105|consensus	241		97.78
KOG0108|consensus	435		97.76
KOG4207|consensus	256		97.68
KOG0117|consensus	506		97.6
KOG0146|consensus	371		97.57
KOG0131|consensus	203		97.54
KOG0533|consensus	243		97.45
KOG0415|consensus	479		97.45
KOG0124|consensus	544		97.45
KOG0131|consensus	203		97.37
KOG0111|consensus	298		97.23
KOG0130|consensus	170		97.08
KOG1548|consensus	382		97.08
KOG0127|consensus	678		97.04
KOG0132|consensus	894		96.92
KOG4212|consensus	608		96.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	96.91
KOG0153|consensus	377		96.72
KOG0116|consensus	419		96.43
KOG4206|consensus	221		96.43
KOG0151|consensus	877		96.39
KOG4212|consensus	608		96.32
KOG4209|consensus	231		96.21
KOG4454|consensus	267		96.09
KOG0110|consensus	725		95.84
KOG0106|consensus	216		95.52
KOG0129|consensus	520		95.49
KOG3152|consensus	278		95.47
KOG0226|consensus	290		95.39
KOG0129|consensus	520		95.39
KOG4661|consensus	940		95.33
KOG4660|consensus	549		95.24
KOG4208|consensus	214		94.6
KOG4210|consensus	285		94.23
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	93.97
KOG1190|consensus	492		93.59
KOG4849|consensus	498		93.47
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	93.29
KOG0110|consensus	725		92.77
KOG0115|consensus	275		92.56
KOG0147|consensus	549		92.1
smart00361	70	RRM_1 RNA recognition motif.	92.07
KOG1457|consensus	284		91.6
KOG0120|consensus	500		91.32
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	89.77
KOG0128|consensus	881		89.58
KOG1855|consensus	484		89.43
KOG0105|consensus	241		86.54
KOG1995|consensus	351		83.85
KOG4211|consensus	510		83.46
KOG4211|consensus	510		82.2
KOG4206|consensus	221		81.28
KOG4454|consensus	267		80.63
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	80.58
KOG1190|consensus	492		80.49

>KOG0149|consensus

Probab=99.13  E-value=5.6e-11  Score=84.41  Aligned_cols=41  Identities=37%  Similarity=0.673  Sum_probs=40.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|||||+|+|.++.+.|+++|++||+|.++.|+.|+. |+||
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rsk   54 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSK   54 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCcccc
Confidence            8999999999999999999999999999999999999 9986

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=98.96  E-value=1.6e-09  Score=72.27  Aligned_cols=44  Identities=32%  Similarity=0.557  Sum_probs=40.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..+++|||+|||+.+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~k   76 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSR   76 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcc
Confidence            3458999999999999999999999999999999999987 7765

>KOG0148|consensus

Probab=98.92  E-value=2.1e-09  Score=78.06  Aligned_cols=73  Identities=21%  Similarity=0.439  Sum_probs=62.5

Q ss_pred             CCcccchhhhhccccccccCCCcCCCcccccccCCC------------------CCCceEEEecCCCCCCHHHHHHhhcC
Q psy10284         24 LSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPL------------------PPDKKLFVGMLSKQQNEDDVRKIFAP   85 (103)
Q Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~lfVgnL~~~~te~~l~~~F~~   85 (103)
                      |.++.+.|.....++.+|+..++++   .||+.++.                  ++++.+||||++..+||+++++.|+.
T Consensus       111 f~~k~dAEnAI~~MnGqWlG~R~IR---TNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~  187 (321)
T KOG0148|consen  111 FPNKEDAENAIQQMNGQWLGRRTIR---TNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSP  187 (321)
T ss_pred             ccchHHHHHHHHHhCCeeeccceee---ccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhccc
Confidence            4556677888889999999998776   58876443                  48899999999999999999999999


Q ss_pred             CCceeEEEEeeCCC
Q psy10284         86 FGTIEECTVLKGPD   99 (103)
Q Consensus        86 ~G~i~~~~v~~d~~   99 (103)
                      ||.|.+|+|.+|+.
T Consensus       188 fG~I~EVRvFk~qG  201 (321)
T KOG0148|consen  188 FGPIQEVRVFKDQG  201 (321)
T ss_pred             CCcceEEEEecccc
Confidence            99999999998873

>KOG0126|consensus

Probab=98.89  E-value=4.8e-10  Score=77.43  Aligned_cols=42  Identities=24%  Similarity=0.538  Sum_probs=39.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.-|||||||+..||.++-.+|++||+|.++.+++|+. |+|+
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSK   77 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSK   77 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCccc
Confidence            35699999999999999999999999999999999999 9986

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.82  E-value=8.7e-09  Score=76.22  Aligned_cols=41  Identities=27%  Similarity=0.628  Sum_probs=38.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+|||+|||..+++++|+++|++||.|.+|+|++|+. |++|
T Consensus         4 ~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~   45 (352)
T TIGR01661         4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSL   45 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccc
Confidence            7899999999999999999999999999999999987 8765

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.75  E-value=1.9e-08  Score=74.42  Aligned_cols=42  Identities=24%  Similarity=0.487  Sum_probs=38.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +..|||+|||+.+++++|+++|++||.|.+|+|++|+. |++|
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~sk  311 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCK  311 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCcc
Confidence            44799999999999999999999999999999999996 7765

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.71  E-value=3.8e-08  Score=74.01  Aligned_cols=43  Identities=28%  Similarity=0.554  Sum_probs=39.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...+|||+|||..+|+++|+++|++||.|.+|.|++|+. |++|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~k  235 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPR  235 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccc
Confidence            457899999999999999999999999999999999987 7764

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.71  E-value=3.5e-08  Score=74.25  Aligned_cols=44  Identities=20%  Similarity=0.477  Sum_probs=40.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|++|+. |++|
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~sr  149 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSF  149 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccC
Confidence            4668999999999999999999999999999999999987 7764

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).

>KOG0144|consensus

Probab=98.70  E-value=6.6e-09  Score=79.38  Aligned_cols=43  Identities=58%  Similarity=1.070  Sum_probs=40.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ...|||||.|+..+||.+++++|++||.|++|+|++|.+|.||
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sR  165 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSR  165 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheeccccccc
Confidence            3689999999999999999999999999999999999998876

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

Probab=98.69  E-value=4.1e-08  Score=77.24  Aligned_cols=77  Identities=25%  Similarity=0.420  Sum_probs=55.0

Q ss_pred             CceeEEecCCcccchhhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         16 DKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        16 ~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ++.++|+...++.+++........    ..       ...........+|||+||+..+|+++|+++|++||.|.+|+++
T Consensus       250 g~~l~v~~a~~k~er~~~~~~~~~----~~-------~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~  318 (562)
T TIGR01628       250 GKKLYVGRAQKRAEREAELRRKFE----EL-------QQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVM  318 (562)
T ss_pred             ceeeEeecccChhhhHHHHHhhHH----hh-------hhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEE
Confidence            888999988877666443321110    00       0000112345789999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q psy10284         96 KGPDGTSK  103 (103)
Q Consensus        96 ~d~~G~sr  103 (103)
                      .|..|++|
T Consensus       319 ~d~~g~~~  326 (562)
T TIGR01628       319 LDEKGVSR  326 (562)
T ss_pred             ECCCCCcC
Confidence            99657664

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PF00076 RRM_1: RNA recognition motif

Probab=98.69  E-value=2.1e-08  Score=57.53  Aligned_cols=36  Identities=36%  Similarity=0.767  Sum_probs=33.0

Q ss_pred             EEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        65 lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      |||+|||..+|+++|+++|++||.|..+.++.+..|
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~   36 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSG   36 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTS
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccc
Confidence            799999999999999999999999999999987333

(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 ....

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=98.67  E-value=4.5e-08  Score=77.82  Aligned_cols=47  Identities=21%  Similarity=0.369  Sum_probs=41.9

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        57 ~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      .+....++|||+|||++++|++|+++|++||.|.+++|++|..|++|
T Consensus        53 ~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sR   99 (578)
T TIGR01648        53 VQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNR   99 (578)
T ss_pred             CCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCcc
Confidence            33456799999999999999999999999999999999999558775

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.

>KOG0144|consensus

Probab=98.62  E-value=3.1e-08  Score=75.79  Aligned_cols=47  Identities=34%  Similarity=0.651  Sum_probs=42.5

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        57 ~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++....|+|||.+|+.++|.+|+++|++||.|.+|.|++|+. |.+|
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~   76 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSK   76 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCccc
Confidence            3445668999999999999999999999999999999999998 7764

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

Probab=98.60  E-value=1.2e-07  Score=74.71  Aligned_cols=67  Identities=36%  Similarity=0.590  Sum_probs=52.5

Q ss_pred             CCCCCceeEEecCCcccchhhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeE
Q psy10284         12 PLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE   91 (103)
Q Consensus        12 ~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~   91 (103)
                      ..+++++++|+.+.++.++...                        .....++|||+|||.++|+++|+++|+.||.|.+
T Consensus       152 ~~~~~~~i~v~~~~~~~~~~~~------------------------~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~  207 (562)
T TIGR01628       152 MLLNDKEVYVGRFIKKHEREAA------------------------PLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITS  207 (562)
T ss_pred             cEecCceEEEeccccccccccc------------------------cccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEE
Confidence            5577888888877766555311                        1112278999999999999999999999999999


Q ss_pred             EEEeeCCCCCC
Q psy10284         92 CTVLKGPDGTS  102 (103)
Q Consensus        92 ~~v~~d~~G~s  102 (103)
                      +.+++|..|++
T Consensus       208 ~~i~~~~~g~~  218 (562)
T TIGR01628       208 AAVMKDGSGRS  218 (562)
T ss_pred             EEEEECCCCCc
Confidence            99999877655

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG4205|consensus

Probab=98.60  E-value=6.3e-08  Score=71.92  Aligned_cols=43  Identities=37%  Similarity=0.814  Sum_probs=40.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..+++|||+|+|.++++.|+++|.+||+|.+|.+|+|+. |++|
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsr   48 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSR   48 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcc
Confidence            459999999999999999999999999999999999998 8875

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.54  E-value=1.3e-07  Score=68.56  Aligned_cols=37  Identities=22%  Similarity=0.331  Sum_probs=35.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++|||||||+.+|+++|+++|+.||.|.+|.|++|+.
T Consensus         5 rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~   41 (260)
T PLN03120          5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE   41 (260)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC
Confidence            7899999999999999999999999999999999874

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=98.54  E-value=2.1e-07  Score=74.45  Aligned_cols=42  Identities=24%  Similarity=0.602  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||+||+.++++++|+++|+.||.|.+|+|++|+. |++|
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksK  246 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHK  246 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcC
Confidence            37899999999999999999999999999999999987 6654

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=98.54  E-value=1.7e-07  Score=68.28  Aligned_cols=88  Identities=26%  Similarity=0.442  Sum_probs=61.9

Q ss_pred             CceeEEecCCcccchhhhhc---cccccccCCCcCCCcccccccCCCC-------CCceEEEecCCCCCCHHHHHHhhcC
Q psy10284         16 DKKLFVGMLSKQQNEDDNLS---HCFHLLFPHLQCFPWDLIWTCTPLP-------PDKKLFVGMLSKQQNEDDVRKIFAP   85 (103)
Q Consensus        16 ~~~~~V~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~lfVgnL~~~~te~~l~~~F~~   85 (103)
                      -|-+|||.+.+...++.-..   ..+...--.+-..+++++|+..|..       ....+|||.|...++.+.||+.|.+
T Consensus         6 prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~p   85 (321)
T KOG0148|consen    6 PRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAP   85 (321)
T ss_pred             CceEEeeccChhhHHHHHHHHHHhccccccceeehhhhccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhcc
Confidence            36799999998876654221   1111000011123455666554432       3457999999999999999999999


Q ss_pred             CCceeEEEEeeCCC-CCCC
Q psy10284         86 FGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        86 ~G~i~~~~v~~d~~-G~sr  103 (103)
                      ||+|.+++|++|.. ++||
T Consensus        86 FGevS~akvirD~~T~KsK  104 (321)
T KOG0148|consen   86 FGEVSDAKVIRDMNTGKSK  104 (321)
T ss_pred             ccccccceEeecccCCccc
Confidence            99999999999999 8886

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.53  E-value=1.7e-07  Score=54.28  Aligned_cols=37  Identities=30%  Similarity=0.716  Sum_probs=32.2

Q ss_pred             EEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCC
Q psy10284         65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT  101 (103)
Q Consensus        65 lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~  101 (103)
                      |||+|||+++++++|+++|+.||.|..+.+..++.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~   37 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQ   37 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSS
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccc
Confidence            7999999999999999999999999999999987543

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 ....

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=98.51  E-value=1.9e-07  Score=74.72  Aligned_cols=43  Identities=33%  Similarity=0.588  Sum_probs=40.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||||||+.+++++|+++|++||.|.+|.+++|+. |++|
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~Tgksk  149 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHK  149 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcC
Confidence            458999999999999999999999999999999999987 8765

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.49  E-value=2.6e-07  Score=66.35  Aligned_cols=38  Identities=26%  Similarity=0.385  Sum_probs=35.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +..+||+||++.+|+++|+++|+.||+|.+|+|++|..
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e   42 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE   42 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC
Confidence            47899999999999999999999999999999999865

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=98.47  E-value=6.5e-07  Score=68.56  Aligned_cols=42  Identities=43%  Similarity=0.760  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..+|||+|||..+|+++|+++|++||.|..|.+++|+. |+++
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~  228 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSK  228 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccc
Confidence            58899999999999999999999999999999999987 6654

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0145|consensus

Probab=98.47  E-value=5e-08  Score=70.93  Aligned_cols=60  Identities=27%  Similarity=0.432  Sum_probs=52.7

Q ss_pred             CCcCCCcccccccCCCC--CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         44 HLQCFPWDLIWTCTPLP--PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        44 ~~~~~~~~~~~~~~~~~--~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|.++++++|+++...  +..+|||.+||..+|..+|+++|++||.|...+|+.|.. |.||
T Consensus       107 rLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~sr  169 (360)
T KOG0145|consen  107 RLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSR  169 (360)
T ss_pred             eeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceec
Confidence            45778888999886664  788999999999999999999999999999999999887 7664

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=98.38  E-value=7.4e-07  Score=68.26  Aligned_cols=43  Identities=26%  Similarity=0.470  Sum_probs=39.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..+.|||+|||..+++++|+++|++||.|.+|.+++|+. |++|
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~sk  131 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSK  131 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcc
Confidence            457899999999999999999999999999999999987 7664

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.

>KOG0113|consensus

Probab=98.36  E-value=7.7e-07  Score=65.51  Aligned_cols=41  Identities=32%  Similarity=0.567  Sum_probs=39.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.|||+-|+.+++|..|+..|+.||.|..+.|++|+. |+||
T Consensus       102 ~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgksk  143 (335)
T KOG0113|consen  102 KTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSK  143 (335)
T ss_pred             ceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCcc
Confidence            7899999999999999999999999999999999998 9886

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.36  E-value=7.7e-07  Score=61.37  Aligned_cols=42  Identities=31%  Similarity=0.711  Sum_probs=38.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...|||||||..+|+++|+++|.+||.|..+.+..|+. |++|
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~  157 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR  157 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccC
Confidence            48999999999999999999999999999999999985 7654

>KOG0117|consensus

Probab=98.36  E-value=6.5e-07  Score=68.86  Aligned_cols=50  Identities=28%  Similarity=0.595  Sum_probs=45.2

Q ss_pred             cccCCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         54 WTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        54 ~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      |...+.+.++.||||.||.++.|++|..+|++-|+|-+++||+|+. |.+|
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nR  125 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNR  125 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCc
Confidence            5555567899999999999999999999999999999999999987 8765

>KOG0109|consensus

Probab=98.35  E-value=2.9e-07  Score=67.68  Aligned_cols=36  Identities=33%  Similarity=0.788  Sum_probs=33.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+|||||||..+++.+|+.+|++||+|.+|.|+++-
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNY   38 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKNY   38 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeeccc
Confidence            689999999999999999999999999999998763

>KOG0121|consensus

Probab=98.34  E-value=3.6e-07  Score=60.20  Aligned_cols=39  Identities=21%  Similarity=0.278  Sum_probs=35.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++.||||||++.++|+++.++|+.+|+|..+-+-.|+.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~   73 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRF   73 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccC
Confidence            448999999999999999999999999999998777775

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.33  E-value=1.3e-06  Score=67.76  Aligned_cols=43  Identities=23%  Similarity=0.569  Sum_probs=39.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...+|||||||..+++++|+++|++||.|..+.+++|.. |+++
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~  337 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSK  337 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcC
Confidence            457999999999999999999999999999999999987 7654

Members of this subfamily are found in plants, metazoa and fungi.

>PLN03213 repressor of silencing 3; Provisional

Probab=98.32  E-value=9.4e-07  Score=69.11  Aligned_cols=38  Identities=32%  Similarity=0.581  Sum_probs=35.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+.+||||||++.+++++|+.+|+.||.|.+|.|+++.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET   46 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK   46 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc
Confidence            34899999999999999999999999999999999654

>KOG0122|consensus

Probab=98.24  E-value=1.7e-06  Score=62.21  Aligned_cols=43  Identities=33%  Similarity=0.570  Sum_probs=40.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +...|-|.|||.+++|++|+++|..||.|.++.|++|+. |.+|
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~k  231 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSK  231 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCccc
Confidence            456799999999999999999999999999999999999 9886

>KOG0125|consensus

Probab=98.23  E-value=1.6e-06  Score=64.64  Aligned_cols=42  Identities=21%  Similarity=0.431  Sum_probs=38.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      +...++|+|.|||+..-|.||+.+|++||.|.+|.|+.+..|
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG  134 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG  134 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC
Confidence            346689999999999999999999999999999999998763

>KOG0107|consensus

Probab=98.23  E-value=1.9e-06  Score=59.37  Aligned_cols=39  Identities=23%  Similarity=0.618  Sum_probs=36.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      .++||||||+..+++.+|+.+|..||.+.+|+|.+.+.|
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPG   48 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPG   48 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCC
Confidence            489999999999999999999999999999999987655

>KOG4205|consensus

Probab=98.21  E-value=2.9e-06  Score=63.12  Aligned_cols=42  Identities=26%  Similarity=0.591  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+||..+++++++++|++||.|.++.++.|+. +++|
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~r  139 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPR  139 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccc
Confidence            47999999999999999999999999999999999998 6654

>KOG0147|consensus

Probab=98.19  E-value=1.5e-06  Score=67.99  Aligned_cols=83  Identities=31%  Similarity=0.375  Sum_probs=59.8

Q ss_pred             hhhhcCCCCCCceeEEecCCcccchhhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHHHHHhhcC
Q psy10284          6 LIWTCTPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAP   85 (103)
Q Consensus         6 ~~~~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~   85 (103)
                      +|..+..++-+-+|+|......+++......       .++...        -.....++|||||.+++++++++.+|+.
T Consensus       237 aiaLsGqrllg~pv~vq~sEaeknr~a~~s~-------a~~~k~--------~~~p~~rl~vgnLHfNite~~lr~ifep  301 (549)
T KOG0147|consen  237 AIALSGQRLLGVPVIVQLSEAEKNRAANASP-------ALQGKG--------FTGPMRRLYVGNLHFNITEDMLRGIFEP  301 (549)
T ss_pred             HhhhcCCcccCceeEecccHHHHHHHHhccc-------cccccc--------cccchhhhhhcccccCchHHHHhhhccC
Confidence            4566677888889998887776666332211       000000        0111244999999999999999999999


Q ss_pred             CCceeEEEEeeCCC-CCCC
Q psy10284         86 FGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        86 ~G~i~~~~v~~d~~-G~sr  103 (103)
                      ||.|+.+.+++|.+ |++|
T Consensus       302 fg~Ie~v~l~~d~~tG~sk  320 (549)
T KOG0147|consen  302 FGKIENVQLTKDSETGRSK  320 (549)
T ss_pred             cccceeeeecccccccccc
Confidence            99999999999986 8775

>smart00362 RRM_2 RNA recognition motif

Probab=98.17  E-value=4.4e-06  Score=46.91  Aligned_cols=35  Identities=37%  Similarity=0.718  Sum_probs=32.8

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +|||+|||..+++++++++|.+||.|..+.+..++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~   35 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT   35 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC
Confidence            48999999999999999999999999999988876

>KOG0146|consensus

Probab=98.16  E-value=1.7e-06  Score=63.23  Aligned_cols=44  Identities=75%  Similarity=1.285  Sum_probs=40.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      .+.++||||.|...-.|+|++.+|..||.|++|.+.+..+|.||
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sK   60 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSK   60 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCC
Confidence            35699999999999999999999999999999999999887665

>KOG0127|consensus

Probab=98.16  E-value=3.6e-06  Score=66.30  Aligned_cols=43  Identities=30%  Similarity=0.570  Sum_probs=40.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ....+||.|||+++|+++|.++|++||+|..+.++.|++ |+|+
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~sk  334 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSK  334 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcc
Confidence            457899999999999999999999999999999999999 8774

>KOG0124|consensus

Probab=98.10  E-value=2.5e-06  Score=64.70  Aligned_cols=81  Identities=19%  Similarity=0.364  Sum_probs=57.0

Q ss_pred             CCcchhhhcC----CCCCCceeEEecCCcccch---hhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCC
Q psy10284          2 LPLDLIWTCT----PLPPDKKLFVGMLSKQQNE---DDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQ   74 (103)
Q Consensus         2 ~~~~~~~~~~----~~~~~~~~~V~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~   74 (103)
                      +|+.+-.+.+    .++.||++.||+-+.-...   .+...+             ....+        .++||..+..+.
T Consensus       164 vPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqe-------------eAk~f--------nRiYVaSvHpDL  222 (544)
T KOG0124|consen  164 VPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQE-------------EAKKF--------NRIYVASVHPDL  222 (544)
T ss_pred             CcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHH-------------HHHhh--------heEEeeecCCCc
Confidence            3455444444    6789999999964432111   111110             01234        789999999999


Q ss_pred             CHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         75 NEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        75 te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|+|++.+|+.||+|..|.+.++.. +.+|
T Consensus       223 Se~DiKSVFEAFG~I~~C~LAr~pt~~~Hk  252 (544)
T KOG0124|consen  223 SETDIKSVFEAFGEIVKCQLARAPTGRGHK  252 (544)
T ss_pred             cHHHHHHHHHhhcceeeEEeeccCCCCCcc
Confidence            9999999999999999999999998 4443

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=98.08  E-value=4.8e-06  Score=64.84  Aligned_cols=37  Identities=24%  Similarity=0.398  Sum_probs=34.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +.|||+|||+.+++++|+++|++||.|.+|.+++++.
T Consensus         3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~   39 (481)
T TIGR01649         3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKR   39 (481)
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCC
Confidence            7799999999999999999999999999999987653

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).

>KOG0109|consensus

Probab=98.07  E-value=3.8e-06  Score=61.84  Aligned_cols=64  Identities=19%  Similarity=0.312  Sum_probs=48.1

Q ss_pred             hhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         32 DNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +..+..+|+.+.++.+.   +..+.....-+.+++||||...++..+++..|++||.|.+|.+++|-
T Consensus        51 dairNLhgYtLhg~nIn---VeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy  114 (346)
T KOG0109|consen   51 DAIRNLHGYTLHGVNIN---VEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDY  114 (346)
T ss_pred             HHHhhcccceecceEEE---EEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecce
Confidence            33445566666665543   23333344466899999999999999999999999999999988773

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=98.06  E-value=8.1e-06  Score=63.61  Aligned_cols=39  Identities=26%  Similarity=0.481  Sum_probs=35.9

Q ss_pred             CCceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++.|||+||++ .+|+++|+++|+.||.|.+|++++++.
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~  313 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKK  313 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC
Confidence            567999999998 699999999999999999999999864

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=98.03  E-value=1e-05  Score=51.63  Aligned_cols=42  Identities=17%  Similarity=0.407  Sum_probs=36.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      |...++-|||.|||+.+|.+++.++|..||.|..++|--++.
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~   55 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE   55 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC
Confidence            334457799999999999999999999999999999876665

>KOG0123|consensus

Probab=98.02  E-value=9.8e-06  Score=61.60  Aligned_cols=72  Identities=21%  Similarity=0.481  Sum_probs=59.0

Q ss_pred             CCCCCCceeEEecCCcccchhhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHHHHHhhcCCCcee
Q psy10284         11 TPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE   90 (103)
Q Consensus        11 ~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~   90 (103)
                      .++++|+++|||.+.++.++......                     ....-.++|+.+++.+++++.+...|.++|.|.
T Consensus       137 g~ll~~kki~vg~~~~~~er~~~~~~---------------------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~  195 (369)
T KOG0123|consen  137 GMLLNGKKIYVGLFERKEEREAPLGE---------------------YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSIT  195 (369)
T ss_pred             CcccCCCeeEEeeccchhhhcccccc---------------------hhhhhhhhheeccccccchHHHHHhhcccCcce
Confidence            37899999999999999777544321                     111227899999999999999999999999999


Q ss_pred             EEEEeeCCCCCCC
Q psy10284         91 ECTVLKGPDGTSK  103 (103)
Q Consensus        91 ~~~v~~d~~G~sr  103 (103)
                      ++.++.+..|+++
T Consensus       196 s~~v~~~~~g~~~  208 (369)
T KOG0123|consen  196 SVAVMRDSIGKSK  208 (369)
T ss_pred             EEEEeecCCCCCC
Confidence            9999999886653

>KOG0145|consensus

Probab=97.98  E-value=1.1e-05  Score=58.88  Aligned_cols=43  Identities=28%  Similarity=0.621  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|.|.-||..+|.++++.+|...|+|++|++++|+- |+|
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqS   82 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQS   82 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccc
Confidence            3447899999999999999999999999999999999998 876

>smart00360 RRM RNA recognition motif

Probab=97.95  E-value=1.3e-05  Score=44.64  Aligned_cols=36  Identities=36%  Similarity=0.733  Sum_probs=32.0

Q ss_pred             EecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         67 VGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        67 VgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      |+|||..+++++++++|++||.|..+.+..++. +++
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~   37 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKS   37 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCC
Confidence            579999999999999999999999999998875 443

>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=97.93  E-value=2.7e-05  Score=43.81  Aligned_cols=36  Identities=36%  Similarity=0.776  Sum_probs=33.3

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +|+|+|||..+++++++++|+.||.|..+.+..++.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~   36 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD   36 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC
Confidence            389999999999999999999999999999988764

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).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=97.92  E-value=2.3e-05  Score=62.63  Aligned_cols=37  Identities=27%  Similarity=0.451  Sum_probs=33.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCC--CceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPF--GTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~--G~i~~~~v~~d   97 (103)
                      ..++|||+||++.+++++|+++|++|  |.|.+|.++++
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg  270 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD  270 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC
Confidence            34789999999999999999999999  99999988765

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.

>KOG0123|consensus

Probab=97.81  E-value=2.7e-05  Score=59.21  Aligned_cols=69  Identities=16%  Similarity=0.368  Sum_probs=49.0

Q ss_pred             cccchhhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         26 KQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      ...+.+...+..++..+.+..+   ..-|+.   .+..-+||.||+..++..+|.+.|+.||.|.+|+|++|..|
T Consensus        46 ~~~da~~A~~~~n~~~~~~~~~---rim~s~---rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g  114 (369)
T KOG0123|consen   46 QPADAERALDTMNFDVLKGKPI---RIMWSQ---RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG  114 (369)
T ss_pred             CHHHHHHHHHHcCCcccCCcEE---Eeehhc---cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC
Confidence            3334555555555544544333   333322   22344999999999999999999999999999999999876

>KOG0105|consensus

Probab=97.78  E-value=2.3e-05  Score=54.70  Aligned_cols=35  Identities=23%  Similarity=0.564  Sum_probs=32.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ..++|||||||-++.+.+++++|-+||.|..+.|.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK   39 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELK   39 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEec
Confidence            45899999999999999999999999999998763

>KOG0108|consensus

Probab=97.76  E-value=3.2e-05  Score=59.97  Aligned_cols=41  Identities=22%  Similarity=0.464  Sum_probs=39.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.+||||+|+++++++|..+|+..|.|.+++++.|++ |++|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~   60 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPK   60 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcC
Confidence            7899999999999999999999999999999999999 8875

>KOG4207|consensus

Probab=97.68  E-value=4.2e-05  Score=54.19  Aligned_cols=43  Identities=21%  Similarity=0.384  Sum_probs=39.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ....|-|-||.+.++.++|+.+|++||.|.+|.|.+|+. +++|
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sR   55 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSR   55 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceeccccccccccc
Confidence            447899999999999999999999999999999999998 7654

>KOG0117|consensus

Probab=97.60  E-value=6.9e-05  Score=57.95  Aligned_cols=38  Identities=26%  Similarity=0.452  Sum_probs=34.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +-+-|||.||+.++|++.|+++|++||.|++|+.++|-
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rDY  295 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRDY  295 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccce
Confidence            45779999999999999999999999999999888773

>KOG0146|consensus

Probab=97.57  E-value=0.0001  Score=54.06  Aligned_cols=45  Identities=27%  Similarity=0.456  Sum_probs=41.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++++|+|||-.||.+..+.+|...|..||.|.+.+|..|+. ++||
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSK  327 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSK  327 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhcccccc
Confidence            46899999999999999999999999999999999999998 7665

>KOG0131|consensus

Probab=97.54  E-value=7.5e-05  Score=51.82  Aligned_cols=43  Identities=30%  Similarity=0.580  Sum_probs=37.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEE-EEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~-~v~~d~~-G~sr  103 (103)
                      .+.++|||||...++|..|.+.|+.||.+.+. .+++|.+ |.++
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~  139 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPK  139 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCC
Confidence            34789999999999999999999999998874 7899988 7653

>KOG0533|consensus

Probab=97.45  E-value=0.00017  Score=52.16  Aligned_cols=42  Identities=26%  Similarity=0.399  Sum_probs=38.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ...+++|.|||..+++++|+++|+.||.+..+-|-.|+.|+|
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s  123 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRS  123 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCC
Confidence            447899999999999999999999999999999999998765

>KOG0415|consensus

Probab=97.45  E-value=0.00013  Score=55.29  Aligned_cols=42  Identities=36%  Similarity=0.714  Sum_probs=38.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ....|||.-|..-+|+++|.-+|+.||.|.+|.|++|.. |-|
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgds  280 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDS  280 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccch
Confidence            346799999999999999999999999999999999997 754

>KOG0124|consensus

Probab=97.45  E-value=6.8e-05  Score=57.06  Aligned_cols=43  Identities=33%  Similarity=0.588  Sum_probs=40.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      -.|++|||.++++..|+.+|..|..||.|.++.+..|+. |++|
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHK  155 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHK  155 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeeccccccccccc
Confidence            348999999999999999999999999999999999998 8775

>KOG0131|consensus

Probab=97.37  E-value=0.00015  Score=50.41  Aligned_cols=39  Identities=23%  Similarity=0.386  Sum_probs=36.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +..+||||||+..++++.|.++|-+.|.|.++.+++|+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv   46 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRV   46 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhh
Confidence            447899999999999999999999999999999999986

>KOG0111|consensus

Probab=97.23  E-value=0.00015  Score=51.92  Aligned_cols=41  Identities=24%  Similarity=0.499  Sum_probs=38.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.||||+|..++||.-|-..|-+||.|.++.++.|-+ +++|
T Consensus        11 rtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHR   52 (298)
T KOG0111|consen   11 RTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHR   52 (298)
T ss_pred             eeEEeccchHHHHHHHHHhccccccchhhcccccchhccccc
Confidence            7899999999999999999999999999999999998 7775

>KOG0130|consensus

Probab=97.08  E-value=0.00062  Score=45.47  Aligned_cols=40  Identities=23%  Similarity=0.378  Sum_probs=36.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      --|||.++...+||+++.+.|..||+|..+.+-.|+. |-.
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~  113 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYV  113 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccc
Confidence            4599999999999999999999999999999999987 754

>KOG1548|consensus

Probab=97.08  E-value=0.0012  Score=49.78  Aligned_cols=44  Identities=14%  Similarity=0.267  Sum_probs=34.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeE--------EEEeeCCCCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPDGTS  102 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~--------~~v~~d~~G~s  102 (103)
                      ...+.+|||.|||.++|-+++.++|+.||-|.+        |++-+|..|+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~l  182 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKL  182 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCc
Confidence            346688999999999999999999999997654        55555555543

>KOG0127|consensus

Probab=97.04  E-value=0.00094  Score=53.07  Aligned_cols=41  Identities=20%  Similarity=0.393  Sum_probs=38.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..|||++||++++.++|.+.|+.+|.|..|.++.++. +.+|
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~R   47 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKR   47 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCccccc
Confidence            7899999999999999999999999999999999987 6654

>KOG0132|consensus

Probab=96.92  E-value=0.00072  Score=55.42  Aligned_cols=38  Identities=26%  Similarity=0.528  Sum_probs=33.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      -++.||||+|+..+++.+|..+|+.||+|.++.++-.+
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R  457 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR  457 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC
Confidence            34889999999999999999999999999998765443

>KOG4212|consensus

Probab=96.92  E-value=0.0014  Score=51.03  Aligned_cols=43  Identities=16%  Similarity=0.370  Sum_probs=38.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcC-CCceeEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAP-FGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~-~G~i~~~~v~~d~~G~sr  103 (103)
                      ..+.+||.|||+++.+.+|+++|.. -|+|+.|.+..|..|++|
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~r   86 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKAR   86 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcC
Confidence            3466999999999999999999975 799999999999998876

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=96.91  E-value=0.0016  Score=50.61  Aligned_cols=27  Identities=22%  Similarity=0.445  Sum_probs=24.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPF   86 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~   86 (103)
                      ...++|||||||+.+|+++|+++|.+|
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~  199 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDL  199 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHH
Confidence            356899999999999999999999975

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0153|consensus

Probab=96.72  E-value=0.0024  Score=48.24  Aligned_cols=38  Identities=29%  Similarity=0.505  Sum_probs=33.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .-..||||+|-..++|.+++++|.+||+|.++.++..+
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~  264 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK  264 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc
Confidence            44789999999999999999999999999999876543

>KOG0116|consensus

Probab=96.43  E-value=0.003  Score=48.93  Aligned_cols=34  Identities=24%  Similarity=0.449  Sum_probs=31.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEee
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   96 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~   96 (103)
                      ..|||+|||.+++..+|++.|.+||.|....|..
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~v  322 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQV  322 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEE
Confidence            4499999999999999999999999999987754

>KOG4206|consensus

Probab=96.43  E-value=0.0061  Score=43.43  Aligned_cols=36  Identities=25%  Similarity=0.669  Sum_probs=31.8

Q ss_pred             ceEEEecCCCCCCHHHHHH----hhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~----~F~~~G~i~~~~v~~d~   98 (103)
                      ..|||.||+..+..++|+.    +|++||+|.++...+..
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~   49 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTP   49 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCC
Confidence            4899999999999999888    99999999999766544

>KOG0151|consensus

Probab=96.39  E-value=0.0038  Score=51.01  Aligned_cols=39  Identities=23%  Similarity=0.486  Sum_probs=35.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +..+++|||||+..++++.|-..|..||.|.++++|.-+
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpR  210 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPR  210 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeeccc
Confidence            577999999999999999999999999999999988644

>KOG4212|consensus

Probab=96.32  E-value=0.003  Score=49.22  Aligned_cols=36  Identities=11%  Similarity=0.152  Sum_probs=33.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      .+.|.|||.|||++.|+..|++-|-.||.|..+.||
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim  569 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM  569 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhh
Confidence            467999999999999999999999999999998873

>KOG4209|consensus

Probab=96.21  E-value=0.0045  Score=44.42  Aligned_cols=44  Identities=23%  Similarity=0.246  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+...+||||+.+.+|-+++..+|+.||.|..+.+..|+. |++|
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k  143 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPK  143 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcc
Confidence            4668899999999999999999999999999999999998 7654

>KOG4454|consensus

Probab=96.09  E-value=0.0021  Score=46.01  Aligned_cols=41  Identities=20%  Similarity=0.351  Sum_probs=37.5

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      .+.|||+|+...++|+-|.++|-+.|.|..+.|..+++|+.
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~   49 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQ   49 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCC
Confidence            37899999999999999999999999999999998888654

>KOG0110|consensus

Probab=95.84  E-value=0.0062  Score=49.55  Aligned_cols=37  Identities=24%  Similarity=0.492  Sum_probs=34.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ..++|.|.|||+..+-.+++++|..||.+.+|+|+.-
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK  648 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK  648 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchh
Confidence            3589999999999999999999999999999999865

>KOG0106|consensus

Probab=95.52  E-value=0.012  Score=41.92  Aligned_cols=32  Identities=25%  Similarity=0.641  Sum_probs=29.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEE
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   94 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v   94 (103)
                      .++|||+||+.+.+.++..+|..||.+.++.+
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m   33 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM   33 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee
Confidence            57999999999999999999999999999854

>KOG0129|consensus

Probab=95.49  E-value=0.041  Score=43.47  Aligned_cols=43  Identities=23%  Similarity=0.511  Sum_probs=37.5

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHhhc-CCCceeEEEEeeCCC
Q psy10284         57 TPLPPDKKLFVGMLSKQQNEDDVRKIFA-PFGTIEECTVLKGPD   99 (103)
Q Consensus        57 ~~~~~~~~lfVgnL~~~~te~~l~~~F~-~~G~i~~~~v~~d~~   99 (103)
                      .+.+-.+.+|||+||.-++-++|-.+|+ .||.|.-+-|=.|++
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k  408 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPK  408 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcc
Confidence            3445668999999999999999999999 699999999888854

>KOG3152|consensus

Probab=95.47  E-value=0.018  Score=41.95  Aligned_cols=38  Identities=8%  Similarity=0.239  Sum_probs=34.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +..-||+++||..+.-..|+++|++||.|.+|.+....
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~  110 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPED  110 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchh
Confidence            56789999999999999999999999999999987543

>KOG0226|consensus

Probab=95.39  E-value=0.017  Score=42.21  Aligned_cols=43  Identities=28%  Similarity=0.553  Sum_probs=40.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...+||+|.|..+++++.|-..|.+|-.....++++|+. |+++
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSk  232 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSK  232 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccc
Confidence            568999999999999999999999999999999999999 9875

>KOG0129|consensus

Probab=95.39  E-value=0.012  Score=46.39  Aligned_cols=30  Identities=30%  Similarity=0.568  Sum_probs=27.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCcee
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIE   90 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~   90 (103)
                      .++++|||+||++++|+.+...|..||.+.
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~  287 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVK  287 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceE
Confidence            568999999999999999999999999854

>KOG4661|consensus

Probab=95.33  E-value=0.014  Score=47.03  Aligned_cols=39  Identities=21%  Similarity=0.468  Sum_probs=35.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      -+++|+|.+|+..+.-.+|+.+|++||.|+-.+|+.+-.
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaR  442 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNAR  442 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCC
Confidence            457899999999999999999999999999999988654

>KOG4660|consensus

Probab=95.24  E-value=0.014  Score=46.43  Aligned_cols=40  Identities=25%  Similarity=0.385  Sum_probs=34.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      ....|+|-|||..+++++|+.+|+.||+|..++.-+.++|
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~  113 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRG  113 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCc
Confidence            4478999999999999999999999999999765554443

>KOG4208|consensus

Probab=94.60  E-value=0.072  Score=37.72  Aligned_cols=44  Identities=20%  Similarity=0.375  Sum_probs=39.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCC-CceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPF-GTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~-G~i~~~~v~~d~~-G~sr  103 (103)
                      ....-+|++.+|..+.+..+..+|.+| |.+.++++.|++. |.||
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSK   92 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSK   92 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcC
Confidence            345779999999999999999999998 8888899889998 9886

>KOG4210|consensus

Probab=94.23  E-value=0.053  Score=40.07  Aligned_cols=42  Identities=29%  Similarity=0.524  Sum_probs=36.6

Q ss_pred             CCceEE-EecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLF-VGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lf-VgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ....+| |+++++.+++++|+.+|..+|.|..++++.++. |.+
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~  226 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDS  226 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccch
Confidence            445566 999999999999999999999999999998887 654

>PF13893 RRM_5: RNA recognition motif

Probab=93.97  E-value=0.066  Score=29.30  Aligned_cols=20  Identities=25%  Similarity=0.635  Sum_probs=16.3

Q ss_pred             HHHhhcCCCceeEEEEeeCC
Q psy10284         79 VRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        79 l~~~F~~~G~i~~~~v~~d~   98 (103)
                      |+++|++||.|.++.+..++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~   20 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK   20 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS
T ss_pred             ChHHhCCcccEEEEEEEeCC
Confidence            67899999999999887655

(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 ....

>KOG1190|consensus

Probab=93.59  E-value=0.096  Score=40.68  Aligned_cols=38  Identities=26%  Similarity=0.471  Sum_probs=33.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .++-+.++|||++++|+++-+++.+||+|+.+.+.+.+
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGk   64 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGK   64 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeeccc
Confidence            44779999999999999999999999999998776554

>KOG4849|consensus

Probab=93.47  E-value=0.027  Score=42.99  Aligned_cols=44  Identities=20%  Similarity=0.268  Sum_probs=33.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCC--ceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G--~i~~~~v~~d~~-G~sr  103 (103)
                      ++...+|||||-|++|+++|.+.....|  .+.+++...++. |+||
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSK  124 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSK  124 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCccc
Confidence            4556799999999999999999888776  344455555555 7765

>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=93.29  E-value=0.12  Score=32.65  Aligned_cols=36  Identities=19%  Similarity=0.386  Sum_probs=21.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +-|++.+++..++.++|++.|++||.|.-|.+.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~   37 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD   37 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC
Confidence            457888899999999999999999999888765543

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0110|consensus

Probab=92.77  E-value=0.096  Score=42.89  Aligned_cols=39  Identities=28%  Similarity=0.435  Sum_probs=34.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||.||++++|.+++..+|...|.|.++.|.+-++
T Consensus       514 ~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd  552 (725)
T KOG0110|consen  514 TETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKD  552 (725)
T ss_pred             cchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEecccc
Confidence            345599999999999999999999999999998876554

>KOG0115|consensus

Probab=92.56  E-value=0.12  Score=37.74  Aligned_cols=39  Identities=26%  Similarity=0.394  Sum_probs=34.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT  101 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~  101 (103)
                      ..|||.||+..++.+.+.+.|+.||.|....+.-|-.|+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k   70 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGK   70 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccccc
Confidence            669999999999999999999999999998777776543

>KOG0147|consensus

Probab=92.10  E-value=0.029  Score=44.54  Aligned_cols=43  Identities=16%  Similarity=0.415  Sum_probs=38.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..+.+|+-.++...+..+|.++|+.+|.|.+|.++.|+. +++|
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rsk  221 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSK  221 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhc
Confidence            447789999999999999999999999999999999998 7654

>smart00361 RRM_1 RNA recognition motif

Probab=92.07  E-value=0.22  Score=28.62  Aligned_cols=23  Identities=17%  Similarity=0.468  Sum_probs=19.0

Q ss_pred             HHHHHHhhc----CCCceeEEE-EeeCC
Q psy10284         76 EDDVRKIFA----PFGTIEECT-VLKGP   98 (103)
Q Consensus        76 e~~l~~~F~----~~G~i~~~~-v~~d~   98 (103)
                      +++|++.|+    .||.|.++. |+.|+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~   29 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDN   29 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCC
Confidence            577888888    999999995 77665

>KOG1457|consensus

Probab=91.60  E-value=0.12  Score=37.37  Aligned_cols=32  Identities=16%  Similarity=0.418  Sum_probs=27.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEE
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   94 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v   94 (103)
                      ..|||.||..++||++|+.+|+.|-....++|
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~  242 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKI  242 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEE
Confidence            46999999999999999999999976555543

>KOG0120|consensus

Probab=91.32  E-value=0.15  Score=40.54  Aligned_cols=43  Identities=33%  Similarity=0.598  Sum_probs=38.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+||...++..++++.+.||.+....++.|.. |-++
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~sk  331 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSK  331 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeeccccccccc
Confidence            557899999999999999999999999999999999987 6553

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=89.77  E-value=0.41  Score=26.47  Aligned_cols=31  Identities=26%  Similarity=0.318  Sum_probs=23.0

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      -|-|.|.+.+.. +.+..+|.+||+|.+..+.
T Consensus         3 wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~   33 (53)
T PF14605_consen    3 WISVSGFPPDLA-EEVLEHFASFGEIVDIYVP   33 (53)
T ss_pred             EEEEEeECchHH-HHHHHHHHhcCCEEEEEcC
Confidence            366777765554 4566699999999998765

>KOG0128|consensus

Probab=89.58  E-value=0.22  Score=41.62  Aligned_cols=42  Identities=10%  Similarity=0.185  Sum_probs=37.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      -..+||.|.|+..|.+.++.++..+|.+.++.++..+.|+++
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpk  777 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPK  777 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccc
Confidence            367999999999999999999999999999988887776553

>KOG1855|consensus

Probab=89.43  E-value=0.87  Score=35.67  Aligned_cols=37  Identities=22%  Similarity=0.454  Sum_probs=33.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      .++.|.+-|||.+-.-+.|.++|+.+|.|..++|..-
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckP  266 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKP  266 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCC
Confidence            4478899999999999999999999999999998654

>KOG0105|consensus

Probab=86.54  E-value=1.4  Score=31.22  Aligned_cols=39  Identities=13%  Similarity=0.135  Sum_probs=34.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...++.|.+||.+.++.+|+++.-..|.|+-..+.+|-.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg~  152 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDGV  152 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecccc
Confidence            346899999999999999999999999999988887754

>KOG1995|consensus

Probab=83.85  E-value=1  Score=34.33  Aligned_cols=32  Identities=22%  Similarity=0.328  Sum_probs=28.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeE
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE   91 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~   91 (103)
                      .....+||-+||..+++.++.++|.++|.|..
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikr   95 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKR   95 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceecc
Confidence            35578999999999999999999999997643

>KOG4211|consensus

Probab=83.46  E-value=2.3  Score=33.78  Aligned_cols=34  Identities=18%  Similarity=0.264  Sum_probs=27.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      .-|-+.+|||++|++++.+.|+.++ |..+.+.++
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~   44 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR   44 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc
Confidence            4466689999999999999999995 666655554

>KOG4211|consensus

Probab=82.20  E-value=4  Score=32.52  Aligned_cols=41  Identities=17%  Similarity=0.224  Sum_probs=31.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeE-EEEeeCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEE-CTVLKGPDGTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~-~~v~~d~~G~s  102 (103)
                      ..-|-..+||+.+|++++.+.|+-.=-+.. +.+++|+.|++
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~  144 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRP  144 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCc
Confidence            345777999999999999999998765555 44666666553

>KOG4206|consensus

Probab=81.28  E-value=3.5  Score=29.59  Aligned_cols=40  Identities=18%  Similarity=0.438  Sum_probs=33.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+.+.-+|+-|||..++.+.+..+|++|....+++++...
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~  182 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR  182 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC
Confidence            3455779999999999999999999999988888766533

>KOG4454|consensus

Probab=80.63  E-value=0.45  Score=34.35  Aligned_cols=40  Identities=25%  Similarity=0.434  Sum_probs=34.9

Q ss_pred             ceEEEec----CCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         63 KKLFVGM----LSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        63 ~~lfVgn----L~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      .+++.|+    |....+++.+...|++-|.+..+++.++.+|+.
T Consensus        81 ~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rn  124 (267)
T KOG4454|consen   81 RTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRN  124 (267)
T ss_pred             cccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCc
Confidence            5678888    888889999999999999999999998887654

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=80.58  E-value=4.3  Score=24.93  Aligned_cols=29  Identities=28%  Similarity=0.549  Sum_probs=19.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeE
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEE   91 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~   91 (103)
                      ..+|--..|...-..|+.++|+.||.|.-
T Consensus         9 dHVFhltFPkeWK~~DI~qlFspfG~I~V   37 (87)
T PF08675_consen    9 DHVFHLTFPKEWKTSDIYQLFSPFGQIYV   37 (87)
T ss_dssp             CCEEEEE--TT--HHHHHHHCCCCCCEEE
T ss_pred             ceEEEEeCchHhhhhhHHHHhccCCcEEE
Confidence            34444458999999999999999998764

; 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.

>KOG1190|consensus

Probab=80.49  E-value=2.8  Score=32.86  Aligned_cols=38  Identities=18%  Similarity=0.371  Sum_probs=32.0

Q ss_pred             CceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++-|.|.||.. .+|.+-|-.+|+.||.|.+++|+.++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk  335 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK  335 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC
Confidence            57788888865 458899999999999999999988763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	103
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		6e-15
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-14
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-13
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-10
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-10
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-09

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 75.9 bits (185), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 39/42 (92%)
Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML KQQ ++DVRK+F PFGTI+ECTVL+GPDGTSK
Sbjct: 12  DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSK 53

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 38/44 (86%)
Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           P  +KLFVGML+KQQ+EDDVR++F  FG IEECT+L+GPDG SK
Sbjct: 13  PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK 56

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 39/42 (92%)
Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLFVGML+KQQ+E+DV ++F PFG I+ECTVL+GPDG+SK
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK 56

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLF+GM+SK+  E+D+R +F+ FG IEEC +L+GPDG S+
Sbjct: 95  DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR 136

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 35/42 (83%)
Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLF+GM+SK+  E+D+R +F+ FG IEEC +L+GPDG S+
Sbjct: 107 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR 148

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 33/42 (78%)
Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLF+G +SK+  E+D+R  F+ FG IEEC +L+GPDG S+
Sbjct: 95  DRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSR 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	103
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	8e-10
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-09
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-05
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-08
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-07
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-07
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-07
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	5e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-05
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	9e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-05
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	9e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-04
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-04

>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 = 77.3 bits (191), Expect = 2e-20
 Identities = 30/44 (68%), Positives = 39/44 (88%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+KLFVGML+KQQ+E+DV ++F PFG I+ECTVL+GPDG+SK
Sbjct: 13  GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK 56

>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 = 76.5 bits (189), Expect = 3e-19
 Identities = 24/42 (57%), Positives = 35/42 (83%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           D+KLF+GM+SK+  E+D+R +F+ FG IEEC +L+GPDG S+
Sbjct: 95  DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR 136

>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 = 53.4 bits (129), Expect = 2e-10
 Identities = 12/37 (32%), Positives = 22/37 (59%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
           K+FVG + +  +E D+R++F  +G + E  VL+    
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQ 41

>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 = 65.8 bits (161), Expect = 1e-15
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 54  WTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            +        KLF+G + +  +E D++ +F  FG I E TVLK    G  K
Sbjct: 5   SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHK 55

>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 = 56.0 bits (136), Expect = 2e-11
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             D  L+V  L +   +D +  IF  +G+I +  +L+    G  +
Sbjct: 87  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 131

>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 = 42.2 bits (100), Expect = 3e-06
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          +  L V  L +   + ++  +F   G I  C +++
Sbjct: 3  NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR 37

>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 = 53.8 bits (130), Expect = 4e-11
 Identities = 11/44 (25%), Positives = 22/44 (50%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
               K+ V  +  Q N+ ++R++F+ FG ++   + K   GT  
Sbjct: 13  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGA 56

>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 = 54.5 bits (132), Expect = 8e-11
 Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            L+V  L K   + ++ ++F+ +G I    +L     G S+
Sbjct: 90  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSR 130

>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 = 41.8 bits (99), Expect = 4e-06
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
           L V  L +   +++ R +F   G IE C +++
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR 36

>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 = 51.5 bits (124), Expect = 2e-10
 Identities = 11/40 (27%), Positives = 18/40 (45%)

Query: 58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
                KL VG +S      ++R  F  +G + EC ++K 
Sbjct: 6  SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 51.4 bits (124), Expect = 3e-10
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
           K+FVG +S      ++R +F   G + EC V+K 
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44

>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 = 50.7 bits (122), Expect = 5e-10
 Identities = 11/39 (28%), Positives = 18/39 (46%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
           P  +L+VG L    +   + + F  FG+I     +KG 
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53

>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 = 51.2 bits (123), Expect = 5e-10
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
               KLF+G L+++ NE  ++ +F   G I E  ++K     S+
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR 48

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 50.9 bits (122), Expect = 6e-10
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            P K++    L+    E  ++ +   +G +EE  +L  P      
Sbjct: 4   IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL 48

>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 = 53.2 bits (128), Expect = 7e-10
 Identities = 10/44 (22%), Positives = 19/44 (43%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
                L V  LS   + + + + F+ FG +E+  V+    G + 
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT 137

>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 = 43.5 bits (103), Expect = 2e-06
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          +LFVG L     E+D +++F  +G   E  + +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINR 56

>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 = 50.8 bits (122), Expect = 8e-10
 Identities = 9/46 (19%), Positives = 20/46 (43%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
                  +FV  L  +     ++++F+  G +    +L+  DG S+
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR 56

>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 = 50.3 bits (121), Expect = 8e-10
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
              +LFVG L     E+++RK+F  +G   E  + K 
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD 50

>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 = 49.5 bits (119), Expect = 1e-09
 Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                L+VG L     ED +R IF PFG I+   ++K  D G SK
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK 47

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 49.5 bits (119), Expect = 1e-09
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
           KLF+G L ++  E ++R +F  +G + EC ++K 
Sbjct: 9  VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN 43

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
            +    KL V  L    ++ D++++FA FGT+++  V     G S 
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 129

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 49.6 bits (119), Expect = 2e-09
 Identities = 12/38 (31%), Positives = 20/38 (52%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
            + +LFV        E ++ +IF PFG ++E  +L G
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 66

>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 = 49.1 bits (118), Expect = 2e-09
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           P    ++V  L      +D+ +IF+ +G + + T++K  D   SK
Sbjct: 14  PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK 58

>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 = 50.1 bits (120), Expect = 2e-09
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
            +    KL V  L    ++ D++++FA FGT+++  V     G S 
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 76

>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 = 49.1 bits (118), Expect = 2e-09
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            P+  L V  LS    E D+R++F+ +G I + +++       S+
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 57

>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 = 49.6 bits (119), Expect = 2e-09
 Identities = 13/47 (27%), Positives = 23/47 (48%)

Query: 57  TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             +    KL V  L    ++ D++++FA FGT+++  V     G S 
Sbjct: 24  AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL 70

>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 = 49.6 bits (119), Expect = 2e-09
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
            L++  L    +E ++  +  PFG +    +L+   GTS+
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 66

>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 = 49.2 bits (118), Expect = 2e-09
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             D+ +FVG L  +  E+ + ++F   G + + T+ K  +G  K
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK 57

>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 = 49.2 bits (118), Expect = 3e-09
 Identities = 13/35 (37%), Positives = 18/35 (51%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          K LFV  L+    E+ + K F+ FG +E    LK 
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 48.8 bits (117), Expect = 3e-09
 Identities = 9/44 (20%), Positives = 20/44 (45%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
               KLF+  L     ++++ +I    GT+++  ++    G  K
Sbjct: 15  LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK 58

>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 = 48.9 bits (117), Expect = 3e-09
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 58 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 97
          P   + ++F+G L+     + DV  IF+ +G +  C+V KG
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG 63

>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 = 48.0 bits (115), Expect = 5e-09
 Identities = 13/38 (34%), Positives = 17/38 (44%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
               L+VG L     E D+R  F  FG I   TV++ 
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR 47

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 48.0 bits (115), Expect = 5e-09
 Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 57 TPLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 97
            +PP  +LF+G L  +  +++D+ +IF+P+G I +  +   
Sbjct: 5  HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 46

>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 = 47.9 bits (115), Expect = 6e-09
 Identities = 8/42 (19%), Positives = 19/42 (45%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT 101
               K+ +G L++   +D + +IF+ +G I+   +       
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHP 43

>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 = 49.2 bits (118), Expect = 7e-09
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           PLP   KLF+G L    N+D V+++   FG ++   ++K    G SK
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 136

>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 = 38.4 bits (90), Expect = 8e-05
 Identities = 8/39 (20%), Positives = 15/39 (38%)

Query: 59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          L   ++L+VG +     E+ +   F     +   T   G
Sbjct: 1  LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39

>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 = 48.0 bits (115), Expect = 7e-09
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
            + KLFVG LS   NE  + ++F+ +G I E  V+K
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK 46

>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 = 49.6 bits (119), Expect = 7e-09
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               KLF+G L    N+D V+++   FG ++   ++K    G SK
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156

>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 = 35.8 bits (83), Expect = 7e-04
 Identities = 7/35 (20%), Positives = 14/35 (40%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          ++L+VG +     E+ +   F     +   T   G
Sbjct: 5  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39

>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 = 48.0 bits (115), Expect = 8e-09
 Identities = 12/41 (29%), Positives = 24/41 (58%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
             +FVG +  + +E ++R  FA +G+++E  ++    G SK
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSK 50

>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 = 48.0 bits (115), Expect = 8e-09
 Identities = 7/44 (15%), Positives = 19/44 (43%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
                LF+G L+  ++  +++   +      +  V+    GT++
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNR 58

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 49.6 bits (119), Expect = 8e-09
 Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               +++V  + +  ++DD++ +F  FG I+  T+ + P  G  K
Sbjct: 123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHK 167

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            L    +++VG +  +  ED +R+ FAPFG I+   +         K
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70

>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 = 46.8 bits (112), Expect = 1e-08
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
              + L+VG L+++ ++  +   F PFG I +  +    +    +
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 49

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.4 bits (113), Expect = 1e-08
 Identities = 4/42 (9%), Positives = 15/42 (35%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           ++ +++         DD+++     G +    + +      K
Sbjct: 11  NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK 52

>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 = 46.8 bits (112), Expect = 2e-08
 Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           P + +++G +   Q E+ +  + +  G +    ++  P  G SK
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSK 44

>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 = 46.9 bits (112), Expect = 2e-08
 Identities = 10/37 (27%), Positives = 20/37 (54%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
            LF+  L+    E+ ++ +F+  G I+ CT+ K  + 
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK 43

>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 = 48.0 bits (114), Expect = 2e-08
 Identities = 12/43 (27%), Positives = 21/43 (48%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
             P D K++VG L    N+ ++ + F  +G +    V + P G
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG 111

>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 = 46.8 bits (112), Expect = 2e-08
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               +LFV  LS   +E+D+ K+F+ +G + E            K
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK 50

>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 = 46.5 bits (111), Expect = 2e-08
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
           KL++G LS     DD+R++F          VL 
Sbjct: 9  NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 42

>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 = 47.4 bits (113), Expect = 2e-08
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            P+  L V  LS    E D+R++F+ +G I + +++       S+
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88

>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 = 46.8 bits (112), Expect = 2e-08
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
              + L+VG L+++ ++  +   F PFG I +  +    +    +
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 54

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 47.1 bits (112), Expect = 3e-08
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
              + L+VG L+++ ++  +   F PFG I +  +    +    +
Sbjct: 61  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105

>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 = 46.1 bits (110), Expect = 3e-08
 Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
              K+L V  +  +  + D+R++F  FG I +  ++      SK
Sbjct: 13  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSK 55

>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 = 46.3 bits (110), Expect = 4e-08
 Identities = 7/45 (15%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVLKGPDGTSK 103
             + +LF+G + K +  +++ +  A     + +  V        K
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMK 50

>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 = 47.6 bits (114), Expect = 4e-08
 Identities = 7/44 (15%), Positives = 19/44 (43%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
                LF+G L+  ++  +++   +      +  V+    GT++
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNR 54

>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 = 40.7 bits (96), Expect = 1e-05
 Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
            +   + L    LS    ED+++++F     I   +     DG SK
Sbjct: 95  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSK 136

>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 = 45.8 bits (109), Expect = 5e-08
 Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 58 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 97
                +LF+G L  +  +++D+ +IF+P+G I +  +   
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 58

>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 = 45.7 bits (109), Expect = 5e-08
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             +  + V  LS+   E D++++F PFG+I    + K    G SK
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK 57

>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 = 46.7 bits (111), Expect = 5e-08
 Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            L     L+VG LS    E+ + ++F+  G I++  +       T+ 
Sbjct: 35  LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC 81

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 45.7 bits (109), Expect = 7e-08
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 94
           P  P+K L++  LS +  E D+  +FA F   +   +
Sbjct: 20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI 57

>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 = 45.4 bits (108), Expect = 8e-08
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               +L+VG L     ED +R IF PFG IE   ++   + G SK
Sbjct: 24  AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68

>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 = 45.4 bits (108), Expect = 8e-08
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                +FVG LS +   +D++  FAPFG I +  V+K    G SK
Sbjct: 13  SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSK 57

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 44.9 bits (107), Expect = 8e-08
 Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 1/44 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
               ++FV  L        ++  F   G +    +    +G SK
Sbjct: 6   SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSK 48

>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 = 44.9 bits (107), Expect = 9e-08
 Identities = 9/34 (26%), Positives = 19/34 (55%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
            +FVG  +    ED++R+ F+ +G + +  + K
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK 39

>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 = 1e-07
 Identities = 14/37 (37%), Positives = 18/37 (48%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
           K+FVG L     +  +RK F  FG IEE  V+    
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ 54

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.0 bits (107), Expect = 1e-07
 Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
              K+L V  +  +  + D+R++F  FG I +  ++    G SK
Sbjct: 27  SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SK 69

>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 = 45.0 bits (107), Expect = 1e-07
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
              K L +  LS    E+ ++++F     I+   V +  +G SK
Sbjct: 13  GESKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSK 53

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 45.3 bits (108), Expect = 1e-07
 Identities = 12/38 (31%), Positives = 23/38 (60%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
           +KLF+G LS +  E+ +R  +  +G + +C V++ P 
Sbjct: 27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA 64

>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 = 46.9 bits (112), Expect = 1e-07
 Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK-GPDGTSK 103
           P D  L V  L     +    ++  PFG++E C ++     G SK
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 137

>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 = 45.4 bits (108), Expect = 4e-07
 Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)

Query: 63  KKLFVGMLSKQQNEDD-VRKIFAPFGTIEECTVLKGPDGTSK 103
           + L V  L    N+ D + +  +   +   C +  G DG  K
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLK 226

>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 = 45.0 bits (107), Expect = 1e-07
 Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             K +F+  LS    E+ + ++   FG ++   V+  PD   SK
Sbjct: 14  EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK 57

>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 = 46.1 bits (110), Expect = 1e-07
 Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            +KLF+G LS +  ++ +R  F  +GT+ +C V++ P+   S+
Sbjct: 13  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSR 55

>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 = 45.7 bits (109), Expect = 2e-07
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
              KK+FVG + +   E  +R  F  +G IE   ++     G  +
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR 146

>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 = 44.5 bits (106), Expect = 1e-07
 Identities = 10/38 (26%), Positives = 19/38 (50%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
            K+FVG +     E ++R+ F  FG + E  ++   +
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE 47

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.5 bits (105), Expect = 2e-07
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
           P + + +  L     E +V  +  PFG +    +LKG
Sbjct: 14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 51

>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 = 44.1 bits (105), Expect = 2e-07
 Identities = 7/35 (20%), Positives = 19/35 (54%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
            K+FVG  ++    +++++ F  +G + +  + K
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK 45

>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 = 44.6 bits (106), Expect = 2e-07
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           P    LF+  L ++  + D+ ++F PFG +    V        SK
Sbjct: 23  PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

>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 = 43.7 bits (104), Expect = 2e-07
 Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                L++  L     + D+ K+  P+G I     +        K
Sbjct: 3   SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK 47

>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 = 44.2 bits (105), Expect = 2e-07
 Identities = 9/43 (20%), Positives = 17/43 (39%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
               D +++VG L       D+  +F  +G I +  +     G
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG 60

>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 = 44.1 bits (105), Expect = 2e-07
 Identities = 8/44 (18%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               L V  L+ + + D +R++F  +G + +  + + P     +
Sbjct: 12  GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPR 55

>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 = 43.7 bits (104), Expect = 2e-07
 Identities = 13/38 (34%), Positives = 22/38 (57%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
            K+FVG LS   ++ D++  F  FG + +CT+   P+
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPN 48

>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 = 44.7 bits (106), Expect = 2e-07
 Identities = 8/37 (21%), Positives = 17/37 (45%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
             + L V  +    +E  +R++F  +G IE   ++ 
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC 76

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.9 bits (104), Expect = 2e-07
 Identities = 3/50 (6%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 57  TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGT--IEECTVLKGPD-GTSK 103
                   + +  ++     D +    +P+ +  +    ++K      ++
Sbjct: 4   HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNR 53

>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 = 45.2 bits (108), Expect = 3e-07
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             K+F+G L+    ED++R+ F  +GT+ +  ++K P  G S+
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSR 45

>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 = 45.2 bits (108), Expect = 3e-07
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               K+FVG +       +  + F+ +GTI +  ++   D G S+
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSR 129

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 43.8 bits (104), Expect = 3e-07
 Identities = 8/37 (21%), Positives = 19/37 (51%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
           K++VG L     + ++ + F+ +G +    + + P G
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG 38

>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 = 43.8 bits (104), Expect = 3e-07
 Identities = 11/38 (28%), Positives = 20/38 (52%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
            KLFVG L     ++ +R  F+ +G + +C ++K   
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT 53

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 43.7 bits (104), Expect = 3e-07
 Identities = 7/34 (20%), Positives = 18/34 (52%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          + ++VG L      + V+++F+ FG +    ++ 
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIY 35

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 43.6 bits (103), Expect = 3e-07
 Identities = 8/38 (21%), Positives = 13/38 (34%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          P    + +  L     E D+ +    FG I    V+  
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

>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 = 43.3 bits (103), Expect = 3e-07
 Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            LFVG L+   +++ +R  F  F +     V+     G+S+
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 43

>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 = 43.3 bits (103), Expect = 4e-07
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           PL     +FVG LS +     +   FAPFG I +  V+K    G SK
Sbjct: 2   PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSK 48

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 44.0 bits (104), Expect = 4e-07
 Identities = 7/37 (18%), Positives = 18/37 (48%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
               L V  L+ + + D +R++F  +G + +  + +
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81

>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 = 45.2 bits (106), Expect = 4e-07
 Identities = 9/37 (24%), Positives = 17/37 (45%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
              K LFV  ++    E  +R+ F  +G I+   ++ 
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136

>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 = 43.4 bits (103), Expect = 5e-07
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
            K+F+G LS Q  ++ +R+ F  FG ++EC V++ P 
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

>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 = 43.0 bits (102), Expect = 5e-07
 Identities = 7/33 (21%), Positives = 14/33 (42%)

Query: 58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE 90
           +   + L    LS    ED+++++F     I 
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIR 44

>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 = 43.3 bits (102), Expect = 5e-07
 Identities = 11/38 (28%), Positives = 18/38 (47%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
           P + L +  L  +  E +V  +  PFG +    +LKG
Sbjct: 13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG 50

>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 = 44.1 bits (104), Expect = 6e-07
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                LFV  + ++  ED++++ F  +G I+   +      G SK
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114

>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 = 43.5 bits (103), Expect = 7e-07
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                LFV  + ++  E+D+   FA +G I+   +      G  K
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64

>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 = 43.0 bits (102), Expect = 7e-07
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
             L V  L  +  E D+++ F+ FG +    V K   
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK 52

>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 = 42.9 bits (101), Expect = 7e-07
 Identities = 8/41 (19%), Positives = 15/41 (36%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
            +     + V  L +   E D+ +    FGTI    ++  
Sbjct: 10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF 50

>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 = 43.7 bits (103), Expect = 7e-07
 Identities = 7/36 (19%), Positives = 18/36 (50%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
               L V  L+ + + D +R++F  +G + +  + +
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 43.0 bits (102), Expect = 8e-07
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                LFV  + ++  ED++++ F  +G I+   +      G SK
Sbjct: 24  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 41.7 bits (99), Expect = 1e-06
 Identities = 14/36 (38%), Positives = 24/36 (66%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
          K+F+G LS Q  ++ +R+ F  FG ++EC V++ P 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 37

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
           P    LF+  L ++  + D+   F PFG +    V        SK
Sbjct: 38  PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK 82

>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 = 42.6 bits (101), Expect = 1e-06
 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            L+V  L    +++ +RK F+PFGTI    V+   + G SK
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSK 55

>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 = 43.0 bits (101), Expect = 1e-06
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
           P + + +  L     E +V  +  PFG +    +LKG
Sbjct: 29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66

>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 = 42.3 bits (100), Expect = 1e-06
 Identities = 10/38 (26%), Positives = 19/38 (50%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
          P +  ++ G ++    +  +R+ F+PFG I E  V   
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

>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 = 41.3 bits (98), Expect = 1e-06
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
          K+FVG LS    E+ +R+ F  FG +E   +     
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK 36

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 42.2 bits (100), Expect = 1e-06
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
                LFV  + ++  E+D+   FA +G I+   +      G  K
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65

>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 = 41.9 bits (99), Expect = 1e-06
 Identities = 10/40 (25%), Positives = 14/40 (35%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
             K L+V  L    +E+ + K F          V K  D
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD 52

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 41.3 bits (98), Expect = 2e-06
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
          K+FVG LS     +DV+  F  FG +++  ++    
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT 36

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 41.9 bits (99), Expect = 2e-06
 Identities = 7/33 (21%), Positives = 13/33 (39%)

Query: 65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
           ++G +     E D+  +F  FG I +      
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE 62

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.5 bits (98), Expect = 2e-06
 Identities = 6/34 (17%), Positives = 14/34 (41%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          + +FV    +  +   + + F  FG +    + K
Sbjct: 9  RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK 42

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 41.7 bits (98), Expect = 2e-06
 Identities = 5/34 (14%), Positives = 14/34 (41%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          +KL +  +      + +  +   +G +E C  + 
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN 49

>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 = 41.0 bits (97), Expect = 3e-06
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECT-VLKGPD-GTSK 103
                +F+G L  + +E  +   F+ FG I +   +++ PD G SK
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK 48

>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 = 43.1 bits (102), Expect = 3e-06
 Identities = 10/44 (22%), Positives = 23/44 (52%), Gaps = 3/44 (6%)

Query: 63  KKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKG--PDGTSK 103
           +++ +  LS +  +E+ +R+ F  FG+IE+  +  G      + 
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNN 254

>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 = 40.4 bits (95), Expect = 2e-05
 Identities = 5/43 (11%), Positives = 14/43 (32%), Gaps = 1/43 (2%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 103
           +  L++        + ++R +      +     L      TS+
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSR 159

>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 = 40.4 bits (95), Expect = 2e-05
 Identities = 10/36 (27%), Positives = 13/36 (36%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
           + V  L K  N++ V K F   G I    V      
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK 79

>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 = 3e-06
 Identities = 14/105 (13%), Positives = 35/105 (33%), Gaps = 3/105 (2%)

Query: 2   LPLDLIWTC---TPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTP 58
           +PL+++        L  D  + V  LSK + E   +S     +         ++      
Sbjct: 46  VPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKN 105

Query: 59  LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
              ++ +++         DD+++     G +    + +      K
Sbjct: 106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK 150

>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 = 42.1 bits (99), Expect = 3e-06
 Identities = 11/43 (25%), Positives = 19/43 (44%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
           P  P+ +++V  L+K   E D++ IF  +      T     D
Sbjct: 40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 82

>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 = 41.1 bits (97), Expect = 4e-06
 Identities = 8/36 (22%), Positives = 18/36 (50%)

Query: 61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
           D  ++VG L ++ +E  + ++F   G +    + K
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK 49

>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 = 41.2 bits (97), Expect = 4e-06
 Identities = 7/44 (15%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             + +F   L+ +    D+   F+  G + +  ++   +   SK
Sbjct: 24  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67

>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 = 40.9 bits (96), Expect = 6e-06
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          + ++VG +       D+   F+  G+I   T+L 
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70

>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 = 41.4 bits (98), Expect = 7e-06
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
               LFVG L+   +++ +R  F  F +     V+     G+S+
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 129

>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 = 35.6 bits (83), Expect = 8e-04
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           + L+VG L K   ED +++ F   G I    ++   +  + 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV 41

>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 = 40.3 bits (95), Expect = 7e-06
 Identities = 9/37 (24%), Positives = 19/37 (51%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
             + L+VG LS+   E  + ++F+  G  + C ++ 
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT 49

>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 = 39.4 bits (93), Expect = 9e-06
 Identities = 6/34 (17%), Positives = 16/34 (47%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          + ++VG +      +++   F   G++   T+L 
Sbjct: 7  RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILC 40

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +K+FVG L    +ED++   F  FG +      K    +  
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYF 49

>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 = 41.4 bits (96), Expect = 1e-05
 Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 98
           P+  +++  L+++  +D+++K    IF+ FG I +  V +  
Sbjct: 7  RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL 49

>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 = 40.3 bits (95), Expect = 2e-05
 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +F+  L K  +   +   F+ FG I  C V+      SK
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSK 143

>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 = 35.7 bits (83), Expect = 9e-04
 Identities = 12/40 (30%), Positives = 17/40 (42%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
           P  P   L+VG L     E  + + F+P G I    V +
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR 49

>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 = 39.2 bits (92), Expect = 2e-05
 Identities = 7/37 (18%), Positives = 18/37 (48%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
             + +FVG +  +  E+ ++ IF+  G +    ++ 
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY 42

>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 = 38.9 bits (91), Expect = 3e-05
 Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 59  LPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           LPP+  + L++  L  +   +++  IF  +G I +  V       ++
Sbjct: 3   LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETR 47

>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 = 38.8 bits (91), Expect = 3e-05
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 3/42 (7%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
             +F+  L K  +   +   F+ FG I  C V+   D   SK
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSK 45

>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 = 38.4 bits (90), Expect = 3e-05
 Identities = 10/43 (23%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 98
           P+  +++  L+++  +D+++K    IF+ FG I +  V +  
Sbjct: 6  RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL 48

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 37.8 bits (88), Expect = 9e-05
 Identities = 8/40 (20%), Positives = 13/40 (32%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
            +  +FV  L +    + V   F   G I+       P 
Sbjct: 5  SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPM 44

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 4/46 (8%), Positives = 17/46 (36%), Gaps = 4/46 (8%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLKGP 98
              P + + +  ++ +  ++ ++     + +  G I +  V    
Sbjct: 24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD 69

>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 = 36.1 bits (84), Expect = 2e-04
 Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 103
           P    + V  +    + D++   F  +  I     L     G   
Sbjct: 13  PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57

>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 = 36.1 bits (84), Expect = 3e-04
 Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 2/38 (5%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
               L+V           +R  F+PFG I + ++   
Sbjct: 13 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP 48

>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 = 36.4 bits (84), Expect = 3e-04
 Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 2/39 (5%)

Query: 61 PDKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKG 97
            + L V  G L    + + +  +    G ++   +   
Sbjct: 24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 62

>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 = 36.8 bits (85), Expect = 3e-04
 Identities = 8/41 (19%), Positives = 18/41 (43%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
           PP   L +  +    +E+D++ +F+  G + +       D 
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 158

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 37.1 bits (85), Expect = 3e-04
 Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 9/47 (19%)

Query: 60  PPDKKLFVGMLS---------KQQNEDDVRKIFAPFGTIEECTVLKG 97
             +K L+VG +            Q E  +R +F+  G I+    ++ 
Sbjct: 132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES 178

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 3/44 (6%)

Query: 63  KKLFVGMLSKQQNEDDVRKIFAPFGTIE--ECTVLKGPD-GTSK 103
             ++VG  S    +  + ++    G  +  E    +    G SK
Sbjct: 56  AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99

>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 = 35.6 bits (82), Expect = 4e-04
 Identities = 4/33 (12%), Positives = 13/33 (39%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV 94
             +    L       ++++ F+ FG++    +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL 42

>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 = 35.7 bits (83), Expect = 4e-04
 Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 1/46 (2%)

Query: 58  PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           P  P    F+G L     E+ +++ F     I    + + P    +
Sbjct: 11  PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPER 55

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 35.3 bits (82), Expect = 5e-04
 Identities = 8/31 (25%), Positives = 11/31 (35%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFG 87
           P  P    +VG L     + D+  IF    
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS 40

>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 = 35.0 bits (81), Expect = 6e-04
 Identities = 7/45 (15%), Positives = 13/45 (28%), Gaps = 1/45 (2%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 103
           P    + V  +    + D++   F  +  I     L     G   
Sbjct: 13  PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPT 57

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 35.3 bits (82), Expect = 6e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIF-APFGTIEECTVLKGPDGTSK 103
           P+  LFVG L+   ++  + + F   + +     V+    G SK
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSK 51

>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 = 34.5 bits (80), Expect = 7e-04
 Identities = 5/27 (18%), Positives = 13/27 (48%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIE 90
           L++G L+    ++D+ +     G  +
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVND 29

>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 = 35.2 bits (81), Expect = 8e-04
 Identities = 6/48 (12%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 57  TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL-KGPDGTSK 103
                D  + +  L     ++++ + F+    +     L   P+G   
Sbjct: 37  ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKIT 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	103
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.28
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.19
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.15
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.13
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.1
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.09
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.08
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.07
2div_A	99	TRNA selenocysteine associated protein; structural	99.06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.05
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.05
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.05
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.05
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.04
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.04
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.03
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.03
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.03
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.03
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.02
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.02
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.02
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.02
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.02
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.02
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.02
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.01
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.01
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.01
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.01
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.01
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.0
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.0
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.0
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.0
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.0
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.99
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.99
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.99
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.99
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.99
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.99
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.99
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.98
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.98
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.98
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.98
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.97
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.97
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.97
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.97
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.96
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.96
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.95
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.95
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.95
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.94
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.94
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.94
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.94
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.94
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.94
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.94
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.93
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.93
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	98.93
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.93
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.92
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.92
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.91
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.91
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.91
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.91
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.91
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.91
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.91
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.9
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.9
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.9
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.9
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.89
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.89
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.89
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.89
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.88
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.88
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.88
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.87
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.87
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.87
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.86
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.85
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.85
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.85
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.85
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.84
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.84
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.84
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.83
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.83
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.82
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.82
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.82
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.81
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.81
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.81
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.81
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.81
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.81
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.79
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.79
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.78
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.77
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.77
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.77
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.75
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.75
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.75
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.75
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.74
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.74
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.73
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.73
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.69
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	98.69
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.69
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.67
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.67
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.67
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.65
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.63
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.62
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.61
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.61
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.61
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.6
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.6
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.6
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.6
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.58
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.56
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.54
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.53
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.5
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.49
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.48
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.46
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.46
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.46
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.46
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.46
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.45
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.44
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.43
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.41
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.4
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.36
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.36
1x5p_A	97	Negative elongation factor E; structure genomics,	98.33
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.3
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.3
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.26
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.26
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.25
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.2
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.14
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.04
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	97.89
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	97.86
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	97.78
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	97.26
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	97.08
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	96.91
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	96.62
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	96.34
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	95.38
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	94.99
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	94.34
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	90.7
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	89.59
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	89.33
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	88.16
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	84.7
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	83.46
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	83.44
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	82.38

>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=99.28  E-value=4.9e-12  Score=78.07  Aligned_cols=43  Identities=23%  Similarity=0.526  Sum_probs=39.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++++|||+|||.++|+++|+++|++||.|.+|.+++|+. |++|
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~k   61 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL   61 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCccc
Confidence            458999999999999999999999999999999999988 7754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=3.2e-11  Score=75.04  Aligned_cols=42  Identities=10%  Similarity=0.237  Sum_probs=38.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      .++|||||||+++|+++|+++|++||.|.+|.|++|+.|++|
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~r   52 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK   52 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCc
Confidence            488999999999999999999999999999999999876654

>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=99.16  E-value=6.8e-11  Score=70.43  Aligned_cols=44  Identities=34%  Similarity=0.692  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   53 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSR   53 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccc
Confidence            3458999999999999999999999999999999999987 7653

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.15  E-value=6.9e-11  Score=74.23  Aligned_cols=42  Identities=19%  Similarity=0.302  Sum_probs=39.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||+|||+.+++++|+++|++||.|.+|.|++|+. |++|
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~r   48 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHL   48 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCcee
Confidence            48899999999999999999999999999999999998 8764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=1e-10  Score=69.33  Aligned_cols=43  Identities=19%  Similarity=0.367  Sum_probs=39.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~   47 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK   47 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcC
Confidence            458999999999999999999999999999999999987 7654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.13  E-value=1.7e-10  Score=70.24  Aligned_cols=44  Identities=23%  Similarity=0.530  Sum_probs=40.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++|+. |++|
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   52 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPR   52 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCC
Confidence            3458999999999999999999999999999999999987 7654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=2.5e-10  Score=68.83  Aligned_cols=43  Identities=42%  Similarity=0.696  Sum_probs=39.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~   47 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSK   47 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCcee
Confidence            458999999999999999999999999999999999987 7664

>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=99.10  E-value=9.8e-11  Score=69.54  Aligned_cols=43  Identities=35%  Similarity=0.552  Sum_probs=38.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~   47 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKS   47 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCcc
Confidence            3458999999999999999999999999999999999976 654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.09  E-value=1.8e-10  Score=71.90  Aligned_cols=44  Identities=34%  Similarity=0.681  Sum_probs=38.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~k   67 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR   67 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcC
Confidence            4568999999999999999999999999999999999987 7764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.08  E-value=1.2e-10  Score=67.64  Aligned_cols=41  Identities=37%  Similarity=0.723  Sum_probs=37.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||.++++++|+++|++||.|.++.+++|+. |+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~   42 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR   42 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcC
Confidence            4699999999999999999999999999999999987 7664

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.08  E-value=2.3e-11  Score=73.82  Aligned_cols=41  Identities=24%  Similarity=0.503  Sum_probs=38.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCC-ceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G-~i~~~~v~~d~~-G~sr  103 (103)
                      ..|||+|||.++|+++|+++|++|| .|.+|+|++|+. |++|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~r   44 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSR   44 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcC
Confidence            6799999999999999999999999 899999999998 8775

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.07  E-value=3.6e-10  Score=68.06  Aligned_cols=45  Identities=27%  Similarity=0.539  Sum_probs=40.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ....++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~   58 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK   58 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcc
Confidence            34568999999999999999999999999999999999987 7654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=9.6e-11  Score=73.61  Aligned_cols=40  Identities=25%  Similarity=0.469  Sum_probs=36.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|++|+.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kG   53 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN   53 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCC
Confidence            3458999999999999999999999999999999998763

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.06  E-value=1.7e-10  Score=70.17  Aligned_cols=43  Identities=19%  Similarity=0.337  Sum_probs=39.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCcee-EEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE-ECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~-~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|. ++.+++|+. |++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~   51 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIP   51 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCc
Confidence            3458999999999999999999999999999 999999986 664

>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=99.06  E-value=2.5e-10  Score=67.18  Aligned_cols=40  Identities=28%  Similarity=0.424  Sum_probs=37.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      .+|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~   42 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS   42 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCc
Confidence            6899999999999999999999999999999999976 664

>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=99.06  E-value=4.2e-10  Score=70.14  Aligned_cols=44  Identities=36%  Similarity=0.600  Sum_probs=39.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ....++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~   67 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS   67 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCcc
Confidence            34568999999999999999999999999999999999876 654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.06  E-value=3.4e-10  Score=70.97  Aligned_cols=44  Identities=27%  Similarity=0.489  Sum_probs=40.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||.++++++|+++|++||.|.++.+++|+. |++|
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~   82 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK   82 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcC
Confidence            4568999999999999999999999999999999999987 7664

>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=99.06  E-value=2.3e-10  Score=70.16  Aligned_cols=44  Identities=30%  Similarity=0.394  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   57 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSK   57 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEE
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCcc
Confidence            4558999999999999999999999999999999999987 7653

>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=99.05  E-value=4.2e-10  Score=69.12  Aligned_cols=42  Identities=69%  Similarity=1.258  Sum_probs=38.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ..++|||+|||..+++++|+++|++||.|.+|.|++|+.|++
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~   55 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSS   55 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCc
Confidence            458999999999999999999999999999999999976554

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.05  E-value=3.9e-10  Score=69.10  Aligned_cols=44  Identities=18%  Similarity=0.394  Sum_probs=39.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++|+. |++|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~   55 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPR   55 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCC
Confidence            3458999999999999999999999999999999999987 6654

>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=99.05  E-value=1.4e-10  Score=71.43  Aligned_cols=44  Identities=39%  Similarity=0.620  Sum_probs=40.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   55 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHK   55 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcc
Confidence            4558999999999999999999999999999999999987 7664

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.05  E-value=3.8e-10  Score=68.80  Aligned_cols=45  Identities=20%  Similarity=0.353  Sum_probs=40.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeE--------EEEeeCCC-CCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPD-GTSK  103 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~--------~~v~~d~~-G~sr  103 (103)
                      ....++|||+|||.++++++|+++|++||.|.+        +.+++|+. |++|
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~   63 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK   63 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCee
Confidence            345689999999999999999999999999999        99999987 7653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.05  E-value=1.9e-10  Score=78.89  Aligned_cols=43  Identities=28%  Similarity=0.315  Sum_probs=39.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||||||+++|+++|+++|++||.|.+|+|++|+. |+++
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~   57 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSL   57 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCcc
Confidence            347899999999999999999999999999999999987 7653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.04  E-value=4.6e-10  Score=70.24  Aligned_cols=44  Identities=36%  Similarity=0.606  Sum_probs=40.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+|+++|+++|++||.|.+|.|++|+. |++|
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   59 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSR   59 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccc
Confidence            3458999999999999999999999999999999999987 7664

>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=99.04  E-value=3.6e-10  Score=68.75  Aligned_cols=43  Identities=28%  Similarity=0.425  Sum_probs=39.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||..+++++|+++|++||.|.+|.+++|+. |+++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   50 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK   50 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcC
Confidence            458999999999999999999999999999999999986 7654

>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=99.04  E-value=3.3e-10  Score=70.13  Aligned_cols=43  Identities=28%  Similarity=0.483  Sum_probs=39.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||+.+++++|+++|++||.|.+|.|++|+. |+++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   57 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK   57 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCc
Confidence            458899999999999999999999999999999999987 7654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.04  E-value=2.2e-10  Score=70.46  Aligned_cols=43  Identities=28%  Similarity=0.564  Sum_probs=39.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||+.+++++|+++|++||.|.+|.+++|+. |++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~   57 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQS   57 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCc
Confidence            4568999999999999999999999999999999999976 664

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.04  E-value=1.5e-10  Score=67.12  Aligned_cols=40  Identities=28%  Similarity=0.576  Sum_probs=37.2

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|||+|||.++++++|+++|++||.|.++.+++|+. |+++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   41 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHR   41 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcC
Confidence            589999999999999999999999999999999986 7664

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.04  E-value=2.6e-10  Score=70.06  Aligned_cols=42  Identities=7%  Similarity=0.307  Sum_probs=38.3

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCc--eeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGT--IEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~--i~~~~v~~d~~-G~sr  103 (103)
                      ...|||+|||+.+|+++|+++|++||.  +.+|++++|+. |++|
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~sr   53 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNR   53 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCS
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCc
Confidence            377999999999999999999999995  67999999998 8875

>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=99.03  E-value=4.2e-10  Score=69.11  Aligned_cols=44  Identities=20%  Similarity=0.338  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++|+. |++|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   57 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ   57 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCC
Confidence            3558999999999999999999999999999999999986 6654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.03  E-value=1.4e-10  Score=74.33  Aligned_cols=44  Identities=14%  Similarity=0.340  Sum_probs=39.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeE--EEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--CTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~--~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||+.+|+++|+++|++||.|..  |+|++|+. |++|
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~r   67 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNR   67 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcc
Confidence            35589999999999999999999999999977  99999997 8765

>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=99.03  E-value=3.1e-10  Score=68.53  Aligned_cols=38  Identities=18%  Similarity=0.452  Sum_probs=34.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...+|||||||+++|+++|+++|++||.|.+|.|++|.
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~s   47 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF   47 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCC
Confidence            34899999999999999999999999999999999874

>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=99.03  E-value=5e-10  Score=66.68  Aligned_cols=41  Identities=20%  Similarity=0.416  Sum_probs=38.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   48 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPK   48 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcc
Confidence            7899999999999999999999999999999999986 7654

>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=99.02  E-value=2.4e-10  Score=67.57  Aligned_cols=42  Identities=21%  Similarity=0.460  Sum_probs=38.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~   48 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKH   48 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCcc
Confidence            458999999999999999999999999999999999866 654

>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=99.02  E-value=4.8e-10  Score=69.23  Aligned_cols=44  Identities=14%  Similarity=0.156  Sum_probs=38.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeE-EEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE-CTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~-~~v~~d~~G~sr  103 (103)
                      ...++|||+|||+.+|+++|+++|++||.|.+ +.|++|..|++|
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~   57 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRST   57 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcc
Confidence            34589999999999999999999999999998 888888557764

>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=99.02  E-value=9.2e-10  Score=68.56  Aligned_cols=43  Identities=23%  Similarity=0.550  Sum_probs=38.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.|++|+.|++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~   65 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTS   65 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCc
Confidence            4568999999999999999999999999999999999976543

>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=99.02  E-value=3.2e-10  Score=68.41  Aligned_cols=42  Identities=26%  Similarity=0.518  Sum_probs=38.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ..++|||+|||..+++++|+++|++||.|.+|.+++|+.|++
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~   56 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKP   56 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCC
Confidence            448999999999999999999999999999999999987554

>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=99.02  E-value=1.6e-10  Score=69.49  Aligned_cols=41  Identities=24%  Similarity=0.429  Sum_probs=36.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCC--ceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G--~i~~~~v~~d~~-G~sr  103 (103)
                      .+|||||||+++|+++|+++|++||  .|.++.+++|+. |++|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~k   45 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK   45 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccC
Confidence            5799999999999999999999999  999999999987 7754

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.02  E-value=5.9e-10  Score=67.98  Aligned_cols=43  Identities=19%  Similarity=0.383  Sum_probs=38.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.++.|+.|++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~   57 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKP   57 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCE
Confidence            3458899999999999999999999999999999999886554

>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=99.02  E-value=3.9e-10  Score=68.37  Aligned_cols=42  Identities=19%  Similarity=0.474  Sum_probs=38.6

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   44 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSK   44 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccc
Confidence            37899999999999999999999999999999999987 7654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=4.4e-10  Score=68.86  Aligned_cols=42  Identities=31%  Similarity=0.540  Sum_probs=38.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||..+++++|+++|++||.|.+|.+++|+. |++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~   56 (103)
T 2cq0_A           14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQS   56 (103)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCce
Confidence            458999999999999999999999999999999999976 654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.01  E-value=6.7e-10  Score=69.12  Aligned_cols=43  Identities=21%  Similarity=0.384  Sum_probs=38.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+.|++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~   55 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS   55 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCe
Confidence            3458999999999999999999999999999999999987654

>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=99.01  E-value=6.8e-10  Score=69.36  Aligned_cols=43  Identities=26%  Similarity=0.533  Sum_probs=39.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+. |++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~   66 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS   66 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCc
Confidence            3558999999999999999999999999999999999986 664

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.01  E-value=5.5e-10  Score=68.72  Aligned_cols=44  Identities=23%  Similarity=0.510  Sum_probs=39.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC-CC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG-PD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d-~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++| +. |+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~   58 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR   58 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcC
Confidence            35589999999999999999999999999999999999 44 6653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.01  E-value=3.2e-10  Score=73.94  Aligned_cols=41  Identities=12%  Similarity=0.287  Sum_probs=39.4

Q ss_pred             ceEEEecC----CCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGML----SKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL----~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+||||||    |+.+++.+|+.+|++||+|.+|.++.|+. |+||
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~sl   48 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPL   48 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcee
Confidence            78999999    99999999999999999999999999999 8875

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=5.1e-10  Score=68.40  Aligned_cols=43  Identities=21%  Similarity=0.470  Sum_probs=39.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||..+++++|+++|++||.|.+|.+++|+. |+++
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~   54 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR   54 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcc
Confidence            458999999999999999999999999999999999977 7654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=6.7e-10  Score=69.49  Aligned_cols=42  Identities=31%  Similarity=0.707  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||+|||..+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~   69 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSR   69 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcC
Confidence            38899999999999999999999999999999999987 7654

>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=99.00  E-value=4.3e-10  Score=70.67  Aligned_cols=38  Identities=24%  Similarity=0.516  Sum_probs=35.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..+|||||||+++|+++|+++|++||.|.+|+|++|+.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~   42 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN   42 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC
Confidence            37899999999999999999999999999999999874

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=4.6e-10  Score=68.60  Aligned_cols=44  Identities=36%  Similarity=0.625  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++|+. |++|
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~   54 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSR   54 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcc
Confidence            3558999999999999999999999999999999999987 6654

>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=99.00  E-value=7.1e-10  Score=69.17  Aligned_cols=42  Identities=17%  Similarity=0.412  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||+|||..+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   67 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK   67 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccC
Confidence            37899999999999999999999999999999999987 7654

>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=98.99  E-value=4.2e-10  Score=73.37  Aligned_cols=44  Identities=9%  Similarity=0.054  Sum_probs=39.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCc---eeEEEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT---IEECTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~---i~~~~v~~d~~G~sr  103 (103)
                      ...++|||+|||+++|+++|+++|++||.   |.+|.|++|+.|++|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~sr   88 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS   88 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCC
Confidence            45689999999999999999999999999   899999999887653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=5e-10  Score=67.44  Aligned_cols=42  Identities=29%  Similarity=0.410  Sum_probs=38.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~   56 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS   56 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCc
Confidence            448899999999999999999999999999999999987 654

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=6.2e-10  Score=69.76  Aligned_cols=43  Identities=12%  Similarity=0.070  Sum_probs=39.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCce-eEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTI-EECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i-~~~~v~~d~~G~sr  103 (103)
                      ..++|||+|||+.+|+++|+++|++||.| .+|.|++|+.|++|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~   57 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGL   57 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCS
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcc
Confidence            45889999999999999999999999999 89999999876654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.99  E-value=9.9e-11  Score=71.97  Aligned_cols=42  Identities=14%  Similarity=0.203  Sum_probs=39.0

Q ss_pred             CceEEEecCCC------CCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSK------QQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~------~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++.|||+|||.      .+++++|+++|++||.|.+|.|++|+. |++|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~k   54 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTK   54 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEEC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccc
Confidence            47899999999      999999999999999999999999998 7664

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=5.6e-10  Score=68.64  Aligned_cols=42  Identities=24%  Similarity=0.359  Sum_probs=38.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      .+++|||+|||..+++++|+++|++||.|.+|.+++|+. |++
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~   64 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL   64 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCce
Confidence            458899999999999999999999999999999999987 664

>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=98.99  E-value=6.4e-10  Score=68.78  Aligned_cols=42  Identities=21%  Similarity=0.404  Sum_probs=37.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ..++|||+|||+++|+++|+++|++|| +.+|.|++|+.|++|
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~~g~~~   55 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVT   55 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECCCCCEe
Confidence            448999999999999999999999999 559999999877653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.99  E-value=6.9e-10  Score=69.24  Aligned_cols=43  Identities=37%  Similarity=0.644  Sum_probs=39.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+. |++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~   56 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKS   56 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCc
Confidence            3558999999999999999999999999999999999976 654

>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=98.98  E-value=7.9e-10  Score=68.07  Aligned_cols=44  Identities=30%  Similarity=0.497  Sum_probs=39.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ....++|||+|||..+++++|+++|++||.|.++.+++|+.|++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~   69 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS   69 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCc
Confidence            34568999999999999999999999999999999999986554

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.98  E-value=5.5e-10  Score=67.46  Aligned_cols=42  Identities=31%  Similarity=0.641  Sum_probs=38.6

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEE-EEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~-~v~~d~~-G~sr  103 (103)
                      .++|||+|||..+++++|+++|++||.|.++ .+++|+. |+++
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~   48 (96)
T 1x5t_A            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK   48 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcC
Confidence            4899999999999999999999999999999 9999976 7654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.98  E-value=6.8e-10  Score=68.04  Aligned_cols=42  Identities=24%  Similarity=0.435  Sum_probs=38.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcC-CCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAP-FGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~-~G~i~~~~v~~d~~G~s  102 (103)
                      ..++|||+|||..+|+++|+++|++ ||.|.+|.|++|+.|++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~   50 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS   50 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCc
Confidence            4589999999999999999999999 99999999999976554

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.98  E-value=4.2e-10  Score=74.66  Aligned_cols=43  Identities=19%  Similarity=0.339  Sum_probs=38.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCC--ceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G--~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||||||+++|+++|+++|++||  .|.+|.|++|+. |++|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~sk   99 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK   99 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccc
Confidence            458999999999999999999999999  999999999987 8764

>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=98.97  E-value=1.2e-09  Score=68.90  Aligned_cols=43  Identities=30%  Similarity=0.553  Sum_probs=38.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ..++|||+|||.++++++|+++|++||.|.+|.++.|+.|+++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~   48 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR   48 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcc
Confidence            4489999999999999999999999999999999998866543

>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=98.97  E-value=4.5e-10  Score=70.01  Aligned_cols=39  Identities=13%  Similarity=0.307  Sum_probs=36.1

Q ss_pred             CCceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .+++|||+|||+ .+|+++|+++|++||.|.+|.|++++.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg   53 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN   53 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSS
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCC
Confidence            458999999999 999999999999999999999998763

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.97  E-value=1.1e-09  Score=67.20  Aligned_cols=42  Identities=21%  Similarity=0.392  Sum_probs=38.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||+.+++++|+++|++|| |.+|.+++|+. |++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~   55 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKF   55 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCcc
Confidence            4558999999999999999999999997 99999999987 765

>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=98.97  E-value=6.6e-10  Score=68.84  Aligned_cols=44  Identities=25%  Similarity=0.405  Sum_probs=39.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++|+. |+++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   68 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK   68 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcc
Confidence            3458899999999999999999999999999999999986 7654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.96  E-value=6.4e-10  Score=70.31  Aligned_cols=44  Identities=9%  Similarity=0.086  Sum_probs=39.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCc---eeEEEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT---IEECTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~---i~~~~v~~d~~G~sr  103 (103)
                      ...++|||+|||+++|+++|+++|+.||.   |.+|+|++|+.|++|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~   61 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQS   61 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCC
Confidence            34588999999999999999999999999   899999999877653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.96  E-value=5.9e-10  Score=68.17  Aligned_cols=41  Identities=27%  Similarity=0.640  Sum_probs=37.6

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      .++|||+|||..+++++|+++|++||.|.+|.+++|+.|++
T Consensus         9 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~   49 (102)
T 2xs2_A            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVS   49 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCc
Confidence            38899999999999999999999999999999999876544

>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=98.95  E-value=1.1e-09  Score=70.38  Aligned_cols=44  Identities=27%  Similarity=0.406  Sum_probs=40.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++|+. |++|
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~   88 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR   88 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccc
Confidence            4568999999999999999999999999999999999987 7654

>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=98.95  E-value=2.2e-10  Score=66.27  Aligned_cols=40  Identities=30%  Similarity=0.551  Sum_probs=36.9

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   41 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRR   41 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcC
Confidence            589999999999999999999999999999999987 7654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.95  E-value=1.4e-09  Score=66.62  Aligned_cols=40  Identities=33%  Similarity=0.588  Sum_probs=36.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT  101 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~  101 (103)
                      ..++|||+|||..+|+++|+++|++||.|.+|.+++| .|+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~   53 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGR   53 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCC
Confidence            4589999999999999999999999999999999988 443

>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=98.95  E-value=7.8e-10  Score=72.12  Aligned_cols=42  Identities=33%  Similarity=0.718  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +++|||+|||.++|+++|+++|++||.|.++.+++|+. |++|
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~   45 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSR   45 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCcc
Confidence            38899999999999999999999999999999999987 7764

>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=98.94  E-value=6.5e-10  Score=68.96  Aligned_cols=44  Identities=16%  Similarity=0.074  Sum_probs=39.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCc---eeEEEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT---IEECTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~---i~~~~v~~d~~G~sr  103 (103)
                      ...++|||+|||+++|+++|+++|+.||.   |.+|.|++|+.|++|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~   55 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRR   55 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEe
Confidence            34589999999999999999999999998   999999999877664

>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=98.94  E-value=2.5e-09  Score=65.42  Aligned_cols=40  Identities=23%  Similarity=0.455  Sum_probs=37.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~   52 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER   52 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            4559999999999999999999999999999999998865

>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=98.94  E-value=1.1e-09  Score=70.04  Aligned_cols=39  Identities=26%  Similarity=0.462  Sum_probs=36.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ..+++|||+|||+++|+++|+++|++||.|.+|.|++++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~k   67 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK   67 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGG
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC
Confidence            345889999999999999999999999999999999875

>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=98.94  E-value=2.5e-10  Score=68.34  Aligned_cols=41  Identities=20%  Similarity=0.515  Sum_probs=38.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   43 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPK   43 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcc
Confidence            6799999999999999999999999999999999987 7764

>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=98.94  E-value=1.2e-09  Score=69.08  Aligned_cols=44  Identities=25%  Similarity=0.354  Sum_probs=39.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+|+++|+++|++||.|.+|.|++|+. |+++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   64 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK   64 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccc
Confidence            3458999999999999999999999999999999999986 6653

>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=98.94  E-value=1.2e-09  Score=65.14  Aligned_cols=37  Identities=24%  Similarity=0.500  Sum_probs=34.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .++|||+|||+.+++++|+++|++||.|.+|.++++.
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~   41 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF   41 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCC
Confidence            4899999999999999999999999999999998773

>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=98.94  E-value=1.9e-09  Score=71.87  Aligned_cols=41  Identities=29%  Similarity=0.583  Sum_probs=38.1

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      .++|||+|||..+|+++|+++|++||.|.++.+++|+. |++
T Consensus       104 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~  145 (196)
T 1l3k_A          104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK  145 (196)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCE
T ss_pred             cceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCc
Confidence            48899999999999999999999999999999999986 654

>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=98.93  E-value=2e-09  Score=66.78  Aligned_cols=38  Identities=29%  Similarity=0.515  Sum_probs=35.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+++|||+|||+.+++++|+++|++||.|.++.+++++
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~k   51 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK   51 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCC
Confidence            45889999999999999999999999999999998875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.93  E-value=1.8e-09  Score=68.32  Aligned_cols=44  Identities=30%  Similarity=0.457  Sum_probs=39.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ..+++|||+|||..+++++|+++|++||.|.+|.+++|+.|++|
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~   76 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL   76 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEe
Confidence            45689999999999999999999999999999999998766543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=98.93  E-value=1.7e-09  Score=69.20  Aligned_cols=44  Identities=20%  Similarity=0.460  Sum_probs=40.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++|+. |++|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~  105 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR  105 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCC
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcC
Confidence            4568999999999999999999999999999999999977 7654

>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=98.93  E-value=1.8e-09  Score=66.32  Aligned_cols=42  Identities=19%  Similarity=0.413  Sum_probs=37.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC--CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD--GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~--G~s  102 (103)
                      ...++|||+|||+.+++++|+++|++|| |.+|.|++|+.  |++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~   56 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERL   56 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSB
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCc
Confidence            4458999999999999999999999999 99999999875  544

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.92  E-value=9.7e-10  Score=69.39  Aligned_cols=41  Identities=24%  Similarity=0.443  Sum_probs=38.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||..+|+++|+++|++||.|.+|.+++|+. |+++
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   78 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPK   78 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcc
Confidence            8899999999999999999999999999999999976 7653

>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=98.92  E-value=1.2e-09  Score=76.51  Aligned_cols=43  Identities=23%  Similarity=0.402  Sum_probs=38.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCC--ceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFG--TIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G--~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||+.+|+++|+++|++||  .|.+|.|++|+. |++|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~sk  112 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK  112 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccc
Confidence            568899999999999999999999999  999999999987 7764

>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=98.91  E-value=9.7e-10  Score=67.31  Aligned_cols=43  Identities=21%  Similarity=0.441  Sum_probs=37.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC-C-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP-D-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~-~-G~sr  103 (103)
                      ...++|||+|||.++++++|+++|++|| |.+|.+++|+ . |++|
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~   61 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK   61 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccC
Confidence            3559999999999999999999999999 9999999998 3 7654

>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=98.91  E-value=9.3e-10  Score=65.24  Aligned_cols=38  Identities=21%  Similarity=0.423  Sum_probs=36.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++|||+|||.++++++|+++|++||.|.++.+++|+.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~   41 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERM   41 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCC
Confidence            48899999999999999999999999999999998875

>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=98.91  E-value=9.4e-10  Score=71.98  Aligned_cols=42  Identities=21%  Similarity=0.404  Sum_probs=38.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ..++|||+|||+++|+++|+++|++|| |.+|.|++|+.|++|
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~sr   86 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVT   86 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCc
Confidence            458899999999999999999999999 779999999877764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.91  E-value=2e-09  Score=64.42  Aligned_cols=38  Identities=13%  Similarity=0.106  Sum_probs=35.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.++++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~   43 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME   43 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc
Confidence            34589999999999999999999999999999999885

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=8.1e-10  Score=70.89  Aligned_cols=43  Identities=19%  Similarity=0.216  Sum_probs=38.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCce----eEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTI----EECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i----~~~~v~~d~~G~sr  103 (103)
                      ...+|||+|||+++|+++|+++|++||.|    .+|.|++|+.|++|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~   68 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT   68 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEe
Confidence            45899999999999999999999999975    69999999767754

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.91  E-value=1.9e-09  Score=67.10  Aligned_cols=39  Identities=21%  Similarity=0.284  Sum_probs=35.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ..++.|||+|||+.+|+++|+++|++||.|.++.+++++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~k   57 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK   57 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCC
Confidence            345889999999999999999999999999999998765

>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=98.91  E-value=1.2e-09  Score=72.91  Aligned_cols=42  Identities=33%  Similarity=0.718  Sum_probs=38.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.+++|+. |++
T Consensus        12 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~   54 (196)
T 1l3k_A           12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRS   54 (196)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCc
Confidence            348999999999999999999999999999999999987 765

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.90  E-value=2.1e-09  Score=66.85  Aligned_cols=43  Identities=19%  Similarity=0.377  Sum_probs=38.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCcee--------EEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIE--------ECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~--------~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||..+++++|+++|++||.|.        .|.|++|+. |++|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~   65 (113)
T 2cpe_A           14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK   65 (113)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCee
Confidence            458999999999999999999999999999        699999976 7654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.90  E-value=1e-09  Score=68.92  Aligned_cols=41  Identities=24%  Similarity=0.334  Sum_probs=38.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ..+|||+|||+++|+++|+++|++| .|.+|.|++|+.|++|
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~   56 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNN   56 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCC
Confidence            4789999999999999999999999 8999999999888765

>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=98.90  E-value=2.3e-09  Score=66.46  Aligned_cols=38  Identities=13%  Similarity=0.219  Sum_probs=35.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~   50 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   50 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC
Confidence            34589999999999999999999999999999999876

>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=98.90  E-value=2.6e-09  Score=68.89  Aligned_cols=43  Identities=16%  Similarity=0.221  Sum_probs=38.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCcee--EEEEeeCCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE--ECTVLKGPDGTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~--~~~v~~d~~G~sr  103 (103)
                      ...++|||+|||+++|+++|+++|++| .|.  +|.|++|+.|++|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~Grsr   84 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKIT   84 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCc
Confidence            355889999999999999999999999 677  8999999887765

>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=98.89  E-value=3.5e-09  Score=65.92  Aligned_cols=38  Identities=21%  Similarity=0.179  Sum_probs=35.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+++|||+|||+.+++++|+++|++||.|.++.+++++
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~k   51 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK   51 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCC
Confidence            35889999999999999999999999999999988765

>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=98.89  E-value=9e-10  Score=67.40  Aligned_cols=40  Identities=20%  Similarity=0.534  Sum_probs=37.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus         9 ~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~   49 (104)
T 1p1t_A            9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP   49 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEE
T ss_pred             cEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCcc
Confidence            8899999999999999999999999999999999976 654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.89  E-value=9.1e-10  Score=70.80  Aligned_cols=43  Identities=21%  Similarity=0.417  Sum_probs=39.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|+.||.|.+|.|++|+. |++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~   83 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQS   83 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCc
Confidence            4568999999999999999999999999999999999987 654

>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=98.89  E-value=1.3e-09  Score=71.36  Aligned_cols=44  Identities=18%  Similarity=0.335  Sum_probs=40.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++|+. |++|
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~  112 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR  112 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccc
Confidence            3468999999999999999999999999999999999986 7764

>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=98.88  E-value=1.6e-09  Score=66.93  Aligned_cols=43  Identities=16%  Similarity=0.342  Sum_probs=38.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCc-eeEEEEe-eCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVL-KGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~-i~~~~v~-~d~~-G~sr  103 (103)
                      ..++|||+|||..+++++|+++|++||. |.++.++ .|+. |++|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~   52 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNR   52 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcC
Confidence            3489999999999999999999999998 9999998 7776 6654

>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=98.88  E-value=2.9e-09  Score=69.78  Aligned_cols=43  Identities=23%  Similarity=0.295  Sum_probs=39.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+|+++|+++|++||.|.+|.|++|+. |++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~   80 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA   80 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcc
Confidence            3558999999999999999999999999999999999987 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=98.88  E-value=3e-09  Score=66.32  Aligned_cols=39  Identities=23%  Similarity=0.396  Sum_probs=36.5

Q ss_pred             CCceEEEecCCCCCCHHHHH---HhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVR---KIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~---~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||+.+++++|+   ++|++||.|.+|.|++|+.
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~   55 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS   55 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCC
Confidence            44889999999999999999   9999999999999999886

>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=98.87  E-value=1.9e-09  Score=65.48  Aligned_cols=40  Identities=13%  Similarity=0.250  Sum_probs=37.0

Q ss_pred             CCCceEEEecCCCCCCHHHHH----HhhcCCCceeEEEEeeCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~----~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...++|||+|||+.+++++|+    ++|++||.|.+|.|++|+.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~   50 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD   50 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCC
Confidence            345899999999999999999    9999999999999998875

>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=98.87  E-value=7.6e-10  Score=66.71  Aligned_cols=42  Identities=17%  Similarity=0.190  Sum_probs=37.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||+.+++++|+++|++||.|.++.++.|+. |++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~   56 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMP   56 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCE
Confidence            348999999999999999999999999999999998876 654

>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=98.87  E-value=4.9e-09  Score=68.54  Aligned_cols=42  Identities=31%  Similarity=0.620  Sum_probs=38.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...+|||+|||..+|+++|+++|++||.|.++.+++|+. |++
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~  135 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  135 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSE
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCc
Confidence            458899999999999999999999999999999999975 654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=3.5e-09  Score=65.88  Aligned_cols=42  Identities=21%  Similarity=0.408  Sum_probs=37.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .....++|||+|||..+++++|+++|++||.|.+|.+++|+.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~   66 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER   66 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC
Confidence            334668999999999999999999999999999999998864

>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=98.86  E-value=3.8e-09  Score=64.61  Aligned_cols=40  Identities=23%  Similarity=0.484  Sum_probs=37.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.|++|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   52 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT   52 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC
Confidence            3558999999999999999999999999999999999865

>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=98.85  E-value=2e-09  Score=70.39  Aligned_cols=38  Identities=32%  Similarity=0.652  Sum_probs=36.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++|||+|||.++|+++|+++|++||.|.++.+++|+.
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~   40 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS   40 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECS
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC
Confidence            48999999999999999999999999999999999987

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.85  E-value=5.4e-09  Score=62.58  Aligned_cols=42  Identities=12%  Similarity=0.188  Sum_probs=37.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ...++|||+|||+.+++++|+++|++| .|.++.+++|..|++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~   49 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNK   49 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCC
Confidence            345899999999999999999999999 999999999954765

>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=98.85  E-value=1.2e-09  Score=69.33  Aligned_cols=45  Identities=13%  Similarity=0.228  Sum_probs=37.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      +....++|||+|||+.+|+++|+++|++||.|.++.++.+.. |++
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~   66 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA   66 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCC
Confidence            344568999999999999999999999999999966666555 664

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.85  E-value=3.3e-09  Score=64.26  Aligned_cols=39  Identities=26%  Similarity=0.537  Sum_probs=36.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||+.+++++|+++|++||.|.+|.+++|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   42 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN   42 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            348899999999999999999999999999999998764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=2.9e-09  Score=66.64  Aligned_cols=38  Identities=26%  Similarity=0.479  Sum_probs=34.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||+.+|+++|+++|++||.|. +.++.++.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~   44 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAE   44 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCC
Confidence            458999999999999999999999999999 88887764

>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=98.84  E-value=1.2e-09  Score=66.29  Aligned_cols=42  Identities=17%  Similarity=0.187  Sum_probs=37.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||+.+++++|+++|++||.|.++.++.++. |++
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~   56 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMP   56 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCe
Confidence            458899999999999999999999999999988888876 654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.84  E-value=1.3e-09  Score=65.80  Aligned_cols=40  Identities=15%  Similarity=0.342  Sum_probs=36.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEE-EEeeCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD   99 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~-~v~~d~~   99 (103)
                      ...++|||+|||+.+++++|+++|++||.|.+| .+++|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~   53 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE   53 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC
Confidence            456899999999999999999999999999999 5888875

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=4e-09  Score=63.36  Aligned_cols=38  Identities=29%  Similarity=0.599  Sum_probs=34.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.++++
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~   45 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD   45 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC
Confidence            34589999999999999999999999999999998754

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.83  E-value=1.6e-09  Score=70.09  Aligned_cols=43  Identities=19%  Similarity=0.346  Sum_probs=39.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||..+|+++|+++|++||.|.+|.+++|+. |++|
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~   89 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR   89 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccc
Confidence            458899999999999999999999999999999999986 6654

>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=98.83  E-value=4.1e-09  Score=66.75  Aligned_cols=38  Identities=16%  Similarity=0.364  Sum_probs=35.1

Q ss_pred             CCceEEEecCCCC-CCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~-~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+++|||+|||++ +++++|+++|++||.|.+|.|++++
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~k   62 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK   62 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCC
Confidence            4689999999998 9999999999999999999998765

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=9.9e-09  Score=61.91  Aligned_cols=37  Identities=16%  Similarity=0.377  Sum_probs=33.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||+.+|+++|+++|++||.|.+|  +.|+.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~   43 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKD   43 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCC
Confidence            34799999999999999999999999999987  66655

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=3.2e-09  Score=63.56  Aligned_cols=38  Identities=32%  Similarity=0.552  Sum_probs=34.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ...++|||+|||..+|+++|+++|++||.|.++.++++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~   44 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD   44 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC
Confidence            34589999999999999999999999999999998764

>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=98.82  E-value=5e-09  Score=69.48  Aligned_cols=43  Identities=23%  Similarity=0.390  Sum_probs=38.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|..|.|++++. |++
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~  113 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS  113 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcE
Confidence            3457899999999999999999999999999999999976 654

>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=98.81  E-value=9.2e-09  Score=64.04  Aligned_cols=41  Identities=20%  Similarity=0.422  Sum_probs=36.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...+++|||+|||..+++++|+++|++||.|.+|.+++|..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~   45 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE   45 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC
Confidence            34458999999999999999999999999999999998754

>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=98.81  E-value=6.9e-09  Score=61.20  Aligned_cols=39  Identities=33%  Similarity=0.494  Sum_probs=35.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~k   48 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ   48 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGG
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCC
Confidence            345899999999999999999999999999999998754

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.81  E-value=3.8e-09  Score=62.12  Aligned_cols=40  Identities=25%  Similarity=0.386  Sum_probs=33.9

Q ss_pred             ceEEEecCCCCC------CHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         63 KKLFVGMLSKQQ------NEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~------te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ++|||+|||..+      ++++|+++|++||.|.++.+++ ..|++|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~-~~g~~~   47 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-EDGKTK   47 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC-BTTBCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC-CCCcEe
Confidence            789999999999      6799999999999999999873 225543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.81  E-value=9.5e-09  Score=66.48  Aligned_cols=43  Identities=26%  Similarity=0.384  Sum_probs=39.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ....+|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~  128 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS  128 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCE
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCc
Confidence            3568899999999999999999999999999999999976 654

>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=98.81  E-value=2e-09  Score=70.16  Aligned_cols=42  Identities=26%  Similarity=0.551  Sum_probs=38.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..+|||+|||..+++++|+++|++||.|.++.+++|+. |+++
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~  129 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSR  129 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTS
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccc
Confidence            47899999999999999999999999999999999986 7664

>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=98.81  E-value=6e-09  Score=67.48  Aligned_cols=40  Identities=28%  Similarity=0.634  Sum_probs=37.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ++|||+|||..+++++|+++|+.||.|.++.+++|+. |++
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~   43 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQS   43 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCE
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcc
Confidence            8899999999999999999999999999999999985 765

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.81  E-value=1.5e-08  Score=68.45  Aligned_cols=41  Identities=24%  Similarity=0.656  Sum_probs=38.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      .++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus       125 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~  166 (216)
T 2qfj_A          125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKH  166 (216)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCc
Confidence            48899999999999999999999999999999999976 654

>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=98.79  E-value=6.3e-09  Score=68.00  Aligned_cols=42  Identities=57%  Similarity=1.132  Sum_probs=38.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ..++|||+|||..+|+++|+++|++||.|.++.+++|+.|++
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~  135 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS  135 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCE
Confidence            568999999999999999999999999999999999977654

>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=98.79  E-value=1.2e-08  Score=61.94  Aligned_cols=38  Identities=32%  Similarity=0.594  Sum_probs=35.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ..++|||+|||..+++++|+++|++||.|.++.+++++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~k   51 (99)
T 2cpj_A           14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK   51 (99)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCC
Confidence            45899999999999999999999999999999998765

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.78  E-value=4.2e-09  Score=68.17  Aligned_cols=40  Identities=25%  Similarity=0.427  Sum_probs=36.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ++|||+|||.++|+++|+++|++||.|.++.+++|+.|++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~   40 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKN   40 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCC
Confidence            4799999999999999999999999999999999987654

>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=98.77  E-value=4.9e-09  Score=68.19  Aligned_cols=41  Identities=22%  Similarity=0.562  Sum_probs=37.7

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      +++|||+|||.++++++|+++|++||.|.++.+++++. |++
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~   44 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYS   44 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEE
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCcc
Confidence            38899999999999999999999999999999999876 654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.77  E-value=1.3e-08  Score=60.82  Aligned_cols=36  Identities=31%  Similarity=0.766  Sum_probs=33.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~   41 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII   41 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE
Confidence            455899999999999999999999999999999886

>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=98.77  E-value=1.3e-08  Score=62.82  Aligned_cols=39  Identities=21%  Similarity=0.470  Sum_probs=35.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++|||+|||..+|+++|+++|++||.|.+|.+..+.
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~   58 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR   58 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC
Confidence            355899999999999999999999999999999997664

>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=98.75  E-value=1.4e-08  Score=61.55  Aligned_cols=39  Identities=28%  Similarity=0.512  Sum_probs=35.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.++.++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~   53 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD   53 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCC
Confidence            345899999999999999999999999999999988763

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.75  E-value=3e-08  Score=66.10  Aligned_cols=43  Identities=30%  Similarity=0.616  Sum_probs=39.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            4568999999999999999999999999999999999985 654

>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=98.75  E-value=2.4e-08  Score=64.89  Aligned_cols=43  Identities=26%  Similarity=0.504  Sum_probs=39.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~  130 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP  130 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCc
Confidence            3568999999999999999999999999999999999985 654

>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=98.75  E-value=5.1e-09  Score=65.74  Aligned_cols=37  Identities=14%  Similarity=0.233  Sum_probs=33.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ..++|||+|||+.+++++|+++|++||.|.+|.|+.|
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~   51 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   51 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC
Confidence            4589999999999999999999999999999999875

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.74  E-value=9.4e-09  Score=63.41  Aligned_cols=42  Identities=26%  Similarity=0.385  Sum_probs=35.3

Q ss_pred             CCceEEEecCCCCC------CHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQ------NEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~------te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      .+++|||||||+.+      |+++|+++|++||.|.+|.+++ ..|++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~-~~g~~~   61 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-EDGKTK   61 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC-BTTBSC
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC-CCCCee
Confidence            35899999999999      7899999999999999999883 225543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.74  E-value=1.6e-08  Score=61.53  Aligned_cols=39  Identities=21%  Similarity=0.369  Sum_probs=35.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.+++.+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~   63 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK   63 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTT
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCC
Confidence            345899999999999999999999999999999987544

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.74  E-value=1.2e-08  Score=68.90  Aligned_cols=43  Identities=30%  Similarity=0.484  Sum_probs=38.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ..+++|||+|||..+++++|+++|++||.|.+|.|+.|+.|++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~  128 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS  128 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCE
Confidence            3568999999999999999999999999999999999876554

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.73  E-value=1.3e-08  Score=68.80  Aligned_cols=41  Identities=29%  Similarity=0.510  Sum_probs=36.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||.++|+++|+++|++||.|.+|.+++|+. |+++
T Consensus        29 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~   70 (216)
T 2qfj_A           29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK   70 (216)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccC
Confidence            8899999999999999999999999999999999986 6654

>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=98.73  E-value=2.4e-08  Score=64.63  Aligned_cols=42  Identities=26%  Similarity=0.507  Sum_probs=38.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...+|||+|||..+++++|+++|++||.|.++.+++|+. |++
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~  129 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVS  129 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCc
Confidence            458899999999999999999999999999999999985 654

>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=98.72  E-value=1.7e-08  Score=68.88  Aligned_cols=40  Identities=8%  Similarity=0.204  Sum_probs=37.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ++|||+|||+.+|+++|+++|++||.|.+|++++|..|++
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~  149 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF  149 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCE
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCc
Confidence            7899999999999999999999999999999999876654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.70  E-value=8.2e-09  Score=65.05  Aligned_cols=48  Identities=6%  Similarity=-0.073  Sum_probs=35.1

Q ss_pred             cccccccCCCCCCceEEEecCCCCCCHHHHHHhhcCCC-ceeEEEEeeCC
Q psy10284         50 WDLIWTCTPLPPDKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKGP   98 (103)
Q Consensus        50 ~~~~~~~~~~~~~~~lfVgnL~~~~te~~l~~~F~~~G-~i~~~~v~~d~   98 (103)
                      .+..+... ....++|||+|||+++++++|+++|++|| .|..+.|..++
T Consensus        17 ~~~~~~~~-p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~   65 (111)
T 2jvr_A           17 RGSHMSKL-PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD   65 (111)
T ss_dssp             ---------CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCS
T ss_pred             cchhcCCC-CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCC
Confidence            33455433 33568999999999999999999999999 99999886443

>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=98.69  E-value=1.5e-08  Score=62.08  Aligned_cols=37  Identities=35%  Similarity=0.499  Sum_probs=34.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ..++|||+|||..+|+++|+++|++||.|.+|.++++
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~   46 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD   46 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC
Confidence            4488999999999999999999999999999998754

>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=98.69  E-value=1.2e-08  Score=66.41  Aligned_cols=39  Identities=28%  Similarity=0.606  Sum_probs=36.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++|||||||+.+|+++|+++|++||.|.+|.+++|.
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~  109 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP  109 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCC
Confidence            456899999999999999999999999999999999883

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.14  E-value=2e-09  Score=67.41  Aligned_cols=42  Identities=21%  Similarity=0.396  Sum_probs=37.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeE--------EEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEE--------CTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~--------~~v~~d~~-G~sr  103 (103)
                      .++|||+|||..+++++|+++|++||.|.+        |.+++|+. |++|
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~   57 (116)
T 2lcw_A            7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK   57 (116)
Confidence            488999999999999999999999999999        89999876 6553

>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=98.69  E-value=1.5e-08  Score=62.59  Aligned_cols=39  Identities=26%  Similarity=0.532  Sum_probs=35.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++|||+|||..+++++|+++|++||.|.+|.+++++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~   61 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK   61 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC
Confidence            345899999999999999999999999999999998874

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.67  E-value=1.1e-08  Score=62.24  Aligned_cols=35  Identities=17%  Similarity=0.474  Sum_probs=33.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ++|||+|||..+|+++|+++|++||.|.++.+++|
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~   35 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN   35 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC
Confidence            47999999999999999999999999999999887

>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=98.67  E-value=3.2e-08  Score=67.95  Aligned_cols=40  Identities=28%  Similarity=0.423  Sum_probs=36.3

Q ss_pred             CCceEEEecCC-CCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         61 PDKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        61 ~~~~lfVgnL~-~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      .++.|||+||| +.+|+++|+++|++||.|.+|++++++.|
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g   43 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPG   43 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTT
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCC
Confidence            35889999999 89999999999999999999999987643

>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=98.67  E-value=3.7e-08  Score=69.50  Aligned_cols=42  Identities=19%  Similarity=0.260  Sum_probs=38.0

Q ss_pred             CCceEEEecCCCCC-CHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~-te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ..++|||+|||..+ |+++|+++|+.||.|.++.|++|..|++
T Consensus       183 ~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~  225 (284)
T 3smz_A          183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQL  225 (284)
T ss_dssp             SCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCE
T ss_pred             CccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCc
Confidence            45889999999995 9999999999999999999999977654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.65  E-value=4e-08  Score=61.08  Aligned_cols=36  Identities=31%  Similarity=0.666  Sum_probs=33.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ...++|||+|||..+++++|+++|++||.|.++.++
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~   64 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL   64 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE
Confidence            456899999999999999999999999999999886

>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=98.65  E-value=2e-08  Score=62.67  Aligned_cols=36  Identities=14%  Similarity=0.341  Sum_probs=33.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ++|||+|||..+++++|+++|++||.|.+|.++.++
T Consensus        11 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~   46 (111)
T 1whx_A           11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG   46 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC
Confidence            789999999999999999999999999999887544

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.65  E-value=3.8e-08  Score=59.86  Aligned_cols=39  Identities=26%  Similarity=0.383  Sum_probs=33.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ..++|||+|||..+++++|+++|++||.|   .++++..|++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~   52 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKS   52 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCE
Confidence            45899999999999999999999999987   5666644554

>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=98.63  E-value=4.7e-08  Score=59.55  Aligned_cols=38  Identities=26%  Similarity=0.545  Sum_probs=33.7

Q ss_pred             CCCCCceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEe
Q psy10284         58 PLPPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      +...+++|||+|||+ .+++++|+++|++||.|.++.+.
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~   56 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK   56 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe
Confidence            334669999999998 99999999999999999999874

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.63  E-value=4.1e-08  Score=59.41  Aligned_cols=35  Identities=31%  Similarity=0.732  Sum_probs=32.6

Q ss_pred             CCceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEe
Q psy10284         61 PDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        61 ~~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ..++|||+|||+ .+++++|+++|++||.|.++.+.
T Consensus         9 ~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~   44 (96)
T 2kvi_A            9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK   44 (96)
T ss_dssp             CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe
Confidence            458999999998 99999999999999999999875

>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=98.63  E-value=7.1e-08  Score=59.64  Aligned_cols=35  Identities=29%  Similarity=0.716  Sum_probs=32.4

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHhhcCCCceeEEEE
Q psy10284         60 PPDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTV   94 (103)
Q Consensus        60 ~~~~~lfVgnL~~~-~te~~l~~~F~~~G~i~~~~v   94 (103)
                      ...++|||+|||+. +++++|+++|++||.|.+|.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i   60 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV   60 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE
Confidence            34589999999999 999999999999999999987

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.62  E-value=3.2e-08  Score=59.97  Aligned_cols=38  Identities=13%  Similarity=0.314  Sum_probs=33.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||+.+++++|+++|++||.|. +.++.++.
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~   55 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGP   55 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETT
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCC
Confidence            458999999999999999999999999997 66766543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.61  E-value=3.1e-08  Score=60.45  Aligned_cols=38  Identities=13%  Similarity=0.153  Sum_probs=34.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+.-||||||++.+||++|+++|.+||+|.++.+...+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~k   43 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ   43 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTT
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCC
Confidence            34679999999999999999999999999999987754

>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=98.61  E-value=4.2e-08  Score=74.44  Aligned_cols=43  Identities=23%  Similarity=0.444  Sum_probs=39.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|+.|+. |+++
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~k  144 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPR  144 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCcc
Confidence            457999999999999999999999999999999999976 6653

>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=98.61  E-value=4.1e-08  Score=59.16  Aligned_cols=37  Identities=24%  Similarity=0.616  Sum_probs=33.5

Q ss_pred             CCCceEEEecCCCCCCHHHHH----HhhcCCCceeEEEEee
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLK   96 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~----~~F~~~G~i~~~~v~~   96 (103)
                      ..+++|||+|||..+++++|+    ++|++||.|.++.+++
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~   46 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR   46 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc
Confidence            345899999999999999999    9999999999998763

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.60  E-value=6.7e-08  Score=66.06  Aligned_cols=39  Identities=23%  Similarity=0.460  Sum_probs=36.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...+|||+|||+.+|+++|+++|++||.|.+|.|++|+.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~  140 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN  140 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC
Confidence            457899999999999999999999999999999999864

>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=98.60  E-value=1.1e-08  Score=63.64  Aligned_cols=31  Identities=32%  Similarity=0.524  Sum_probs=28.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCcee
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIE   90 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~   90 (103)
                      ...++|||+|||..+|+++|+++|++||.|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~   53 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKK   53 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcc
Confidence            4568999999999999999999999999994

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.60  E-value=2.6e-09  Score=65.19  Aligned_cols=42  Identities=14%  Similarity=0.282  Sum_probs=35.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||+.+|+++|+++|++||.|.+ .+++|+. |++|
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~   58 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNR   58 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcC
Confidence            4589999999999999999999999999988 6666655 5543

>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=98.60  E-value=1.6e-08  Score=64.24  Aligned_cols=38  Identities=13%  Similarity=0.257  Sum_probs=33.9

Q ss_pred             CCceEEE--ecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfV--gnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+.+|||  |||++.+++++|+++|++||.|.++.++.++
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~r   63 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK   63 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC
Confidence            3578999  7799999999999999999999999887654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=1e-07  Score=57.84  Aligned_cols=36  Identities=25%  Similarity=0.388  Sum_probs=32.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCC--CceeEEEEee
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPF--GTIEECTVLK   96 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~--G~i~~~~v~~   96 (103)
                      ..++|||+|||+.+++++|+++|++|  |.|.++.+++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~   51 (99)
T 2cpd_A           14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR   51 (99)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS
T ss_pred             CcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeC
Confidence            45899999999999999999999999  9999998754

>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=98.56  E-value=4e-08  Score=58.01  Aligned_cols=37  Identities=16%  Similarity=0.356  Sum_probs=34.3

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCC----C-------ceeEEEEeeCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPF----G-------TIEECTVLKGP   98 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~----G-------~i~~~~v~~d~   98 (103)
                      .++|||+|||+.+++++|+++|++|    |       .|.++.+++++
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~k   53 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK   53 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCC
Confidence            4899999999999999999999999    8       99999988765

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.54  E-value=1.4e-07  Score=60.63  Aligned_cols=36  Identities=14%  Similarity=0.133  Sum_probs=32.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEee
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   96 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~   96 (103)
                      ....|||+||++.+|+++|+++|++||.|.+|.|..
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~   59 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK   59 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            346689999999999999999999999999998865

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.53  E-value=1.1e-07  Score=61.08  Aligned_cols=38  Identities=11%  Similarity=0.240  Sum_probs=32.7

Q ss_pred             CCCceEEEecCCCCCCHHHHH----HhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~----~~F~~~G~i~~~~v~~d   97 (103)
                      ...++|||||||+.+++++|+    ++|++||.|.+|.+.++
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~   68 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS   68 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccC
Confidence            346889999999999999876    69999999999987653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.50  E-value=1.5e-07  Score=60.99  Aligned_cols=38  Identities=24%  Similarity=0.333  Sum_probs=33.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .-.+|||+||++.+|+++|+++|++||.|.+|.+..+.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~   64 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN   64 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC
Confidence            34679999999999999999999999999999887643

>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=98.49  E-value=7.9e-08  Score=57.60  Aligned_cols=35  Identities=26%  Similarity=0.416  Sum_probs=30.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCc-eeEEEE
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTV   94 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~-i~~~~v   94 (103)
                      ...++|||+|||..+|+++|+++|++||. |..+.+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~   41 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL   41 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE
Confidence            34589999999999999999999999999 665554

>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=98.48  E-value=1.1e-07  Score=63.94  Aligned_cols=39  Identities=23%  Similarity=0.328  Sum_probs=34.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ....+|||+||++.+|+++|+++|++||.|.++.|..++
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~   82 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN   82 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC
Confidence            345789999999999999999999999999999987554

>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=98.46  E-value=1.9e-07  Score=66.07  Aligned_cols=43  Identities=23%  Similarity=0.466  Sum_probs=38.2

Q ss_pred             CCceEEEecCCCC-CCHHHHHHhhcCCCceeEEEEeeCCC--CCCC
Q psy10284         61 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPD--GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~-~te~~l~~~F~~~G~i~~~~v~~d~~--G~sr  103 (103)
                      ..++|||+|||.. +|+++|+++|++||.|.++.+++|..  |+++
T Consensus       209 ~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~  254 (292)
T 2ghp_A          209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNN  254 (292)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCC
T ss_pred             CCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCc
Confidence            4588999999999 99999999999999999999999876  6553

>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=98.46  E-value=3.7e-07  Score=59.80  Aligned_cols=31  Identities=23%  Similarity=0.307  Sum_probs=28.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEE
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC   92 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~   92 (103)
                      .++|||+|||..+|+++|+++|++||.|..+
T Consensus        99 ~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~  129 (175)
T 1fje_B           99 ARTLLAKNLSFNITEDELKEVFEDALEIRLV  129 (175)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHCTTCSEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe
Confidence            4889999999999999999999999988766

>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=98.46  E-value=1.4e-07  Score=66.42  Aligned_cols=42  Identities=24%  Similarity=0.368  Sum_probs=38.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      ...+|||+|||..+|+++|+++|+.||.|.+|.+++|..|++
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~  136 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRA  136 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCc
Confidence            457999999999999999999999999999999999965764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.46  E-value=1.4e-07  Score=63.25  Aligned_cols=38  Identities=16%  Similarity=0.352  Sum_probs=35.5

Q ss_pred             CceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +++|||+|||. .+++++|+++|++||.|.+|.+++|+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~   41 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK   41 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCC
Confidence            48899999999 999999999999999999999998864

>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=98.46  E-value=1.2e-07  Score=65.40  Aligned_cols=41  Identities=15%  Similarity=0.280  Sum_probs=37.6

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         59 LPPDKKLFVGMLSK-QQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        59 ~~~~~~lfVgnL~~-~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...+++|||+|||. .+++++|+++|++||.|.+|.+++|+.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~   72 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK   72 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCC
Confidence            34678999999999 999999999999999999999998874

>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=98.45  E-value=1.5e-08  Score=65.52  Aligned_cols=34  Identities=24%  Similarity=0.428  Sum_probs=30.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEE
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC   92 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~   92 (103)
                      ...+++|||+|||+.+|+++|+++|++||.|.+|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~   75 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSE   75 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccc
Confidence            3456899999999999999999999999998774

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.44  E-value=3.1e-07  Score=55.76  Aligned_cols=40  Identities=28%  Similarity=0.475  Sum_probs=33.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ...++|||+|||..+++++|+++|+.|+   ++.+++|+. |++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~   53 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSS   53 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSE
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCc
Confidence            3558999999999999999999999874   677888876 654

>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=98.43  E-value=2.6e-07  Score=65.09  Aligned_cols=42  Identities=26%  Similarity=0.527  Sum_probs=38.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ..++|||+|||..+|+++|+++|++||.|.++.+++|+. |++
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~  136 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS  136 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCcc
Confidence            458999999999999999999999999999999999986 765

>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=98.41  E-value=4.3e-07  Score=63.92  Aligned_cols=37  Identities=24%  Similarity=0.634  Sum_probs=33.6

Q ss_pred             CCceEEEecCCCCCCHHHHH----HhhcCCCceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVR----KIFAPFGTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~----~~F~~~G~i~~~~v~~d   97 (103)
                      ..++|||+|||..+|+++|+    ++|++||.|.+|.++++
T Consensus         8 ~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~   48 (282)
T 3pgw_A            8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS   48 (282)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCC
Confidence            45899999999999999977    89999999999998863

>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=98.40  E-value=2.7e-07  Score=65.29  Aligned_cols=41  Identities=24%  Similarity=0.249  Sum_probs=36.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      ...++|||+|||..+|+++|+++|+.||.|.+|.+++|+.|
T Consensus        39 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~   79 (292)
T 2ghp_A           39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK   79 (292)
T ss_dssp             ---CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC
Confidence            45689999999999999999999999999999999998763

>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=98.36  E-value=3.7e-07  Score=64.21  Aligned_cols=38  Identities=26%  Similarity=0.529  Sum_probs=35.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.+.+++
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~k   58 (261)
T 3sde_A           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR   58 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCC
Confidence            44889999999999999999999999999999998765

>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=98.36  E-value=5.1e-07  Score=53.67  Aligned_cols=33  Identities=18%  Similarity=0.399  Sum_probs=31.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      .++|||+|||+.+++++|+++|++| .|.++.+.
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~   37 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD   37 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe
Confidence            4889999999999999999999999 99999885

>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=98.36  E-value=2.4e-07  Score=63.58  Aligned_cols=38  Identities=18%  Similarity=0.254  Sum_probs=34.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCce--eEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTI--EECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i--~~~~v~~d~   98 (103)
                      .+.+|||+|||+++|+++|+++|++||.|  .+++++.|+
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~  161 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK  161 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC
Confidence            35789999999999999999999999999  899988876

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.33  E-value=1.4e-06  Score=52.57  Aligned_cols=36  Identities=22%  Similarity=0.292  Sum_probs=31.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ...++|||+|+  .+|+++|+++|++||.|.+|.+...
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~   48 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP   48 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETT
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCC
Confidence            34589999996  8999999999999999999988643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.30  E-value=3.5e-07  Score=64.74  Aligned_cols=39  Identities=23%  Similarity=0.447  Sum_probs=35.2

Q ss_pred             CCCceEEEecCCCCC---------CHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQQ---------NEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~---------te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      ...++||||||+..+         ++++|+++|++||.|.+|+|+.++
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~k  179 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK  179 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGG
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCC
Confidence            356899999999998         799999999999999999998765

>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=98.30  E-value=9.5e-07  Score=62.16  Aligned_cols=39  Identities=26%  Similarity=0.462  Sum_probs=36.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||..+++++|+++|++||.|.++.++.++.
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~  244 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH  244 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCC
Confidence            457899999999999999999999999999999998763

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.26  E-value=5.2e-07  Score=54.17  Aligned_cols=32  Identities=22%  Similarity=0.300  Sum_probs=29.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEE
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC   92 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~   92 (103)
                      ..++|||+|||..+++++|+++|++||.|..+
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~   46 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV   46 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe
Confidence            34899999999999999999999999988766

>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=98.26  E-value=7.6e-06  Score=56.30  Aligned_cols=37  Identities=16%  Similarity=0.432  Sum_probs=34.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCC-ceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G-~i~~~~v~~d   97 (103)
                      ..++|||+|||..+++++|+++|++|| .|.++.++.+
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~  187 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  187 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC
Confidence            468999999999999999999999999 9999998653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.25  E-value=5.6e-06  Score=55.27  Aligned_cols=38  Identities=16%  Similarity=0.414  Sum_probs=34.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCC-ceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFG-TIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G-~i~~~~v~~d~   98 (103)
                      .++.|||+|||..+++++|+++|++|| .|.++.++.+.
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~  157 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD  157 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC
Confidence            468899999999999999999999999 99999987644

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.20  E-value=1.6e-06  Score=55.52  Aligned_cols=39  Identities=15%  Similarity=0.174  Sum_probs=36.3

Q ss_pred             CCceEEEecCCCC-CCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~-~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++-|||+||+.. +++++|+++|++||+|..|.+++|..
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~   56 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK   56 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC
Confidence            4588999999999 99999999999999999999988875

>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=98.07  E-value=2.2e-06  Score=63.46  Aligned_cols=38  Identities=11%  Similarity=0.193  Sum_probs=32.9

Q ss_pred             CCCceEEEec--CCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         60 PPDKKLFVGM--LSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        60 ~~~~~lfVgn--L~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ..+.+|||||  |++.+|+++|+++|++||+|.++.+..+
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~   55 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN   55 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTT
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC
Confidence            3458999998  6899999999999999999999877543

>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=98.07  E-value=2.6e-07  Score=60.53  Aligned_cols=32  Identities=13%  Similarity=0.271  Sum_probs=28.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeE
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE   91 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~   91 (103)
                      ...++|||+|||..+|+++|+++|++||.+..
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~   42 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKND   42 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce
Confidence            34589999999999999999999999998766

>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=98.04  E-value=2.6e-06  Score=55.34  Aligned_cols=37  Identities=16%  Similarity=0.356  Sum_probs=32.7

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCC----C-------ceeEEEEeeCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPF----G-------TIEECTVLKGP   98 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~----G-------~i~~~~v~~d~   98 (103)
                      .++|||+|||.++|+++|+++|++|    |       .|.++.+.+++
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~   51 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK   51 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTT
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCC
Confidence            3899999999999999999999999    7       78888776654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=97.89  E-value=1e-05  Score=53.62  Aligned_cols=37  Identities=16%  Similarity=0.356  Sum_probs=31.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCC----C-------ceeEEEEeeCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPF----G-------TIEECTVLKGP   98 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~----G-------~i~~~~v~~d~   98 (103)
                      +++|||+|||.++|+++|+++|++|    |       .|.++.+.+++
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~   51 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK   51 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTT
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCC
Confidence            4899999999999999999999999    5       66777665443

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.86  E-value=2e-05  Score=48.56  Aligned_cols=30  Identities=17%  Similarity=0.293  Sum_probs=26.1

Q ss_pred             ceEEEecCCCCCCHHH----HHHhhcCC-CceeEE
Q psy10284         63 KKLFVGMLSKQQNEDD----VRKIFAPF-GTIEEC   92 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~----l~~~F~~~-G~i~~~   92 (103)
                      +-|||+|||+.+++++    |+++|++| |+|.++
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V   44 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI   44 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE
Confidence            4499999999999987    55899999 599887

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=97.78  E-value=5.7e-05  Score=46.64  Aligned_cols=38  Identities=13%  Similarity=0.385  Sum_probs=31.8

Q ss_pred             CceEEEecCCC-----CCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSK-----QQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~-----~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++.|++.|+..     +.++++|++.|++||.|.+|.|++|+.
T Consensus         8 s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~   50 (105)
T 2pe8_A            8 TKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPG   50 (105)
T ss_dssp             CSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSS
T ss_pred             CCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCC
Confidence            47799999973     237899999999999999999999864

>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=97.26  E-value=2e-05  Score=48.59  Aligned_cols=36  Identities=14%  Similarity=0.267  Sum_probs=29.2

Q ss_pred             EecCCCCCCHHHHHHhh------------cCCCceeEEEEeeCCCCCC
Q psy10284         67 VGMLSKQQNEDDVRKIF------------APFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        67 VgnL~~~~te~~l~~~F------------~~~G~i~~~~v~~d~~G~s  102 (103)
                      +.|||+.+++++|++.|            ++||.|.+|.|++|+.|++
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~   67 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHL   67 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSS
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCc
Confidence            56788888888877776            9999999999999876554

>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=97.08  E-value=0.0011  Score=40.78  Aligned_cols=38  Identities=13%  Similarity=0.273  Sum_probs=29.8

Q ss_pred             CCceEEEecCCCCCC-----------HHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQN-----------EDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~t-----------e~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++.|+|.||....+           +++|+++|++||.|.+|.| .|+.
T Consensus        14 ~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~   62 (112)
T 2dit_A           14 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRH   62 (112)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTC
T ss_pred             CceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCC
Confidence            347899999954433           5799999999999999955 5553

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.91  E-value=0.00096  Score=40.84  Aligned_cols=25  Identities=8%  Similarity=0.235  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHhhcCCCceeEEEEee
Q psy10284         72 KQQNEDDVRKIFAPFGTIEECTVLK   96 (103)
Q Consensus        72 ~~~te~~l~~~F~~~G~i~~~~v~~   96 (103)
                      ..+++++|+++|++||.|.+|.|+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~   51 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSS   51 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEES
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEcc
Confidence            4689999999999999999999874

>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=96.62  E-value=0.002  Score=39.45  Aligned_cols=37  Identities=16%  Similarity=0.271  Sum_probs=29.3

Q ss_pred             ceEEEecC--CCCCC--------HHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         63 KKLFVGML--SKQQN--------EDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        63 ~~lfVgnL--~~~~t--------e~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +-|.+.|+  |....        +++|++.|++||.|.++.|++|+.
T Consensus         6 ~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~   52 (105)
T 3v4m_A            6 EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVD   52 (105)
T ss_dssp             SEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBT
T ss_pred             eEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCC
Confidence            56777887  33333        368999999999999999999875

>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=96.34  E-value=0.0045  Score=38.85  Aligned_cols=38  Identities=11%  Similarity=0.262  Sum_probs=30.4

Q ss_pred             CceEEEecCCCC-----CCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQ-----QNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~-----~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++.|++.|+-..     --+++|++.|++||.|.+|.|++|+.
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~   62 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQ   62 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCC
Confidence            377899998421     23589999999999999999998864

>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=95.38  E-value=0.011  Score=36.76  Aligned_cols=23  Identities=26%  Similarity=0.198  Sum_probs=20.3

Q ss_pred             HHHHHhhcCCCceeEEEEeeCCC
Q psy10284         77 DDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        77 ~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++|++.|++||.|.++.|.++..
T Consensus        32 edl~~~f~kfG~V~~v~i~~~~~   54 (114)
T 3s6e_A           32 DDVIEECNKHGGVIHIYVDKNSA   54 (114)
T ss_dssp             HHHHHHHTTTTCCSEEEECTTCT
T ss_pred             HHHHHHHhccCCEEEEEEecCCC
Confidence            58899999999999999987764

>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=94.99  E-value=0.0069  Score=37.18  Aligned_cols=47  Identities=15%  Similarity=0.282  Sum_probs=12.6

Q ss_pred             CCCCCCceeEEecCCcccchhhhhccccccccCCCcCCCcccccccCCCCCCceEEEecCCCCCCHHH
Q psy10284         11 TPLPPDKKLFVGMLSKQQNEDDNLSHCFHLLFPHLQCFPWDLIWTCTPLPPDKKLFVGMLSKQQNEDD   78 (103)
Q Consensus        11 ~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~   78 (103)
                      ...++|++|.|.....+..+......                     ......++||+|||.++|++.
T Consensus        67 ~~~~~g~~i~V~~a~~~~~~~~~~~~---------------------~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           67 GMLLNDRKVFVGRFKSRKEREAELGA---------------------RAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             TCEETTEECEEEESSCCCC-------------------------------------------------
T ss_pred             CCEECCEEEEEEECCCcccccccccc---------------------ccCCCCceEeCCCCCCccccc
Confidence            35577788888776655443322110                     011236899999999999863

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.34  E-value=0.061  Score=32.50  Aligned_cols=36  Identities=19%  Similarity=0.333  Sum_probs=26.6

Q ss_pred             ceEEEecCCC----CCCH----HHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSK----QQNE----DDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~----~~te----~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+++|...+.    ..-+    .+|.+.|++||+|..++++.|+
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~   51 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK   51 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC
Confidence            5667766551    2223    5789999999999999998875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=90.70  E-value=0.3  Score=30.70  Aligned_cols=43  Identities=9%  Similarity=0.062  Sum_probs=36.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHhhcCC-----CceeEEEEeeCCCC
Q psy10284         58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPF-----GTIEECTVLKGPDG  100 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~~~te~~l~~~F~~~-----G~i~~~~v~~d~~G  100 (103)
                      ++...+.+-+-|||..+++..++.+.+.+     |.+..+.+..|..|
T Consensus        17 ~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~G   64 (117)
T 2l9w_A           17 SKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG   64 (117)
T ss_dssp             TTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTE
T ss_pred             CccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCc
Confidence            33445788899999999999999999999     99999998888754

>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=89.59  E-value=0.24  Score=30.10  Aligned_cols=39  Identities=23%  Similarity=0.396  Sum_probs=29.1

Q ss_pred             CCCceEEEecCCCC------CCH---HHHHHhhcCCCceeEEEEeeCC
Q psy10284         60 PPDKKLFVGMLSKQ------QNE---DDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        60 ~~~~~lfVgnL~~~------~te---~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +...+++|..++..      .++   .+|.+.|++||+|..++++.|+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~   60 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ   60 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc
Confidence            34477888877643      232   4688999999999999988775

>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=89.33  E-value=0.61  Score=28.54  Aligned_cols=27  Identities=22%  Similarity=0.498  Sum_probs=22.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCce
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTI   89 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i   89 (103)
                      ..+|+-+.|.+..-.||.++|+.||.|
T Consensus        16 ~HVf~l~FP~ewKt~DI~~lFs~fggv   42 (100)
T 1whv_A           16 DHVLHVTFPKEWKTSDLYQLFSAFGNI   42 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSC
T ss_pred             CeEEEEeCChhhhhHHHHHHhhccCCE
Confidence            445555999999999999999999954

>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=88.16  E-value=1.3  Score=26.44  Aligned_cols=34  Identities=9%  Similarity=0.235  Sum_probs=29.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEee
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   96 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~   96 (103)
                      +|+-|.+||..+|++++.+.++.+..+....-..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~   35 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFS   35 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeC
Confidence            6899999999999999999999998776655443

>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=84.70  E-value=0.71  Score=30.90  Aligned_cols=26  Identities=15%  Similarity=0.350  Sum_probs=21.9

Q ss_pred             CCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         74 QNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        74 ~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      -.++++++.|++||.|.++.|.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~  166 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQ  166 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEEC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCC
Confidence            35678999999999999999986654

>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=83.46  E-value=1.5  Score=26.87  Aligned_cols=25  Identities=20%  Similarity=0.478  Sum_probs=21.2

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCc
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGT   88 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~   88 (103)
                      .+|+-+.|.+..-.||.++|+.||.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fgg   31 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGN   31 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEE
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCC
Confidence            3444499999999999999999994

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=83.44  E-value=0.66  Score=35.50  Aligned_cols=33  Identities=15%  Similarity=0.363  Sum_probs=26.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEee
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   96 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~   96 (103)
                      +.+||. .|...++.+|.++|++||.|.++..-.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~   86 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYE   86 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEEC
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEc
Confidence            779996 699999999999999999999985443

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.38  E-value=3.5  Score=25.32  Aligned_cols=33  Identities=12%  Similarity=0.016  Sum_probs=27.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcC----C-CceeEEEE
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAP----F-GTIEECTV   94 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~----~-G~i~~~~v   94 (103)
                      ..+|.|.|||..+.++.|.-+|++    . |+|.++..
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~   45 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQR   45 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEE
Confidence            378999999999999999999998    2 57777654

---

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	103
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-05
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-04
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-04
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-04
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-04
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-04
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	6e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.001
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.001
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.001
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.001
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.002
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	0.002
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.002
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.003
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	0.003
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.003

>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 = 42.5 bits (100), Expect = 4e-07
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 58 PLPPDKKLFVGMLSKQQ-NEDDVRKIFAPFGTIEECTVLKG 97
          P   + ++F+G L+     + DV  IF+ +G I  C+V KG
Sbjct: 11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG 51

>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 = 41.5 bits (97), Expect = 8e-07
 Identities = 11/44 (25%), Positives = 22/44 (50%)

Query: 60  PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
               K+ V  +  Q N+ ++R++F+ FG ++   + K   GT  
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGA 49

>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 = 40.3 bits (94), Expect = 2e-06
 Identities = 10/37 (27%), Positives = 19/37 (51%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          P +  ++ G ++    +  +R+ F+PFG I E  V  
Sbjct: 16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP 52

>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 = 40.0 bits (92), Expect = 1e-05
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
           +KLF+G LS +  ++ +R  F  +GT+ +C
Sbjct: 6  LRKLFIGGLSFETTDESLRSHFEQWGTLTDC 36

>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 = 38.4 bits (89), Expect = 1e-05
 Identities = 10/33 (30%), Positives = 15/33 (45%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
           L+VG L     E  + + F+P G I    V +
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR 34

>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 = 38.0 bits (88), Expect = 1e-05
 Identities = 11/33 (33%), Positives = 20/33 (60%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KL V  L    ++ D++++FA FGT+++  V  
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHY 34

>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 = 38.0 bits (88), Expect = 1e-05
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          D  L+V  L +   +D +  IF  +G+I + 
Sbjct: 6  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQK 36

>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 = 37.3 bits (86), Expect = 3e-05
 Identities = 7/31 (22%), Positives = 13/31 (41%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          +  L V  L +   + ++  +F   G I  C
Sbjct: 2  NTNLIVNYLPQDMTDRELYALFRAIGPINTC 32

>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 = 36.6 bits (84), Expect = 5e-05
 Identities = 8/31 (25%), Positives = 16/31 (51%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          D  L+V  L K   + ++ ++F+ +G I   
Sbjct: 6  DANLYVSGLPKTMTQKELEQLFSQYGRIITS 36

>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 = 36.6 bits (84), Expect = 5e-05
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
           P+  L V  LS    E D+R++F+ +G I + 
Sbjct: 7  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADV 39

>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 = 36.3 bits (83), Expect = 7e-05
 Identities = 7/36 (19%), Positives = 14/36 (38%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
          ++L+VG +     E+ +   F     +   T   G 
Sbjct: 2  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN 37

>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 = 35.7 bits (82), Expect = 1e-04
 Identities = 12/29 (41%), Positives = 20/29 (68%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          K+F+G LS Q  ++ +R+ F  FG ++EC
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKEC 30

>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 = 35.8 bits (82), Expect = 1e-04
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
            D  ++VG L ++ +E  + ++F   G +   
Sbjct: 7  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNT 39

>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 = 35.3 bits (81), Expect = 1e-04
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          K+FVG LS    E+ +R+ F  FG +E  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESI 29

>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 = 35.8 bits (82), Expect = 2e-04
 Identities = 9/36 (25%), Positives = 19/36 (52%), Gaps = 2/36 (5%)

Query: 59 LPPD--KKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          LPP+  + L++  L  +   +++  IF  +G I + 
Sbjct: 2  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI 37

>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 = 35.0 bits (80), Expect = 2e-04
 Identities = 10/39 (25%), Positives = 20/39 (51%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           LF+  L+    E+ ++ +F+  G I+ CT+ K  +    
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGV 39

>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 = 34.7 bits (79), Expect = 3e-04
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK 96
          KL++G LS     DD+R++F          VL 
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 35

>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 = 34.9 bits (80), Expect = 3e-04
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          L     L+VG LS    E+ + ++F+  G I++ 
Sbjct: 4  LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKI 37

>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 = 34.3 bits (78), Expect = 3e-04
 Identities = 9/39 (23%), Positives = 17/39 (43%)

Query: 65  LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK 103
           +F+G L  + +E  +   F+ FG I +   +     T  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGN 39

>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 = 34.2 bits (78), Expect = 4e-04
 Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 62  DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK 103
            +KLF+G LS +  ++ +R  F  +GT+ +C V++ P+   S+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSR 48

>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 = 33.9 bits (77), Expect = 5e-04
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
             + L+VG L+++ ++  +   F PFG I + 
Sbjct: 3  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 35

>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 = 33.9 bits (77), Expect = 6e-04
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
             K+L V  +  +  + D+R++F  FG I + 
Sbjct: 9  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV 41

>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 = 33.9 bits (77), Expect = 7e-04
 Identities = 8/33 (24%), Positives = 15/33 (45%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
            D +++VG L       D+  +F  +G I + 
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI 44

>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 = 34.0 bits (77), Expect = 7e-04
 Identities = 7/39 (17%), Positives = 14/39 (35%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP 98
            +  ++V  L+     DD+   F   G ++       P
Sbjct: 6  SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQP 44

>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 = 33.4 bits (76), Expect = 8e-04
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          +LFVG L     E+++RK+F  +G   E 
Sbjct: 10 RLFVGNLPPDITEEEMRKLFEKYGKAGEV 38

>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 = 33.5 bits (76), Expect = 9e-04
 Identities = 10/37 (27%), Positives = 17/37 (45%)

Query: 64  KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
            +F+  L K  +   +   F+ FG I  C V+   +G
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG 46

>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 = 33.5 bits (76), Expect = 9e-04
 Identities = 5/30 (16%), Positives = 13/30 (43%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          + +F   L+ +    D+   F+  G + + 
Sbjct: 19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDV 48

>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 = 33.1 bits (75), Expect = 0.001
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
             + L+VG LS+   E  + ++F+  G  + C
Sbjct: 6  GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSC 38

>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 = 33.6 bits (76), Expect = 0.001
 Identities = 9/37 (24%), Positives = 16/37 (43%)

Query: 63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
             F G L  Q   +D+  +F+  G I+    ++G  
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK 48

>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 = 32.6 bits (74), Expect = 0.001
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD 99
          K+F+G LS    + D++  F+ FG + +CT+   P 
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI 36

>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 = 33.1 bits (75), Expect = 0.001
 Identities = 5/29 (17%), Positives = 13/29 (44%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          +LF+G + K +  +++ +  A        
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLD 31

>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 = 33.1 bits (75), Expect = 0.001
 Identities = 12/40 (30%), Positives = 23/40 (57%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG 100
             +KLF+G LS +  E+ +R  +  +G + +C V++ P  
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPAS 58

>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 = 32.5 bits (73), Expect = 0.002
 Identities = 2/31 (6%), Positives = 10/31 (32%)

Query: 62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          +  L++        + ++R +      +   
Sbjct: 1  ECTLWMTNFPPSYTQRNIRDLLQDINVVALS 31

>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 = 32.0 bits (72), Expect = 0.002
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 64 KLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          K+FVG LS     +DV+  F  FG +++ 
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDA 29

>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 = 32.3 bits (73), Expect = 0.002
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
           P  +L+VG L    +   + + F  FG+I   
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI 47

>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 = 32.0 bits (72), Expect = 0.003
 Identities = 9/33 (27%), Positives = 17/33 (51%)

Query: 60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
          P    LF+  L ++  + D+ ++F PFG +   
Sbjct: 16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA 48

>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 = 31.9 bits (72), Expect = 0.003
 Identities = 8/41 (19%), Positives = 15/41 (36%)

Query: 61  PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGT 101
             + L    LS    ED+++++F     I   +      G 
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGI 55

>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 = 32.1 bits (72), Expect = 0.003
 Identities = 11/36 (30%), Positives = 18/36 (50%)

Query: 57 TPLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC 92
           P  P+K L++  LS +  E D+  +FA F   +  
Sbjct: 13 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGP 48

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	103
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.36
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.34
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.32
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.31
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.28
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.28
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.27
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.26
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.25
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.21
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.2
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.2
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.2
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.19
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.19
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.18
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.18
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.18
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.17
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.16
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.16
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.15
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.15
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.15
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.14
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.13
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.11
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.1
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.08
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.08
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.07
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.05
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.05
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.03
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.01
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.0
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.0
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.97
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.97
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.97
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.97
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.97
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.96
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.95
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.95
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.92
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.91
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.9
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.89
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.89
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.87
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.85
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.83
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.81
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.8
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.8
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.77
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.77
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.76
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.74
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.73
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.73
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.73
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.7
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.62
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.61
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.58
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.58
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.57
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.43
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.41
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.41
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.37
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.37
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.32
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.01
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	97.83
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	97.65
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.23
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	96.11
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	91.63
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	84.14

>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=99.36  E-value=3e-13  Score=78.99  Aligned_cols=41  Identities=37%  Similarity=0.723  Sum_probs=39.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      |+|||+|||+++|+++|+++|++||.|.++.|++|+. |++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~k   42 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR   42 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCcc
Confidence            6899999999999999999999999999999999998 8876

>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=99.34  E-value=6e-13  Score=79.85  Aligned_cols=43  Identities=30%  Similarity=0.405  Sum_probs=40.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|++|+. |++|
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~sr   50 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSK   50 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccC
Confidence            458899999999999999999999999999999999998 8764

>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=99.32  E-value=4.7e-13  Score=77.87  Aligned_cols=40  Identities=30%  Similarity=0.551  Sum_probs=38.1

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|||||||+++|+++|+++|++||.|.+|.|++|+. |++|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~r   41 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRR   41 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTT
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccc
Confidence            699999999999999999999999999999999998 8875

>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=99.31  E-value=1.2e-12  Score=77.39  Aligned_cols=43  Identities=26%  Similarity=0.516  Sum_probs=39.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++++|||||||..+|+++|+++|++||.|.++++++|+. |++|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~k   48 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSR   48 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCC
Confidence            348899999999999999999999999999999999987 7653

>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=99.28  E-value=2.6e-12  Score=75.99  Aligned_cols=41  Identities=34%  Similarity=0.677  Sum_probs=38.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+|||||||..+|+++|+++|++||+|.+++|++|+. |++|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~r   43 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK   43 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccc
Confidence            5799999999999999999999999999999999998 8875

>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=99.28  E-value=3.6e-12  Score=77.89  Aligned_cols=42  Identities=38%  Similarity=0.633  Sum_probs=39.6

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||||||+.+++++|+++|++||.|.++.|++|+. |++|
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~k   52 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSR   52 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCC
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccC
Confidence            37899999999999999999999999999999999998 8875

>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=99.27  E-value=1.6e-12  Score=75.31  Aligned_cols=40  Identities=35%  Similarity=0.714  Sum_probs=37.9

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|||||||+++|+++|+++|++||+|.++.|++|+. |++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~k   41 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSR   41 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcC
Confidence            599999999999999999999999999999999998 8775

>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=99.26  E-value=5.6e-12  Score=74.36  Aligned_cols=43  Identities=26%  Similarity=0.545  Sum_probs=39.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++++|||+|||.++++++|+++|++||.|.++++++|+. |++|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~   48 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR   48 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCc
Confidence            347899999999999999999999999999999999988 8764

>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=99.25  E-value=3.6e-12  Score=75.30  Aligned_cols=41  Identities=34%  Similarity=0.791  Sum_probs=38.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||||||+.+|+++|+++|++||.|.++.|++|+. |++|
T Consensus         7 ~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~k   48 (84)
T d1l3ka1           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSR   48 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEE
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcc
Confidence            7899999999999999999999999999999999998 8764

>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=99.21  E-value=7.7e-12  Score=73.38  Aligned_cols=42  Identities=26%  Similarity=0.371  Sum_probs=38.7

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++.|||+|||..+|+++|+++|++||.|.+|.|++|+. |++|
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~   51 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR   51 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccc
Confidence            37899999999999999999999999999999999988 7653

>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=99.20  E-value=9.6e-12  Score=74.63  Aligned_cols=43  Identities=23%  Similarity=0.278  Sum_probs=39.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .+++|||||||.++|+++|+++|++||.|.+|.+++|+. |++|
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~k   49 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC   49 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceecccccccccccc
Confidence            358999999999999999999999999999999999988 7653

>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=99.20  E-value=5.1e-12  Score=73.84  Aligned_cols=41  Identities=22%  Similarity=0.527  Sum_probs=38.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||.++|+++|+++|++||.|.++.+++|+. |++|
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~   44 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSY   44 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCcc
Confidence            7899999999999999999999999999999999987 7654

>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=99.20  E-value=1.3e-11  Score=74.68  Aligned_cols=43  Identities=28%  Similarity=0.425  Sum_probs=39.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||+.+++++|+++|++||.|.+|.+++|+. |++|
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~   50 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPK   50 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccC
Confidence            458899999999999999999999999999999999988 8765

>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=99.19  E-value=8.7e-12  Score=74.15  Aligned_cols=41  Identities=22%  Similarity=0.488  Sum_probs=39.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.|||||||+++|+++|+++|++||.|.+|.+++|+. |++|
T Consensus         6 ~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~k   47 (89)
T d2cqba1           6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR   47 (89)
T ss_dssp             SCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCS
T ss_pred             cEEEEeCCCCcCCHHHHHHHHhhCCeEEeccccccccccccc
Confidence            7899999999999999999999999999999999998 8775

>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=99.19  E-value=1.6e-11  Score=75.13  Aligned_cols=41  Identities=32%  Similarity=0.761  Sum_probs=38.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||||||+++|+++|+++|++||.|.++.|++|+. |++|
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~k   62 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSR   62 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCcc
Confidence            7899999999999999999999999999999999988 6664

>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=99.18  E-value=1.7e-11  Score=71.03  Aligned_cols=40  Identities=30%  Similarity=0.621  Sum_probs=37.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ++|||||||+++|+++|+++|++||.|..+.++.|+. |++
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~   43 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK   43 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCccc
Confidence            7899999999999999999999999999999999987 665

>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=99.18  E-value=1.7e-11  Score=73.55  Aligned_cols=42  Identities=21%  Similarity=0.362  Sum_probs=39.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||||||..+|+++|+++|++||.|.++.|++|+. |++|
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~k   51 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ   51 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccc
Confidence            47899999999999999999999999999999999987 7764

>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=99.18  E-value=1.5e-11  Score=71.66  Aligned_cols=40  Identities=28%  Similarity=0.634  Sum_probs=37.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ++|||+|||.++++++|+++|++||.|.+|++++|.. |++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~   43 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQS   43 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCc
Confidence            6799999999999999999999999999999999987 765

>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=99.17  E-value=1.4e-11  Score=71.84  Aligned_cols=40  Identities=28%  Similarity=0.304  Sum_probs=37.5

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .|||||||..+|+++|+++|++||.|.+++|++|+. |++|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~   42 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSL   42 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCC
Confidence            499999999999999999999999999999999998 7753

>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=99.16  E-value=4.8e-11  Score=72.43  Aligned_cols=45  Identities=22%  Similarity=0.504  Sum_probs=39.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      .....++|||+|||.++++++|+++|++||.|.++.+..+..|++
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~   58 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTS   58 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccccccc
Confidence            334558999999999999999999999999999999998866654

>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=99.16  E-value=2.8e-11  Score=73.75  Aligned_cols=41  Identities=17%  Similarity=0.425  Sum_probs=39.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.|||+|||+.+|+++|+++|++||.|.+|.+++|+. |++|
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~k   60 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK   60 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCcccc
Confidence            6799999999999999999999999999999999988 8875

>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=99.15  E-value=1.4e-11  Score=71.56  Aligned_cols=40  Identities=33%  Similarity=0.526  Sum_probs=37.7

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      +|||+|||+++++++|+++|++||.|.+++|++|+.|++|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~   41 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL   41 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccc
Confidence            6999999999999999999999999999999999887764

>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=99.15  E-value=2.9e-11  Score=72.60  Aligned_cols=43  Identities=23%  Similarity=0.503  Sum_probs=38.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC--CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD--GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~--G~sr  103 (103)
                      .+.+|||+|||..+++++|+++|++||.|.+|.|++|..  |++|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~r   51 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR   51 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcc
Confidence            448899999999999999999999999999999998864  7664

>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=99.15  E-value=3.6e-11  Score=73.15  Aligned_cols=44  Identities=27%  Similarity=0.545  Sum_probs=39.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +.+++|||+|||+++++++|+++|++||.|.++.+++|+. |++|
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~k   60 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK   60 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCc
Confidence            3457899999999999999999999999999999999987 7654

>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=99.14  E-value=2.9e-11  Score=71.73  Aligned_cols=43  Identities=26%  Similarity=0.428  Sum_probs=39.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++..|||+|||..+|+++|+++|++||.|.++++++|+. |++|
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~   49 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK   49 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccc
Confidence            347899999999999999999999999999999999987 8764

>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=99.13  E-value=3.6e-11  Score=71.53  Aligned_cols=43  Identities=33%  Similarity=0.552  Sum_probs=39.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||+|||..+++++|+++|++||.|.++.|++|+. |++|
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~r   50 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSK   50 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccc
Confidence            347899999999999999999999999999999999987 7653

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=2.7e-11  Score=71.89  Aligned_cols=42  Identities=38%  Similarity=0.657  Sum_probs=38.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      .++|||||||+++++++|+++|++||.|.++.+++++. |++|
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~   47 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSR   47 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeecccccccccc
Confidence            48899999999999999999999999999999999887 7764

>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=99.10  E-value=2.8e-11  Score=69.33  Aligned_cols=40  Identities=28%  Similarity=0.576  Sum_probs=37.0

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      +|||||||.++|+++|+++|++||.|..+.+++++. |+++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~   41 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHR   41 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccC
Confidence            599999999999999999999999999999999887 7653

>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=99.08  E-value=8.8e-11  Score=69.27  Aligned_cols=41  Identities=10%  Similarity=0.225  Sum_probs=37.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ++|||+|||.++|+++|+++|+.||.|.+|.|.+++.|++|
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~k   47 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK   47 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcc
Confidence            78999999999999999999999999999999988777653

>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=99.08  E-value=3e-11  Score=73.54  Aligned_cols=41  Identities=22%  Similarity=0.547  Sum_probs=38.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||.++|+++|+++|++||.|.+|+|++|+. |++|
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~   50 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPK   50 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEE
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccC
Confidence            6799999999999999999999999999999999987 7653

>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=99.07  E-value=1e-10  Score=70.00  Aligned_cols=43  Identities=28%  Similarity=0.483  Sum_probs=39.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++++|||||||+++|+++|+++|++||.|.++.++.++. |++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~   50 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSK   50 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeecccccccccc
Confidence            458899999999999999999999999999999999887 6654

>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=99.05  E-value=1.5e-10  Score=65.93  Aligned_cols=39  Identities=21%  Similarity=0.422  Sum_probs=36.4

Q ss_pred             EEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        65 lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      |||+|||.++|+++|+++|++||.|.++.+.+++. |+++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~   40 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK   40 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccccccccccccccc
Confidence            79999999999999999999999999999999987 7654

>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=99.05  E-value=5e-11  Score=75.88  Aligned_cols=43  Identities=21%  Similarity=0.443  Sum_probs=38.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..++|||||||+++|+++|+++|++||.|.++.|++|+. |++|
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~r   84 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR   84 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhcccccccccccccccccc
Confidence            346899999999999999999999999999999999987 7653

>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=99.03  E-value=1.9e-10  Score=68.29  Aligned_cols=39  Identities=23%  Similarity=0.510  Sum_probs=36.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||||||.++|+++|+++|++||.|.+|.+++|+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~   45 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT   45 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccC
Confidence            347899999999999999999999999999999999887

>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=99.01  E-value=9.2e-11  Score=68.24  Aligned_cols=41  Identities=12%  Similarity=0.229  Sum_probs=33.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+.. |++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~   43 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSR   43 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------C
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeeccccccccc
Confidence            7899999999999999999999999999998888776 7664

>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=99.00  E-value=4.9e-10  Score=66.89  Aligned_cols=39  Identities=23%  Similarity=0.463  Sum_probs=36.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||+.+++++|+++|++||.|.+|.++.|+.
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~   48 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER   48 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc
Confidence            348899999999999999999999999999999999876

>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=99.00  E-value=4.1e-10  Score=69.22  Aligned_cols=41  Identities=20%  Similarity=0.422  Sum_probs=36.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ...++.|||+|||..+|+++|+++|++||.|.+|++..+..
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~   44 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE   44 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCC
Confidence            34458899999999999999999999999999999987653

>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=98.97  E-value=1.9e-10  Score=67.11  Aligned_cols=39  Identities=33%  Similarity=0.694  Sum_probs=35.4

Q ss_pred             EEEecCCCCCCHHHHHHhhcCCCceeEE-EEeeCCC-CCCC
Q psy10284         65 LFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPD-GTSK  103 (103)
Q Consensus        65 lfVgnL~~~~te~~l~~~F~~~G~i~~~-~v~~d~~-G~sr  103 (103)
                      |||+|||.++|+++|+++|++||.|.++ .+++|+. |+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~   41 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK   41 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccC
Confidence            7999999999999999999999999775 7888988 8765

>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=98.97  E-value=3e-10  Score=66.55  Aligned_cols=35  Identities=29%  Similarity=0.618  Sum_probs=33.7

Q ss_pred             EEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        65 lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      |||+|||+++|+++|+++|++||.|.++.|++|+.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~   35 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN   35 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEEC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccc
Confidence            79999999999999999999999999999998876

>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=98.97  E-value=1.5e-10  Score=69.45  Aligned_cols=42  Identities=14%  Similarity=0.318  Sum_probs=37.3

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCc-eeEEEEeeCCC--CCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGT-IEECTVLKGPD--GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~-i~~~~v~~d~~--G~sr  103 (103)
                      +|+|||||||.++++++|+++|++||. |.++.+++|..  |++|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~r   45 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNR   45 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCC
Confidence            389999999999999999999999996 99999998864  6654

>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=98.97  E-value=3.1e-10  Score=65.44  Aligned_cols=38  Identities=26%  Similarity=0.315  Sum_probs=35.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      +.|||+|||+++++++|+++|++||.|.++++.+|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~   38 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK   38 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc
Confidence            36999999999999999999999999999999999874

>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=98.97  E-value=3.3e-10  Score=66.97  Aligned_cols=38  Identities=24%  Similarity=0.484  Sum_probs=34.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +++|||+|||+.+|+++|+++|++||.|.+|.++.+..
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~   42 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR   42 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccC
Confidence            48999999999999999999999999999998776543

>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=98.96  E-value=6.7e-10  Score=65.47  Aligned_cols=38  Identities=32%  Similarity=0.596  Sum_probs=35.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++|||+|||.++++++|+++|++||.|.+|.+.+++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~   45 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG   45 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccc
Confidence            47899999999999999999999999999999988764

>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=98.95  E-value=2.6e-10  Score=67.21  Aligned_cols=42  Identities=24%  Similarity=0.457  Sum_probs=34.1

Q ss_pred             CceEEEecCCCCCC-HHHHHHhhcCCCceeEEEEeeCC-C-CCCC
Q psy10284         62 DKKLFVGMLSKQQN-EDDVRKIFAPFGTIEECTVLKGP-D-GTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~t-e~~l~~~F~~~G~i~~~~v~~d~-~-G~sr  103 (103)
                      +++|||+|||++++ +++|+++|++||.|.+|.|.++. . |++|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~k   48 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNN   48 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccc
Confidence            48999999999986 45699999999999999987754 3 6654

>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=98.95  E-value=2.8e-10  Score=67.59  Aligned_cols=39  Identities=23%  Similarity=0.399  Sum_probs=35.5

Q ss_pred             ceEEEecCCCCCCHHHH---HHhhcCCCceeEEEEeeCCC-CC
Q psy10284         63 KKLFVGMLSKQQNEDDV---RKIFAPFGTIEECTVLKGPD-GT  101 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l---~~~F~~~G~i~~~~v~~d~~-G~  101 (103)
                      ..|||+|||+.+++++|   +++|++||.|.+|.+++|+. +.
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~   51 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG   51 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCS
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCC
Confidence            66999999999999999   67899999999999999986 44

>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=98.92  E-value=8.2e-10  Score=65.31  Aligned_cols=37  Identities=24%  Similarity=0.525  Sum_probs=35.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .+|||+|||.++|+++|+++|++||.|.++.|+.|+.
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~   45 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN   45 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC
Confidence            6799999999999999999999999999999999875

>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=98.91  E-value=1.5e-09  Score=63.31  Aligned_cols=39  Identities=21%  Similarity=0.362  Sum_probs=35.7

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      ++.|||+|||..+|+++|+++|++||.|.++++++++.|
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g   46 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD   46 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCS
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccce
Confidence            478999999999999999999999999999999877643

>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=98.90  E-value=1.3e-09  Score=65.13  Aligned_cols=40  Identities=20%  Similarity=0.459  Sum_probs=35.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..+++|||+|||.++|+++|+++|++||.|..+.+..+..
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~   51 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG   51 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccccc
Confidence            4558899999999999999999999999999998876554

>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=98.89  E-value=6e-10  Score=67.00  Aligned_cols=39  Identities=23%  Similarity=0.468  Sum_probs=36.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..++|||+|||..+++++|+++|++||.|.++++++|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg   55 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG   55 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTT
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecce
Confidence            347899999999999999999999999999999998864

>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=98.89  E-value=4.3e-10  Score=66.35  Aligned_cols=34  Identities=15%  Similarity=0.216  Sum_probs=32.3

Q ss_pred             eEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         64 KLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        64 ~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      +|||||||+.+++++|+++|++||.|.++.+.+|
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~   35 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   35 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc
Confidence            6999999999999999999999999999998766

>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=98.87  E-value=8.2e-10  Score=72.10  Aligned_cols=40  Identities=35%  Similarity=0.788  Sum_probs=37.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ++|||||||+.+|+++|+++|++||.|.++.+++|.. |++
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~   47 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRS   47 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCc
Confidence            7899999999999999999999999999999999987 765

>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=98.85  E-value=2.1e-09  Score=64.97  Aligned_cols=41  Identities=20%  Similarity=0.420  Sum_probs=35.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC--CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD--GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~--G~s  102 (103)
                      ..++|||+|||+++|+++|+++|++|| +.++.++++..  |++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~   56 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERL   56 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSB
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCc
Confidence            348899999999999999999999999 77888887764  554

>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=98.83  E-value=1e-09  Score=67.08  Aligned_cols=38  Identities=21%  Similarity=0.286  Sum_probs=35.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..+|||+|||+.+|+++|+++|++||.|.++.+++++.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~   44 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN   44 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETT
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCC
Confidence            37899999999999999999999999999999988765

>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=98.81  E-value=1.7e-09  Score=65.72  Aligned_cols=39  Identities=15%  Similarity=0.352  Sum_probs=34.9

Q ss_pred             CceEEEecCC-CCCCHHHHHHhhcCCCceeEEEEeeCCCC
Q psy10284         62 DKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTVLKGPDG  100 (103)
Q Consensus        62 ~~~lfVgnL~-~~~te~~l~~~F~~~G~i~~~~v~~d~~G  100 (103)
                      ++.|||+||+ ..+|+++|+++|++||.|.+|.|++|+.|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg   41 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE   41 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccc
Confidence            3789999995 56999999999999999999999998754

>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=98.80  E-value=1.1e-10  Score=69.69  Aligned_cols=42  Identities=17%  Similarity=0.311  Sum_probs=36.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      ..+|||+|||+.+|+++|+++|++||.|.++.|+.+..|++|
T Consensus        13 ~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~k   54 (91)
T d1fjeb1          13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNR   54 (91)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTT
T ss_pred             CcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCcc
Confidence            478999999999999999999999999999988765547664

>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=98.80  E-value=3.6e-09  Score=63.42  Aligned_cols=42  Identities=17%  Similarity=0.361  Sum_probs=35.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCcee--------EEEEeeCCC-CCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIE--------ECTVLKGPD-GTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~--------~~~v~~d~~-G~s  102 (103)
                      ...+|||+|||..+|+++|+++|++||.|.        .+.+.+|+. |++
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~   57 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP   57 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSB
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccc
Confidence            458999999999999999999999999884        456667766 654

>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=98.80  E-value=5.6e-09  Score=61.38  Aligned_cols=39  Identities=28%  Similarity=0.520  Sum_probs=35.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++.|||+|||..+++++|+++|++||.|.++.++.++.
T Consensus         7 Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~   45 (88)
T d2cq1a1           7 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN   45 (88)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccce
Confidence            348899999999999999999999999999999887653

>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=98.77  E-value=5.1e-09  Score=62.73  Aligned_cols=38  Identities=26%  Similarity=0.471  Sum_probs=35.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++|||+|||.++++++|+++|++||.|..+.+.+++.
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~   54 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS   54 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecccc
Confidence            47899999999999999999999999999999987753

>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=98.77  E-value=7.8e-09  Score=67.29  Aligned_cols=43  Identities=28%  Similarity=0.539  Sum_probs=39.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      ....+|||+|||+.+|+++|+++|+.||.|..+.|+.|+. |++
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~  138 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK  138 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCcc
Confidence            3458899999999999999999999999999999999987 764

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.76  E-value=7.6e-09  Score=62.24  Aligned_cols=37  Identities=19%  Similarity=0.222  Sum_probs=33.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      ...+|||+|||+.+++++|+++|++||+|.++.+.++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~   50 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD   50 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc
Confidence            3478999999999999999999999999999998754

>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=98.74  E-value=4.6e-10  Score=67.68  Aligned_cols=45  Identities=24%  Similarity=0.298  Sum_probs=38.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         59 LPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        59 ~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ...+++|||+|||..+++++|+++|++||.|..+.++.+.. |+++
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~   60 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR   60 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeeccccccccc
Confidence            34468899999999999999999999999999998888765 6553

>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=98.73  E-value=1.2e-08  Score=61.72  Aligned_cols=43  Identities=14%  Similarity=0.124  Sum_probs=36.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ....|||+|||+++|+++|+++|..||.+..+.++.+.. |+++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~k   57 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRST   57 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcc
Confidence            446799999999999999999999999998876666555 6653

>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=98.73  E-value=4.2e-09  Score=64.03  Aligned_cols=36  Identities=14%  Similarity=0.341  Sum_probs=32.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +.|||+|||..+++++|+++|++||.|.+|.|...+
T Consensus        11 ~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~k   46 (111)
T d1whxa_          11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG   46 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSS
T ss_pred             CEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccC
Confidence            689999999999999999999999999999875443

>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=98.73  E-value=4.1e-09  Score=64.94  Aligned_cols=37  Identities=24%  Similarity=0.411  Sum_probs=34.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ..+||||||..+|+++|+++|++||+|.+|.|++++.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg   48 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK   48 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCc
Confidence            5579999999999999999999999999999998764

>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=98.70  E-value=2e-08  Score=60.78  Aligned_cols=38  Identities=21%  Similarity=0.179  Sum_probs=35.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+..|||+|||..+|+++|+++|++||.|..+.+.+++
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k   51 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK   51 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc
Confidence            45789999999999999999999999999999988765

>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=98.70  E-value=9.5e-09  Score=59.32  Aligned_cols=37  Identities=22%  Similarity=0.301  Sum_probs=32.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +++.|||+|++  +|+++|+++|++||.|.++.+.+++.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~   40 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRN   40 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTT
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCC
Confidence            45789999986  89999999999999999999987653

>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=98.68  E-value=9.6e-09  Score=60.77  Aligned_cols=39  Identities=13%  Similarity=0.286  Sum_probs=34.8

Q ss_pred             CCceEEEecCCCC-CCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~-~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++.|||+|||.. +|+++|.++|++||.|.++.++.++.
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~   46 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN   46 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSS
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccce
Confidence            3478999999986 78999999999999999999987764

>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=98.68  E-value=1.2e-08  Score=61.39  Aligned_cols=39  Identities=15%  Similarity=0.359  Sum_probs=34.8

Q ss_pred             CCceEEEecCCCC-CCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         61 PDKKLFVGMLSKQ-QNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        61 ~~~~lfVgnL~~~-~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      .++.|||+|||.. +|+++|.++|++||.|.++.+++++.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~   56 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS   56 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTT
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCC
Confidence            3478999999985 89999999999999999999988763

>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=98.66  E-value=2.1e-08  Score=58.76  Aligned_cols=38  Identities=16%  Similarity=0.283  Sum_probs=33.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++.|||+|||.++++++|+++|++||.|.++.+..++.
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~   47 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD   47 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecc
Confidence            37799999999999999999999999999987766554

>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=98.66  E-value=2.8e-09  Score=61.85  Aligned_cols=36  Identities=31%  Similarity=0.405  Sum_probs=32.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+|||||||.++|+++|+++|++||.|.++.+++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~r   37 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS   37 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEET
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEeccc
Confidence            579999999999999999999999999888777655

>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=98.62  E-value=1.9e-08  Score=60.56  Aligned_cols=41  Identities=10%  Similarity=0.011  Sum_probs=34.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~sr  103 (103)
                      ..|||+|||+++|+++|+++|+.||.|..+.++.+.. |+++
T Consensus         9 ~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~   50 (103)
T d2cpya1           9 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGL   50 (103)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCS
T ss_pred             eEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcC
Confidence            5699999999999999999999999998755555444 7764

>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=98.61  E-value=3.2e-08  Score=59.58  Aligned_cols=41  Identities=22%  Similarity=0.413  Sum_probs=35.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCC
Q psy10284         61 PDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTS  102 (103)
Q Consensus        61 ~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~s  102 (103)
                      .+..|||+|||+++|+++|+++|+.|| +.++.++++..|++
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~   54 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRV   54 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcc
Confidence            346899999999999999999999998 56788888877654

>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=98.58  E-value=2.7e-08  Score=59.77  Aligned_cols=36  Identities=31%  Similarity=0.637  Sum_probs=31.4

Q ss_pred             CCCceEEEecCC-CCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         60 PPDKKLFVGMLS-KQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        60 ~~~~~lfVgnL~-~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ...++|||+||| ..+++++|+++|++||.|.++.|.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~   49 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH   49 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe
Confidence            345789999996 578889999999999999999874

>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=98.58  E-value=1.3e-08  Score=62.43  Aligned_cols=45  Identities=13%  Similarity=0.228  Sum_probs=35.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC-CCC
Q psy10284         58 PLPPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD-GTS  102 (103)
Q Consensus        58 ~~~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~-G~s  102 (103)
                      +......|||+|||+.+|+++|+++|+.||.+..+.++.+.. |++
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~   59 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA   59 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccce
Confidence            334557899999999999999999999999998765554443 654

>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=98.58  E-value=4.3e-08  Score=57.12  Aligned_cols=37  Identities=24%  Similarity=0.108  Sum_probs=33.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+.|||+|||..+++++|+++|++||.|..+.+.+.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~r   44 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR   44 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcccc
Confidence            3789999999999999999999999999888776544

>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=98.57  E-value=1.3e-08  Score=59.32  Aligned_cols=41  Identities=12%  Similarity=0.143  Sum_probs=33.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEE-EEeeCCCCCC
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEEC-TVLKGPDGTS  102 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~-~v~~d~~G~s  102 (103)
                      ...|||+|||+++++++|+++|+.||.+..+ .+..+..|++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~   50 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMP   50 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCc
Confidence            4679999999999999999999999999874 4455544654

>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=98.43  E-value=7e-08  Score=57.41  Aligned_cols=32  Identities=22%  Similarity=0.313  Sum_probs=29.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEE
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECT   93 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~   93 (103)
                      .+.|||+|||+++|+++|+++|++||.|..+.
T Consensus        16 ~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~   47 (96)
T d1fjca_          16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVS   47 (96)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHHCSEEEECCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcccceeee
Confidence            48899999999999999999999999987764

>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=98.41  E-value=1.3e-07  Score=55.51  Aligned_cols=32  Identities=19%  Similarity=0.454  Sum_probs=27.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhcCCCceeEEEE
Q psy10284         62 DKKLFVGMLSKQQNEDDVRKIFAPFGTIEECTV   94 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v   94 (103)
                      +.+|||+|||.++++++|+++|++|| +..+.+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~   36 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV   36 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee
Confidence            37899999999999999999999999 333443

>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=98.41  E-value=7.8e-09  Score=60.92  Aligned_cols=33  Identities=18%  Similarity=0.278  Sum_probs=30.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEe
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVL   95 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~   95 (103)
                      ++|||||||..+|+++|+++|++||.+.++.+.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~   34 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA   34 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEe
Confidence            789999999999999999999999988876654

>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=98.37  E-value=2.5e-07  Score=52.76  Aligned_cols=31  Identities=16%  Similarity=0.413  Sum_probs=26.8

Q ss_pred             EEEecCCCCCCHHHHHHhhcCCCceeEEEEee
Q psy10284         65 LFVGMLSKQQNEDDVRKIFAPFGTIEECTVLK   96 (103)
Q Consensus        65 lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~   96 (103)
                      |||+|||.++++++|+++|++|| +..+.+.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~   31 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK   31 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc
Confidence            79999999999999999999999 55555543

>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=98.37  E-value=1.4e-07  Score=55.49  Aligned_cols=35  Identities=26%  Similarity=0.621  Sum_probs=30.4

Q ss_pred             CceEEEecCCCCCCHHHHHH----hhcCCCceeEEEEee
Q psy10284         62 DKKLFVGMLSKQQNEDDVRK----IFAPFGTIEECTVLK   96 (103)
Q Consensus        62 ~~~lfVgnL~~~~te~~l~~----~F~~~G~i~~~~v~~   96 (103)
                      +++|||||||..+++++|++    +|++||+|.+|.+..
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~   41 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR   41 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee
Confidence            37899999999999998864    689999999998754

>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=98.32  E-value=1.2e-07  Score=57.16  Aligned_cols=38  Identities=13%  Similarity=0.248  Sum_probs=33.5

Q ss_pred             CceEEE--ecCCCCCCHHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFV--GMLSKQQNEDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfV--gnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      +..+||  ||||..+|+++|+++|++||.|.++.++.++.
T Consensus        18 t~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~   57 (101)
T d2cq2a1          18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP   57 (101)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCS
T ss_pred             CceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCcc
Confidence            467888  55999999999999999999999999887764

>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=98.01  E-value=1.2e-06  Score=52.81  Aligned_cols=38  Identities=11%  Similarity=0.160  Sum_probs=32.0

Q ss_pred             CCceEEEecCCCCC-CH----HHHHHhhcCCCceeEEEEeeCC
Q psy10284         61 PDKKLFVGMLSKQQ-NE----DDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        61 ~~~~lfVgnL~~~~-te----~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      .+.+|||+||+.++ ++    ++|+++|++||.|.++.+++.+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~   46 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF   46 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC
Confidence            34889999999886 43    4689999999999999998765

>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=97.83  E-value=4.3e-06  Score=48.30  Aligned_cols=35  Identities=14%  Similarity=0.060  Sum_probs=29.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGP   98 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~   98 (103)
                      +.++|+|+|.+.+++.| ++|++||+|.++++.+++
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~   39 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG   39 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSS
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCC
Confidence            66999999999987655 579999999999886655

>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=97.65  E-value=3.3e-07  Score=55.49  Aligned_cols=41  Identities=12%  Similarity=0.087  Sum_probs=35.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeCCCCCCC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKGPDGTSK  103 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d~~G~sr  103 (103)
                      .+++|.+++..+++++++++|++||+|.+|.|+++..|++|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~   68 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLV   68 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEe
Confidence            56888888889999999999999999999999888667654

>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=96.23  E-value=0.0011  Score=39.16  Aligned_cols=38  Identities=16%  Similarity=0.264  Sum_probs=29.7

Q ss_pred             CceEEEecC--CCCCC--------HHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGML--SKQQN--------EDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL--~~~~t--------e~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++.|.+.|+  +....        .+++++.|++||.|.+|.|+++..
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~   51 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVD   51 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTT
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCC
Confidence            366888998  44442        247899999999999999988765

>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=96.11  E-value=0.0029  Score=36.90  Aligned_cols=38  Identities=13%  Similarity=0.307  Sum_probs=30.0

Q ss_pred             CceEEEecC--CCCCC---------HHHHHHhhcCCCceeEEEEeeCCC
Q psy10284         62 DKKLFVGML--SKQQN---------EDDVRKIFAPFGTIEECTVLKGPD   99 (103)
Q Consensus        62 ~~~lfVgnL--~~~~t---------e~~l~~~F~~~G~i~~~~v~~d~~   99 (103)
                      ++.|++.|+  |.+..         ++++++.|++||.|..+.+..++.
T Consensus         8 ~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~   56 (99)
T d2dita1           8 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHP   56 (99)
T ss_dssp             CCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCT
T ss_pred             ccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCC
Confidence            477999998  44321         257999999999999999887765

>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=91.63  E-value=0.31  Score=27.82  Aligned_cols=35  Identities=9%  Similarity=0.232  Sum_probs=30.5

Q ss_pred             ceEEEecCCCCCCHHHHHHhhcCCCceeEEEEeeC
Q psy10284         63 KKLFVGMLSKQQNEDDVRKIFAPFGTIEECTVLKG   97 (103)
Q Consensus        63 ~~lfVgnL~~~~te~~l~~~F~~~G~i~~~~v~~d   97 (103)
                      +||-|..||...|++++.+.++..|++....-...
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~G   36 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSN   36 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEES
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCC
Confidence            68999999999999999999999999887765543

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.14  E-value=1.2  Score=25.81  Aligned_cols=32  Identities=22%  Similarity=0.480  Sum_probs=27.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhcCCCceeE
Q psy10284         60 PPDKKLFVGMLSKQQNEDDVRKIFAPFGTIEE   91 (103)
Q Consensus        60 ~~~~~lfVgnL~~~~te~~l~~~F~~~G~i~~   91 (103)
                      +....+|.-..|......++.++|+.||.|.-
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V   44 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI   44 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEE
Confidence            44567999999999999999999999998754